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4.2 Chromosomes and Packaging
Within eukaryotic cells, DNA is organized into long linear structures called chromosomes (Figure 4.8). A chromosome is a deoxyribonucleic acid (DNA) molecule with part or all of the genetic material (genome) of an organism. The replicated arms of a chromosome are called chromatids. Before being separated into the daughter cells during mitosis, replicated chromatids are held together by a chromosomal structure called the centromere.
Figure 4.8 Diagram of Replicated and Condensed Eukaryotic Chromosome. (1) Chromatid - one of the two identical parts of the chromosome after S phase. (2) Centromere - the point where the two chromatids are joined together. (3) Short arm is termed p; Long arm is termed q
Image by: Magnus Manske, Dietzel65, and Tryphon
Eukaryotic organisms (animals, plants, fungi and protists) store most of their DNA inside the cell nucleus as linear nuclear DNA, and some in the mitochondria as circular mitochondrial DNA or in chloroplasts as circular chloroplast DNA. In contrast, prokaryotes (bacteria and archaea) do not have organelle structures and thus, store their DNA only in a region of the cytoplasm known as the nucleoid region. Prokaryotic chromosomes consist of double–stranded circular DNA.
The genome of a cell is often significantly larger than the cell itself. For example, if the DNA from a human cell containing 46 chromosomes were stretched out in a line, it would extend more that 6 feet (2 meters)! How is it possible that the genetic information not only fits into the cell, but fits into the cell nucleus? Eukaryota solves this problem by a combination of supercoiling and packaging DNA around the histone family of proteins (described below). Prokaryotes do not contain histones (with a few exceptions). Prokaryotes tend to compress their DNA using nucleoid-associated-proteins (NAPs)and supercoiling(Figure 4.9).
DNA supercoilingrefers to the over- or under-winding of a DNA strand, and is an expression of the strain on that strand (Figure 4.9). Supercoiling is important in a number of biological processes, such as compacting DNA, and by regulating access to the genetic code. DNA supercoiling strongly affects DNA metabolism and possibly gene expression. Additionally, certain enzymes such as topoisomerases are able to change DNA topology to facilitate functions such as DNA replication or transcription.
In a "relaxed" double-helical segment of B-DNA, the two strands twist around the helical axis once every 10.4–10.5 base pairs of sequence. Adding or subtracting twists, as some enzymes can do, imposes strain. If a DNA segment under twist strain were closed into a circle by joining its two ends and then allowed to move freely, the circular DNA would contort into a new shape, such as a simple figure-eight (Figure 4.9). Such a contortion is a supercoil. The noun form "supercoil" is often used in the context of DNA topology.
Figure 4.9 DNA Supercoiling. The supercoiled structure of linear DNA molecules with constrained ends. The helical nature of the DNA duplex is omitted for clarity.
Image by: Richard Wheeler
Positively supercoiled (overwound) DNA is transiently generated during DNA replication and transcription, and, if not promptly relaxed, inhibits (regulates) these processes. The simple figure eight is the simplest supercoil, and is the shape a circular DNA assumes to accommodate one too many or one too few helical twists. The two lobes of the figure eight will appear rotated either clockwise or counterclockwise with respect to one another, depending on whether the helix is over- or underwound. For each additional helical twist being accommodated, the lobes will show one more rotation about their axis. As a general rule, the DNA of most organisms is negatively supercoiled.
Lobal contortions of a circular DNA, such as the rotation of the figure-eight lobes above, are referred to as writhe. The above example illustrates that twist and writhe are interconvertible. Supercoiling can be represented mathematically by the sum of twist and writhe (Figure 4.9). The twistis the number of helical turns in the DNA and the writhe is the number of times the double helix crosses over on itself (these are the supercoils). Extra helical twists are positive and lead to positive supercoiling, while subtractive twisting causes negative supercoiling. Many topoisomerase enzymes sense supercoiling and either generate or dissipate it as they change DNA topology.
In part because chromosomes may be very large, segments in the middle may act as if their ends are anchored. As a result, they may be unable to distribute excess twist to the rest of the chromosome or to absorb twist to recover from underwinding—the segments may become supercoiled, in other words. In response to supercoiling, they will assume an amount of writhe, just as if their ends were joined.
Supercoiled circular DNA forms two major structures; a plectoneme or a toroid, or a combination of both (Figure 4.9). A negatively supercoiled DNA molecule will produce either a one-start left-handed helix, the toroid, or a two-start right-handed helix with terminal loops, the plectoneme. Plectonemes are typically more common in nature, and this is the shape most bacterial plasmids will take (Figure 4.10). For larger molecules it is common for hybrid structures to form – a loop on a toroid can extend into a plectoneme (Figure 4.10). DNA supercoiling is an important for DNA packaging within all cells, and seems to also play a role in gene expression.
Figure 4.10 Bacterial DNA Supercoiling. Atomic force microscopy (AFM) visualization of torsionally relaxed (A), and negativey supercoiled (B) bacterial plasmids pBR322. (C) Electron microscopy image of the E. coli chromosomal DNA displaying a hybrid toroidal-plectoneme structure.
Image A and B from: Witz, G. and Stasiak, A. (2009) Nucleic Acids Research 38(7):2119-2133.
Image C from: Prokaryotic Chromosomes
In addition to forming supercoiled structure, circular chromosomes from bacteria have been shown to undergo the processes of catenation and knotting upon the inhibition of topoisomerase enzymes. Catenationis the process by which two circular DNA strands are linked together like chain links, whereas DNA knotting is the interlooping structures occurring within a single circular DNA structure. In vivo, the action of topoisomerase enzymes is critical to keep knots and catenoids from tangling the DNA structure.
Figure 4.11 DNA Catenation and Knotting. Upper structure shows the negative supercoiled form of bacterial DNA. The inhibition of topoisomerase enzyme activity leads to the relaxation, catenation and knotting of the chromosomal structure.
Image from: Harms, A. et al. (2015) Cell Reports 12(9):1497-1507.
Note the circular nature of chloroplast and mitochondrial DNA, suggesting a bacterial origin for both of these organelle structures. Sequence alignments further lend support for the endosymbiotic theory, which proposes that bacteria were engulfed by early eukaryotic organisms and subsequently became symbiotic to their eukaryotic counterpart, rather than being digested.
In the cells of extant organisms, the vast majority of the proteins present in the mitochondria (numbering approximately 1500 different types in mammals) are coded for by nuclear DNA. However, sequencing of the human mitochondrial genome has revealed 16,569 base pairs encoding for 13 proteins (Figure 4.12). Many of the mitochondrially produced proteins are required for electron transport during the production of ATP (Figure 4.12).
Figure 4.12 Mitochondrial Genome. Mitochondria are organelle structures containing a double membrane, thought to have originated as an independent prokaryotic organism that was originally engulfed by a eukaryotic organism, where it became a symbiotic counterpart. Mitochondria contain circular chromosomal DNA that shares high sequence similarity with alphaprotobacteria. The human mitochondrial genome contains 16,569 base pairs encoding for 13 proteins and ribosomal RNA (rRNA) components.
Images adapted from: The National Human Genome Research Institute and Shanel, Knopfkind, and JHC.
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Within eukaryotic chromosomes, chromatin proteins, known as histones, compact and organize DNA. These compacting structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.
Histones are highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes. They are the chief protein components of chromatin, acting as spools around which DNA winds, and playing a role in gene regulation. Without histones, the unwound DNA in chromosomes would be very long (a length to width ratio of more than 10 million to 1 in human DNA). For example, each human diploid cell (containing 23 pairs of chromosomes) has about 1.8 meters of DNA; wound on the histones, the diploid cell has about 90 micrometers (0.09 mm) of chromatin.
Five major families of histones exist: H1/H5, H2A, H2B, H3, and H4. Histones H2A, H2B, H3 and H4 are known as the core histones, while histones H1/H5 are known as the linker histones.
The core histones all exist as dimers, which are similar in that they all possess the histone fold domain: three alpha helices linked by two loops (Figure 4.13). It is this helical structure that allows for interaction between distinct dimers, particularly in a head-tail fashion (also called the handshake motif). The resulting four distinct dimers then come together to form one octameric nucleosome core, approximately 63 Angstroms in diameter. Around 146 base pairs (bp) of DNA wrap around this core particle 1.65 times in a left-handed super-helical turn to give a particle of around 100 Angstroms across, called a nucleosome.
Figure 4.13 Nucleosome Core Structure. Histones H2A and H2B dimerize, and Histones H3 and H4 dimerize. Two dimers of each join to form a histone core octomer. The DNA double helix winds 1.65 times around the octomer core forming the nucleosome structure.
Image adapted from: Nucleosome Structure
The linker histone H1 binds the nucleosome at the entry and exit sites of the DNA, thus locking the DNA into place and allowing the formation of higher order structure (Figure 4.14). The most basic such formation is the 10 nm fiber or beads on a string conformation. This involves the wrapping of DNA around nucleosomes with approximately 50 base pairs of DNA separating each pair of nucleosomes (also referred to as linker DNA).
The nucleosome contains over 120 direct protein-DNA interactions and several hundred water-mediated ones. Direct protein - DNA interactions are not spread evenly about the octamer surface but rather located at discrete sites. These are due to the formation of two types of DNA binding sites within the octamer; the α1α1 site, which uses the α1 helix from two adjacent histones, and the L1L2 site formed by the L1 and L2 loops. Salt links and hydrogen bonding between both side-chain basic and hydroxyl groups and main-chain amides with the DNA backbone phosphates form the bulk of interactions with the DNA. This is important, given that the ubiquitous distribution of nucleosomes along genomes requires it to be a non-sequence-specific DNA-binding factor. Although nucleosomes tend to prefer some DNA sequences over others, they are capable of binding practically to any sequence, which is thought to be due to the flexibility in the formation of these water-mediated interactions. In addition, non-polar interactions are made between protein side-chains and the deoxyribose groups, and an arginine side-chain intercalates into the DNA minor groove at all 14 sites where it faces the octamer surface. The distribution and strength of DNA-binding sites about the octamer surface distorts the DNA within the nucleosome core. The DNA is non-uniformly bent and also contains twist defects. The twist of free B-form DNA in solution is 10.5 bp per turn. However, the overall twist of nucleosomal DNA is only 10.2 bp per turn, varying from a value of 9.4 to 10.9 bp per turn.
The histone tail extensions constitute up to 30% by mass of histones, but are not visible in the crystal structures of nucleosomes due to their high intrinsic flexibility, and have been thought to be largely unstructured (Figure 4.14). The N-terminal tails of histones H3 and H2B pass through a channel formed by the minor grooves of the two DNA strands, protruding from the DNA every 20 bp. The N-terminal tail of histone H4, on the other hand, has a region of highly basic amino acids (16-25), which, in the crystal structure, forms an interaction with the highly acidic surface region of a H2A-H2B dimer of another nucleosome, being potentially relevant for the higher-order structure of nucleosomes. This interaction is thought to occur under physiological conditions also, and suggests that acetylation of the H4 tail distorts the higher-order structure of chromatin.
Figure 4.14 Overall Nucleosome Structure. (A) Side view diagram of the nucleosome structure with the histone octomer shown in blue, the DNA double helix in red, and the histone H1 linker in green. (B) Shows a top view rendering of the histone octomer with the associated DNA helix. Note that the Histone tails from H3 and H2B protude from the DNA.
Image A from: Darekk2 Image B from: EMW
The formation of the DNA double helix represents the first order packaging of the chromosome structure (Figure 4.15). The formation of nucleosomes represent the second level of packaging for eukaryotic chromosomes. In vitro data suggests that nucleosomes are then arranged into either a solenoid structure which consists of 6 nucleosomes linked together by the Histone H1 linker proteins or a zigzag structure that is similar to the solenoid construct (Figure 4.15). Both the solenoid and zigzag structures are approximately 30 nm in diamater. The solenoid and zigzag structures reported from in vitro data have not yet been confirmed to occur in vivo.
During interphase, each chromosome occupies a spatially limited, roughly elliptical domain which is known as a chromosome territory (CT). Each chromosome territory is comprised of higher order chromatin units of ~1 Mb each. These units are likely built up from smaller loop domains that contain the solenoid/zigzag structural motifs. On the other hand, 1Mb domains can themselves serve as smaller units in higher-order chromatin structures.
Chromosome territories are known to be arranged radially around the nucleus. This arrangement is both cell and tissue-type specific and is also evolutionary conserved. The radial organization of chromosome territories was shown to correlate with their gene density and size. In this case, the gene-rich chromosomes occupy interior positions, whereas larger, gene-poor chromosomes, tend to be located around the periphery. Chromosome territories are also dynamic structures, with genes able to relocate from the periphery towards the interior once they have been ‘switched on’. In other cases, genes may move in the opposite direction, or simply maintain their position. The eviction of genes from their chromosome territories into the interchromatin compartment or a neighboring chromosome territory is often accompanied by the formation of large decondensed chromatin loops.
Figure 4.15 Chromosome Structure. (1) DNA double helix is approximately 2 nm in diameter. (2) The nucleosome core structure is approximately 11 nm in diameter. (3) The solenoid/zigzag structure is approximately 30 nm in diameter and is proposed to form chromosome loops (4) during cellular interphase and more condensed chromosome territories (5) during mitosis.
Image by: MBInfo
Models describing chromosome territory arrangement
With the development of high-throughput biochemical techniques, such as 3C (‘chromosome conformation capture’) and 4C (‘chromosome conformation capture-on-chip’ and ‘circular chromosome conformation capture’), numerous spatial interactions between neighbouring chromatin territories have been described (Figure 4.16). These descriptions have been supplemented with the construction of spatial proximity maps for the entire genome (e.g., for a human lymphoblastoid cell line). Together, these observations and physical simulations have led to the proposal of various models that aim to define the structural organization of chromosome territories:
Figure 4.16 Computer Models of Chromosome Territory (CT) Structure. On the CT-IC model, the space between discrete CTs can be visualized in light and electron microscope and is called interchromatin compartment (IC). Transcription factories (TF, green color) are localized predominantly in perichromatin region. In the ICN model, interchromatin compartment is not apparent. Instead, the space between CTs is occupied by intermingling decondensed chromatin loops, which often share the same transcription factories.
Image by: MBInfo
1. The chromosome territory-interchromatin compartment (CT-IC) model describes two principal compartments: chromosome territories (CTs) and an interchromatin compartment (IC). In this model, chromosome territories build up an interconnected chromatin network that is associated with an adjacent 3D space called the interchromatin compartment. The latter can be observed using both light and electron microscopy.
Within a single chromosome territory, the interphase chromosome is divided into defined regions based on the level of chromosome condensation. Here, the inner part of the interphase chromosome is comprised of more condensed chromatin domains or higher-order chromatin fibers, while a thin (<200 nm) layer of more decondensed chromatin, known as the perichromatin region, can be found around the chromosomal periphery. Functionally, the perichromatin region represents the major transcriptional compartment, and is also the region where most co-transcriptional RNA splicing takes place. DNA replication  and DNA repair  is also predominately carried out within the perichromatin region. Finally, nascent RNA transcripts, referred to as perichromatin fibrils, are also generated in the perichromatin region. Perichromatin fibrils are then subjected to the splicing events by the factors, provided from the interchromatin compartment.
The lattice model, proposed by Dehgani et al. is based on reports that transcription also occurs within the inner, more condensed chromosome territories and not only at the interface between the interchromatin compartment and the perichromatin region. Using ESI (electron spectroscopic imaging), Dehgani et al. showed that chromatin was organized as an array of deoxy-ribonucleoprotein fibers of 10–30 nm in diameter. In this study, the interchromatin compartments, which are described in the CT-IC model as large channels between chromosome territories, were not apparent. Instead, chromatin fibers created a loose meshwork of chromatin throughout the nucleus that intermingled at the periphery of chromosome territories. Thus, inter- and intra-chromosomal spaces within this meshwork are essentially contiguous and together form the intra-nuclear space.
2. The interchromatin network (ICN) model predicts that intermingling chromatin fibers/loops can make both cis- (within the same chromosome) and trans- (between different chromosomes) contacts. This intermingling is uniform and makes distinction between the chromosome territory and interchromatin compartment functionally meaningless. The advantage of the ICN model is that it permits high chromatin dynamics and diffusion-like movements. The authors propose that ongoing transcription influences the degree of intermingling between specific chromosomes by stabilizing associations between particular loci. Such interactions are likely to depend on the transcriptional activity of the loci, and are therefore cell-type specific.
The cell type-specific organization of chromosome territories has been studied by measuring the volume and frequency of intermingling between heterologous chromosomes. By using 3C (chromosome conformation capture) and FISH (fluorescence in situ hybridization) to map the regions of chromosome intermingling, it was revealed that these regions contain a higher density of active genes and are enriched with markers of transcriptional activation and repression, such as activated RNAPII. By comparing the positions of the CTs in undifferentiated mouse embryonic stem (ES) cells, ES cells in early stages of differentiation, and terminally differentiated NIH3T3 cells, it was shown that fully differentiated cells had a higher enrichment of RNAPII, compared to undifferentiated or less-differentiated cells. The findings support the notion that the intermingling regions have functional significance in the nucleus and provide a basis for understanding how the radial and relative positions of chromosomal territories evolve during the process of differentiation, explaining their organization in a cell type-dependent manner.
3. The Fraser and Bickmore model emphasizes the functional importance of giant chromatin loops, which originate from chromosome territories and expand across the nuclear space in order to share transcription factories. In this case, both cis- and trans- loops of decondensed chromatin can be co-expressed and co-regulated by the same transcription factory.
4. The Chromatin polymer models assume a broad range of chromatin loop sizes and predict the observed distances between genomic loci and chromosome territories, as well as the probabilities of contacts being formed between given loci. These models apply physics-based approaches that highlight the importance of entropy for understanding nuclear organization. By proposing the existence of conformational chromatin ensembles with structures based on three possible homopolymer states, these models also provide alternative structures to the traditional 30 nm chromatin fiber, which has been brought into question following recent studies.
With a lack of experimental evidence to support these described models, it must be remembered that they serve only to hypothesize the structural and chemical properties of intermediate chromatin structures, and to highlight unanswered questions. For example, the mechanisms that exist to control the rate and the extent of chromatin movement remain to be defined
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Thought Question: Why are histones alkaline?
At the ends of the linear chromosomes are specialized regions of DNA called telomeres (Figure 4.17). The main function of these regions is to allow the cell to replicate chromosome ends using the enzyme telomerase, as the enzymes that normally replicate DNA cannot copy the extreme 3′ ends of chromosomes. These specialized chromosome caps also help protect the DNA ends, and stop the DNA repair systems in the cell from treating them as damage to be corrected. In human cells, telomeres are usually lengths of single-stranded DNA containing several thousand repeats of a simple TTAGGG sequence.
During DNA replication, the double stranded DNA is unwound and DNA polymerase synthesizes new strands. However, as DNA polymerase moves in a unidirectional manner (from 5’ to 3’), only the leading strand can be replicated continuously. In the case of the lagging strand, DNA replication is discontinuous. In humans small RNA primers attach to the lagging strand DNA, and the DNA is synthesized in small stretches of about 100-200 nucleotides, which are termed Okazaki fragments. The RNA primers are removed, replaced with DNA and the Okazaki fragments ligated together. At the end of the lagging strand, it is impossible to attach an RNA primer, meaning that there will be a small amount of DNA lost each time the cell divides. This ‘end replication problem’ has serious consequences for the cell as it means the DNA sequence cannot be replicated correctly, with the loss of genetic information.
In order to prevent this, telomeres are repeated hundreds to thousands of times at the end of the chromosomes. Each time cell division occurs, a small section of telomeric sequences are lost to the end replication problem, thereby protecting the genetic information. At some point, the telomeres become critically short. This attrition leads to cell senescence, where the cell is unable to divide, or apoptotic cell death. Telomeres are the basis for the Hayflick limit, the number of times a cell is able to divide before reaching senescence.
Telomeres can be restored by the enzyme telomerase, which extends telomeres length (Figure 4.17). Telomerase activity is found in cells that undergo regular division, such as stem cells and lymphocyte cells of the immune system. Telomeres can also be extended through the Alternative Lengthening of Telomeres (ALT) pathway. In this case, rather than being extended, telomeres are switched between chromosomes by homologous recombination. As a result of the telomere swap, one set of daughter cells will have shorter telomeres, and the other set will have longer telomeres.
A downside to telomere extension is the potential for uncontrolled cell division and cancer. Abnormally high telomerase activity has been found in the majority of cancer cells, and non-telomerase tumors often exhibit ALT pathway activation. As well as the potential for losing genetic information, cells with short telomeres are at a high risk for improper chromosome recombination, which can lead to genetic instability and aneuploidy (an abnormal number of chromosomes).
Figure 4.17 Telomere Structure. (A) Telomeres are located at the end of chromosomes, where they help protect against the loss of DNA during replication. (B) DNA quadruplex formed by telomere repeats. The looped conformation of the DNA backbone is very different from the typical DNA helix. The green spheres in the center represent potassium ions.
Image (A) by: MBInfo and Image (B) by: Thomas Splettstoesser
These guanine-rich telomere sequences may also stabilize chromosome ends by forming structures of stacked sets of four-base units, rather than the usual base pairs found in other DNA molecules (Figure 4.17). Here, four guanine bases form a flat plate and these flat four-base units then stack on top of each other, to form a stable G-quadruplex structure. These structures are stabilized by hydrogen bonding between the edges of the bases and chelation of a metal ion in the centre of each four-base unit. Other structures can also be formed, with the central set of four bases coming from either a single strand folded around the bases, or several different parallel strands, each contributing one base to the central structure.
In addition to these stacked structures, telomeres also form large loop structures called telomere loops, or T-loops. Here, the single-stranded DNA curls around in a long circle stabilized by telomere-binding proteins. At the very end of the T-loop, the single-stranded telomere DNA is held onto a region of double-stranded DNA by the telomere strand disrupting the double-helical DNA and base pairing to one of the two strands. This triple-stranded structure is called a displacement loop or D-loop.
Chromosome and DNA MCQs
DNA molecule is located in the nucleus of each cell, the thread-like structures in which DNA is packaged are called chromosomes. Each chromosome is made up of DNA tightly coiled many times around proteins called histones that support its structure.
Chromosome and DNA MCQs
1. Which is incorrect?
A. Chromosomes 1st observed by Walther Fleming
B. Chromosomal theory of inheritance 1st formulated by Walter Sutton
C. 1st evidence of hereditary nature of DNA provided by Friedrich Meischer
D. Sex chromosomes discovered by Thomas Hunt Morgan
2. A chromosome is made of
A. 2 chromatids +1 centromere +secondary constriction
B. 1 chromatids + 1 centromere + primary constriction
C. 2 chromatids + 1 centromere + primary constriction
D. 2 chromatids + 2 centromere + secondary constriction
3. Chromosomes are composed of
A. 40% protein and 60% DNA
B. 50% protein and 50% DNA
C. 70% protein and 30% DNA
D. 60% protein and 40% DNA
4. A typical human chromosome contains _________ nucleotides in its DNA
A. 240 million
B. 140 million
C. 150 million
D. 160 million
5. Histones have an abundance of amino acids
A. Valine and lysine
B. Arginine and lysine
C. Valine and arginine
D. Histidine and threonine
6. A torsion of chromatin that is condensed only during cell division is
7. Transfer of genetic material from one cell to another that can alter the genetic makeup of recipient cell is called
8. Who discovered DNA?
B. Frederick Griffith
C. Friedrich Miescher
D. Rosalind Franklin
9. DNA contains
A. Purines (A and G) pyrimidines (U and (c)
B. Purines (T and (c) pyrimidines (A and G)
C. Purines (A and (c) pyrimidines (U and G)
D. Purines (A and G) pyrimidines (T and (c)
10. In DNA
A. A forms two bonds with T
B. G forms three bonds with C
C. A forms three bonds with T
D. Both a and b
Click On Below Page Numbers To Go To Next/Previous Page of Chromosome and DNA MCQs
Researchers Measure Mass of Human Chromosomes
Each human cell, at metaphase, normally contains 23 pairs of chromosomes, or 46 in total. Within these are four copies of 3.5 billion base pairs of DNA. In a new study, a team of scientists from the United Kingdom and the United States used a method called phase-sensitive X-ray ptychography to determine the number of electrons in a spread of all 46 human chromosomes they found that the chromosomes were about 20 times heavier than the DNA they contained — a much larger mass than previously expected, suggesting there might be missing components yet to be discovered.
The spread of 46 human chromosomes. Image credit: Bhatiya et al., doi: 10.1007/s10577-021-09660-7.
“Chromosomes have been investigated by scientists for 130 years but there are still parts of these complex structures that are poorly understood,” said Professor Ian Robinson, a researcher in the London Centre for Nanotechnology at University College London and the Condensed Matter Physics and Materials Science Division at Brookhaven National Lab.
“The mass of DNA we know from the Human Genome Project, but this is the first time we have been able to precisely measure the masses of chromosomes that include this DNA.”
“A better understanding of chromosomes may have important implications for human health,” said Archana Bhartiya, a Ph.D. student in the London Centre for Nanotechnology at University College London.
“A vast amount of study of chromosomes is undertaken in medical labs to diagnose cancer from patient samples. Any improvements in our abilities to image chromosomes would therefore be highly valuable.”
In the study, Professor Robinson, Bhartiya and their colleagues used X-ray ptychography — which involves stitching together the diffraction patterns that occur as the X-ray beam passes through the chromosomes — to create a highly sensitive 3D reconstruction.
The fine resolution was possible as the beam deployed at the UK’s Diamond Light Source was billions of times brighter than the Sun.
The chromosomes were imaged in metaphase, just before they were about to divide into two daughter cells.
This is when packaging proteins wind up the DNA into very compact, precise structures.
“Our measurement suggests the 46 chromosomes in each of our cells weigh 242 picograms (trillionths of a gram),” Professor Robinson said.
“This is heavier than we would expect, and, if replicated, points to unexplained excess mass in chromosomes.”
The results were published in the journal Chromosome Research.
A. Bhartiya et al. 2021. X-ray Ptychography Imaging of Human Chromosomes After Low-dose Irradiation. Chromosome Res 29, 107-126 doi: 10.1007/s10577-021-09660-7
8.2 Human Inheritance
Characteristics that are encoded in DNA are called genetic traits. Different types of human traits are inherited in different ways. Some human traits have simple inheritance patterns like the traits that Gregor Mendel studied in pea plants. Other human traits have more complex inheritance patterns.
Mendelian Inheritance in Humans
Mendelian inheritance refers to the inheritance of traits controlled by a single gene with two alleles, one of which may be dominant to the other. Not many human traits are controlled by a single gene with two alleles, but they are a good starting point for understanding human heredity. How Mendelian traits are inherited depends on whether the traits are controlled by genes on autosomes or the X chromosome.
Autosomal traits are controlled by genes on one of the 22 human autosomes. Consider earlobe attachment. A single autosomal gene with two alleles determines whether you have attached earlobes or free-hanging earlobes. The allele for free-hanging earlobes (F) is dominant to the allele for attached earlobes (f). Other single-gene autosomal traits include widow’s peak and hitchhiker’s thumb. The dominant and recessive forms of these traits are shown in Figure below. Which form of these traits do you have? What are your possible genotypes for the traits? The chart in Figure below is called a pedigree. It shows how the earlobe trait was passed from generation to generation within a family. Pedigrees are useful tools for studying inheritance patterns.
You can watch a video explaining how pedigrees are used and what they reveal at this link: http://www.youtube.com/watch?v=HbIHjsn5cHo.
CMIcreationstation – Pain in Pedigree Pups
Other single-gene autosomal traits include widow’s peak and hitchhiker’s thumb. The dominant and recessive forms of these traits are shown in Figure below. Which form of these traits do you have? What are your possible genotypes for the traits?
Traits controlled by genes on the sex chromosomes are called sex-linked traits, or X-linked traits in the case of the X chromosome. Single-gene X-linked traits have a different pattern of inheritance than single-gene autosomal traits. Do you know why? It’s because males have just one X chromosome. In addition, they always inherit their X chromosome from their mother, and they pass it on to all their daughters but none of their sons. This is illustrated in Figure below.
Because males have just one X chromosome, they have only one allele for any X-linked trait. Therefore, a recessive X-linked allele is always expressed in males. Because females have two X chromosomes, they have two alleles for any X-linked trait. Therefore, they must inherit two copies of the recessive allele to express the recessive trait. This explains why X-linked recessive traits are less common in females than males. An example of a recessive X-linked trait is red-green color blindness. People with this trait cannot distinguish between the colors red and green. More than one recessive gene on the X chromosome codes for this trait, which is fairly common in males but relatively rare in females (Figure below). At the link below, you can watch an animation about another X-linked recessive trait called hemophilia A.
Pedigree Analysis Activity
The following link is to a pedigree analysis activity. Autosomal dominant, autosomal recessive and sex-linked recessive inheritance is explored through an interactive activity. CK-12 Pedigree Analysis Animation
Most human traits have more complex modes of inheritance than simple Mendelian inheritance. For example, the traits may be controlled by multiple alleles or multiple genes.
Multiple Allele Traits
The majority of human genes are thought to have more than two alleles. Traits controlled by a single gene with more than two alleles are called multiple allele traits. An example is ABO blood type. There are three common alleles for this trait, which can be represented by the letters A, B, and O. As shown in Table below, there are six possible ABO genotypes but only four phenotypes. This is because alleles A and B are codominant to each other and both are dominant to O.
Blood Types: ABO and Rh (with donuts and sprinkles):
Can we take a break for a second and get some donuts? That was just cruel to have to watch that video and not have a box of donuts sitting on the counter.
Many human traits are controlled by more than one gene. These traits are called polygenic traits (or characteristics). The alleles of each gene have a minor additive effect on the phenotype. There are many possible combinations of alleles, especially if each gene has multiple alleles. Therefore, a whole continuum of phenotypes is possible. An example of a human polygenic trait is adult height. Several genes, each with more than one allele, contribute to this trait, so there are many possible adult heights. For example, one adult’s height might be 1.655 m (5.430 feet), and another adult’s height might be 1.656 m (5.433 feet) tall. Adult height ranges from less than 5 feet to more than 6 feet, but the majority of people fall near the middle of the range, as shown in Figure below.
Many polygenic traits are affected by the environment. For example, adult height might be negatively impacted by poor diet or illness during childhood. Skin color is another polygenic trait. There is a wide range of skin colors in people worldwide. In addition to differences in skin color genes, differences in exposure to UV light explain most of the variation. As shown in Figure below, exposure to UV light darkens the skin.
Sometimes a single gene may affect more than one trait. This is called pleiotropy. An example is the gene that codes for the main protein in collagen, a substance that helps form bones. The gene for this protein also affects the ears and eyes. This was discovered from mutations in the gene. They result in problems not only in bones but also in these sensory organs.
In other cases, one gene affects the expression of another gene. This is called epistasis. Epistasis is similar to dominance, except that it occurs between different genes rather than between different alleles for the same gene. An example is the gene coding for widow’s peak. A gene that codes for baldness would “hide” the widow’s peak trait if it occurred in the same person.
Many genetic disorders are caused by mutations in one or a few genes. Other genetic disorders are caused by abnormal numbers of chromosomes.
Genetic Disorders Caused by Mutations
Table below lists several genetic disorders caused by mutations in just one gene. Some of the disorders are caused by mutations in autosomal genes, others by mutations in X-linked genes. Which disorder would you expect to be more common in males than females?
You can click on any human chromosome at this link to see the genetic disorders associated with it:
|Genetic Disorder||Direct Effect of Mutation||Signs and Symptoms of the Disorder||Mode of Inheritance|
|Marfan syndrome||defective protein in connective tissue||heart and bone defects and unusually long, slender limbs and fingers||autosomal dominant|
|Sickle cell anemia||abnormal hemoglobin protein in red blood cells||sickle-shaped red blood cells that clog tiny blood vessels, causing pain and damaging organs and joints||autosomal recessive|
|Vitamin D-resistant rickets||lack of a substance needed for bones to absorb minerals||soft bones that easily become deformed, leading to bowed legs and other skeletal deformities||X-linked dominant|
|Hemophilia A||reduced activity of a protein needed for blood clotting||internal and external bleeding that occurs easily and is difficult to control||X-linked recessive|
Few genetic disorders are controlled by dominant alleles. A mutant dominant allele is expressed in every individual who inherits even one copy of it. If it causes a serious disorder, affected people may die young and fail to reproduce. Therefore, the mutant dominant allele is likely to die out of the population. A mutant recessive allele, such as the allele that causes sickle cell anemia (see Figure below and the link that follows), is not expressed in people who inherit just one copy of it. These people are called carriers. They do not have the disorder themselves, but they carry the mutant allele and can pass it to their offspring. Thus, the allele is likely to pass on to the next generation rather than die out.
CMIcreationstation – Sickle Cell Anemia – not evidence for evolution
Cystic Fibrosis and Tay-Sachs disease are two additional severe genetic disorders. They are discussed in the following video: http://www.youtube.com/watch?v=8s4he3wLgkM&feature=related (9:31).
Cystic Fibrosis “A Day in the Life”
Mistakes may occur during meiosis that result in nondisjunction. This is the failure of replicated chromosomes to separate during meiosis (the animation at the link below shows how this happens). Some of the resulting gametes will be missing a chromosome, while others will have an extra copy of the chromosome. If such gametes are fertilized and form zygotes, they usually do not survive. If they do survive, the individuals are likely to have serious genetic disorders. Table below lists several genetic disorders that are caused by abnormal numbers of chromosomes. Most chromosomal disorders involve the X chromosome. Look back at the X and Y chromosomes and you will see why. The X and Y chromosomes are very different in size, so nondisjunction of the sex chromosomes occurs relatively often.
A genetic condition where someone has either too many or two few chromosomes is called aneuploidy: https://learn.genetics.utah.edu/content/disorders/extraormissing/
|Genetic Disorder||Genotype||Phenotypic Effects|
|Down syndrome||extra copy (complete or partial) of chromosome 21 (see Figure below)||developmental delays, distinctive facial appearance, and other abnormalities (see Figure below)|
|Turner’s syndrome||one X chromosome but no other sex chromosome (XO)||female with short height and infertility (inability to reproduce)|
|Triple X syndrome||three X chromosomes (XXX)||female with mild developmental delays and menstrual irregularities|
|Klinefelter’s syndrome||one Y chromosome and two or more X chromosomes (XXY, XXXY)||male with problems in sexual development and reduced levels of the male hormone testosterone|
Trisomy 21 (Down Syndrome) Karyotype. A karyotype is a picture of a cell’s chromosomes. Note the extra chromosome 21. Child with Down syndrome, exhibiting characteristic facial appearance.
You may wish to do a search on YouTube for Born This Way episodes.
Diagnosing Genetic Disorders
A genetic disorder that is caused by a mutation can be inherited. Therefore, people with a genetic disorder in their family may be concerned about having children with the disorder. Professionals known as genetic counselors can help them understand the risks of their children being affected. If they decide to have children, they may be advised to have prenatal (“before birth”) testing to see if the fetus has any genetic abnormalities. One method of prenatal testing is amniocentesis. In this procedure, a few fetal cells are extracted from the fluid surrounding the fetus, and the fetal chromosomes are examined.
KQED: Treating Genetic Disorders
The symptoms of genetic disorders can sometimes be treated, but cures for genetic disorders are still in the early stages of development. One potential cure that has already been used with some success is gene therapy. This involves inserting normal genes into cells with mutant genes. At the following link, you can watch the video Sickle Cell Anemia: Hope from Gene Therapy, to learn how scientists are trying to cure sickle-cell anemia with gene therapy.
If you could learn your risk of getting cancer or another genetic disease, would you? Though this is a personal decision, it is a possibility. Some companies now make it easy to order medical genetic tests through the Web. One of these is: https://www.23andme.com/
- A minority of human traits are controlled by single genes with two alleles. They have different inheritance patterns depending on whether they are controlled by autosomal or X-linked genes.
- Most human traits have complex modes of inheritance. They may be controlled by one gene with multiple alleles or by multiple genes. More complexity may be introduced by pleiotropy (one gene, multiple effect) and epistasis (gene-gene interactions).
- Many genetic disorders are caused by mutations in one or a few genes. Other genetic disorders are caused by abnormal numbers of chromosomes.
Lesson Review Questions
1. Describe the inheritance pattern for a single-gene autosomal dominant trait, such as free-hanging earlobes.
2. Give an example of a multiple allele trait and a polygenic trait.
3. Identify factors that influence human skin color.
4. Describe a genetic disorder caused by a mutation in a single gene.
5. What causes Down syndrome?
7. Draw a pedigree for hitchhiker’s thumb. Your pedigree should cover at least two generations and include both dominant and recessive forms of the trait. Label the pedigree with genotypes, using the letter H to represent the dominant allele for the trait and the letter h to represent the recessive allele.
8. How might red-green color blindness affect the health of a person with this trait?
9. Compare and contrast dominance and epistasis.
10. Explain why genetic disorders caused by abnormal numbers of chromosomes most often involve the X chromosome.
Points to Consider
Technology has been developed to cure some genetic disorders with gene therapy. This involves inserting normal genes into cells with mutations. Scientists use genetic technology for other purposes as well.
"Biology" derives from the Ancient Greek words of βίος romanized bíos meaning "life" and -λογία romanized logía (-logy) meaning "branch of study" or "to speak".   Those combined make the Greek word βιολογία romanized biología meaning biology. Despite this, the term βιολογία as a whole didn't exist in Ancient Greek. The first to borrow it was the English and French (biologie). Historically there was another term for "biology" in English, lifelore it is rarely used today.
The Latin-language form of the term first appeared in 1736 when Swedish scientist Carl Linnaeus (Carl von Linné) used biologi in his Bibliotheca Botanica. It was used again in 1766 in a work entitled Philosophiae naturalis sive physicae: tomus III, continens geologian, biologian, phytologian generalis, by Michael Christoph Hanov, a disciple of Christian Wolff. The first German use, Biologie, was in a 1771 translation of Linnaeus' work. In 1797, Theodor Georg August Roose used the term in the preface of a book, Grundzüge der Lehre van der Lebenskraft. Karl Friedrich Burdach used the term in 1800 in a more restricted sense of the study of human beings from a morphological, physiological and psychological perspective (Propädeutik zum Studien der gesammten Heilkunst). The term came into its modern usage with the six-volume treatise Biologie, oder Philosophie der lebenden Natur (1802–22) by Gottfried Reinhold Treviranus, who announced: 
The objects of our research will be the different forms and manifestations of life, the conditions and laws under which these phenomena occur, and the causes through which they have been affected. The science that concerns itself with these objects we will indicate by the name biology [Biologie] or the doctrine of life [Lebenslehre].
The earliest of roots of science, which included medicine, can be traced to ancient Egypt and Mesopotamia in around 3000 to 1200 BCE.   Their contributions later entered and shaped Greek natural philosophy of classical antiquity.     Ancient Greek philosophers such as Aristotle (384–322 BCE) contributed extensively to the development of biological knowledge. His works such as History of Animals were especially important because they revealed his naturalist leanings, and later more empirical works that focused on biological causation and the diversity of life. Aristotle's successor at the Lyceum, Theophrastus, wrote a series of books on botany that survived as the most important contribution of antiquity to the plant sciences, even into the Middle Ages. 
Scholars of the medieval Islamic world who wrote on biology included al-Jahiz (781–869), Al-Dīnawarī (828–896), who wrote on botany,  and Rhazes (865–925) who wrote on anatomy and physiology. Medicine was especially well studied by Islamic scholars working in Greek philosopher traditions, while natural history drew heavily on Aristotelian thought, especially in upholding a fixed hierarchy of life.
Biology began to quickly develop and grow with Anton van Leeuwenhoek's dramatic improvement of the microscope. It was then that scholars discovered spermatozoa, bacteria, infusoria and the diversity of microscopic life. Investigations by Jan Swammerdam led to new interest in entomology and helped to develop the basic techniques of microscopic dissection and staining. 
Advances in microscopy also had a profound impact on biological thinking. In the early 19th century, a number of biologists pointed to the central importance of the cell. Then, in 1838, Schleiden and Schwann began promoting the now universal ideas that (1) the basic unit of organisms is the cell and (2) that individual cells have all the characteristics of life, although they opposed the idea that (3) all cells come from the division of other cells. Thanks to the work of Robert Remak and Rudolf Virchow, however, by the 1860s most biologists accepted all three tenets of what came to be known as cell theory.  
Meanwhile, taxonomy and classification became the focus of natural historians. Carl Linnaeus published a basic taxonomy for the natural world in 1735 (variations of which have been in use ever since), and in the 1750s introduced scientific names for all his species.  Georges-Louis Leclerc, Comte de Buffon, treated species as artificial categories and living forms as malleable—even suggesting the possibility of common descent. Although he was opposed to evolution, Buffon is a key figure in the history of evolutionary thought his work influenced the evolutionary theories of both Lamarck and Darwin. 
Serious evolutionary thinking originated with the works of Jean-Baptiste Lamarck, who was the first to present a coherent theory of evolution.  He posited that evolution was the result of environmental stress on properties of animals, meaning that the more frequently and rigorously an organ was used, the more complex and efficient it would become, thus adapting the animal to its environment. Lamarck believed that these acquired traits could then be passed on to the animal's offspring, who would further develop and perfect them.  However, it was the British naturalist Charles Darwin, combining the biogeographical approach of Humboldt, the uniformitarian geology of Lyell, Malthus's writings on population growth, and his own morphological expertise and extensive natural observations, who forged a more successful evolutionary theory based on natural selection similar reasoning and evidence led Alfred Russel Wallace to independently reach the same conclusions.   Darwin's theory of evolution by natural selection quickly spread through the scientific community and soon became a central axiom of the rapidly developing science of biology.
The basis for modern genetics began with the work of Gregor Mendel, who presented his paper, "Versuche über Pflanzenhybriden" ("Experiments on Plant Hybridization"), in 1865,  which outlined the principles of biological inheritance, serving as the basis for modern genetics.  However, the significance of his work was not realized until the early 20th century when evolution became a unified theory as the modern synthesis reconciled Darwinian evolution with classical genetics.  In the 1940s and early 1950s, a series of experiments by Alfred Hershey and Martha Chase pointed to DNA as the component of chromosomes that held the trait-carrying units that had become known as genes. A focus on new kinds of model organisms such as viruses and bacteria, along with the discovery of the double-helical structure of DNA by James Watson and Francis Crick in 1953, marked the transition to the era of molecular genetics. From the 1950s to the present times, biology has been vastly extended in the molecular domain. The genetic code was cracked by Har Gobind Khorana, Robert W. Holley and Marshall Warren Nirenberg after DNA was understood to contain codons. Finally, the Human Genome Project was launched in 1990 with the goal of mapping the general human genome. This project was essentially completed in 2003,  with further analysis still being published. The Human Genome Project was the first step in a globalized effort to incorporate accumulated knowledge of biology into a functional, molecular definition of the human body and the bodies of other organisms.
Atoms and molecules
All living organisms are made up of matter and all matter is made up of elements.  Oxygen, carbon, hydrogen, and nitrogen are the four elements that account for 96% of all living organisms, with calcium, phosphorus, sulfur, sodium, chlorine, and magnesium accounting for the remaining 3.7%.  Different elements can combine to form compounds such as water, which is fundamental to life.  Life on Earth began from water and remained there for about three billions years prior to migrating onto land.  Matter can exist in different states as a solid, liquid, or gas.
The smallest unit of an element is an atom, which is composed of a nucleus and one or more electrons bound to the nucleus. The nucleus is made of one or more protons and a number of neutrons. Individual atoms can be held together by chemical bonds to form molecules and ionic compounds.  Common types of chemical bonds include ionic bonds, covalent bonds, and hydrogen bonds. Ionic bonding involves the electrostatic attraction between oppositely charged ions, or between two atoms with sharply different electronegativities,  and is the primary interaction occurring in ionic compounds. Ions are atoms (or groups of atoms) with an electrostatic charge. Atoms that gain electrons make negatively charged ions (called anions) whereas those that lose electrons make positively charged ions (called cations).
Unlike ionic bonds, a covalent bond involves the sharing of electron pairs between atoms. These electron pairs and the stable balance of attractive and repulsive forces between atoms, when they share electrons, is known as covalent bonding. 
A hydrogen bond is primarily an electrostatic force of attraction between a hydrogen atom which is covalently bound to a more electronegative atom or group such as oxygen. A ubiquitous example of a hydrogen bond is found between water molecules. In a discrete water molecule, there are two hydrogen atoms and one oxygen atom. Two molecules of water can form a hydrogen bond between them. When more molecules are present, as is the case with liquid water, more bonds are possible because the oxygen of one water molecule has two lone pairs of electrons, each of which can form a hydrogen bond with a hydrogen on another water molecule.
With the exception of water, nearly all the molecules that make up each living organism contain carbon.   Carbon can form very long chains of interconnecting carbon–carbon bonds, which are strong and stable. The simplest form of an organic molecule is the hydrocarbon, which is a large family of organic compounds that are composed of hydrogen atoms bonded to a chain of carbon atoms. A hydrocarbon backbone can be substituted by other atoms. When combined with other elements such as oxygen, hydrogen, phosphorus, and sulfur, carbon can form many groups of important biological compounds such as sugars, fats, amino acids, and nucleotides.
Molecules such as sugars, amino acids, and nucleotides can act as single repeating units called monomers to form chain-like molecules called polymers via a chemical process called condensation.  For example, amino acids can form polypeptides whereas nucleotides can form strands of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). Polymers make up three of the four macromolecules (polysaccharides, lipids, proteins, and nucleic acids) that are found in all living organisms. Each macromolecule plays a specialized role within any given cell. Some polysaccharides, for instance, can function as storage material that can be hydrolyzed to provide cells with sugar. Lipids are the only class of macromolecules that are not made up of polymers and the most biologically important lipids are fats, phospholipids, and steroids.  Proteins are the most diverse of the macromolecules, which include enzymes, transport proteins, large signaling molecules, antibodies, and structural proteins. Finally, nucleic acids store, transmit, and express hereditary information. 
Cell theory states that cells are the fundamental units of life, that all living things are composed of one or more cells, and that all cells arise from preexisting cells through cell division.  Most cells are very small, with diameters ranging from 1 to 100 micrometers and are therefore only visible under a light or electron microscope.  There are generally two types of cells: eukaryotic cells, which contain a nucleus, and prokaryotic cells, which do not. Prokaryotes are single-celled organisms such as bacteria, whereas eukaryotes can be single-celled or multicellular. In multicellular organisms, every cell in the organism's body is derived ultimately from a single cell in a fertilized egg.
Every cell is enclosed within a cell membrane that separates its cytoplasm from the extracellular space.  A cell membrane consists of a lipid bilayer, including cholesterols that sit between phospholipids to maintain their fluidity at various temperatures. Cell membranes are semipermeable, allowing small molecules such as oxygen, carbon dioxide, and water to pass through while restricting the movement of larger molecules and charged particles such as ions.  Cell membranes also contains membrane proteins, including integral membrane proteins that go across the membrane serving as membrane transporters, and peripheral proteins that loosely attach to the outer side of the cell membrane, acting as enzymes shaping the cell.  Cell membranes are involved in various cellular processes such as cell adhesion, storing electrical energy, and cell signalling and serve as the attachment surface for several extracellular structures such as a cell wall, glycocalyx, and cytoskeleton.
Within the cytoplasm of a cell, there are many biomolecules such as proteins and nucleic acids.  In addition to biomolecules, eukaryotic cells have specialized structures called organelles that have their own lipid bilayers or are spatially units. These organelles include the cell nucleus, which contains a cell's genetic information, or mitochondria, which generates adenosine triphosphate (ATP) to power cellular processes. Other organelles such as endoplasmic reticulum and Golgi apparatus play a role in the synthesis and packaging of proteins, respectively. Biomolecules such as proteins can be engulfed by lysosomes, another specialized organelle. Plant cells have additional organelles that distinguish them from animal cells such as a cell wall, chloroplasts, and vacuole.
All cells require energy to sustain cellular processes. Energy is the capacity to do work, which, in thermodynamics, can be calculated using Gibbs free energy. According to the first law of thermodynamics, energy is conserved, i.e., cannot be created or destroyed. Hence, chemical reactions in a cell do not create new energy but are involved instead in the transformation and transfer of energy.  Nevertheless, all energy transfers lead to some loss of usable energy, which increases entropy (or state of disorder) as stated by the second law of thermodynamics. As a result, living organisms such as cells require continuous input of energy to maintain a low state of entropy. In cells, energy can be transferred as electrons during redox (reduction–oxidation) reactions, stored in covalent bonds, and generated by the movement of ions (e.g., hydrogen, sodium, potassium) across a membrane.
Metabolism is the set of life-sustaining chemical reactions in organisms. The three main purposes of metabolism are: the conversion of food to energy to run cellular processes the conversion of food/fuel to building blocks for proteins, lipids, nucleic acids, and some carbohydrates and the elimination of metabolic wastes. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. Metabolic reactions may be categorized as catabolic – the breaking down of compounds (for example, the breaking down of glucose to pyruvate by cellular respiration) or anabolic – the building up (synthesis) of compounds (such as proteins, carbohydrates, lipids, and nucleic acids). Usually, catabolism releases energy, and anabolism consumes energy.
The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, each step being facilitated by a specific enzyme. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy that will not occur by themselves, by coupling them to spontaneous reactions that release energy. Enzymes act as catalysts – they allow a reaction to proceed more rapidly without being consumed by it – by reducing the amount of activation energy needed to convert reactants into products. Enzymes also allow the regulation of the rate of a metabolic reaction, for example in response to changes in the cell's environment or to signals from other cells.
Cellular respiration is a set of metabolic reactions and processes that take place in the cells of organisms to convert chemical energy from nutrients into adenosine triphosphate (ATP), and then release waste products.  The reactions involved in respiration are catabolic reactions, which break large molecules into smaller ones, releasing energy because weak high-energy bonds, in particular in molecular oxygen,  are replaced by stronger bonds in the products. Respiration is one of the key ways a cell releases chemical energy to fuel cellular activity. The overall reaction occurs in a series of biochemical steps, some of which are redox reactions. Although cellular respiration is technically a combustion reaction, it clearly does not resemble one when it occurs in a living cell because of the slow, controlled release of energy from the series of reactions.
Sugar in the form of glucose is the main nutrient used by animal and plant cells in respiration. Cellular respiration involving oxygen is called aerobic respiration, which has four stages: glycolysis, citric acid cycle (or Krebs cycle), electron transport chain, and oxidative phosphorylation.  Glycolysis is a metabolic process that occurs in the cytoplasm whereby glucose is converted into two pyruvates, with two net molecules of ATP being produced at the same time.  Each pyruvate is then oxidized into acetyl-CoA by the pyruvate dehydrogenase complex, which also generates NADH and carbon dioxide. Acetyl-Coa enters the citric acid cycle, which takes places inside the mitochondrial matrix. At the end of the cycle, the total yield from 1 glucose (or 2 pyruvates) is 6 NADH, 2 FADH2, and 2 ATP molecules. Finally, the next stage is oxidative phosphorylation, which in eukaryotes, occurs in the mitochondrial cristae. Oxidative phosphorylation comprises the electron transport chain, which is a series of four protein complexes that transfer electrons from one complex to another, thereby releasing energy from NADH and FADH2 that is coupled to the pumping of protons (hydrogen ions) across the inner mitochondrial membrane (chemiosmosis), which generates a proton motive force.  Energy from the proton motive force drives the enzyme ATP synthase to synthesize more ATPs by phosphorylating ADPs. The transfer of electrons terminates with molecular oxygen being the final electron acceptor.
If oxygen were not present, pyruvate would not be metabolized by cellular respiration but undergoes a process of fermentation. The pyruvate is not transported into the mitochondrion but remains in the cytoplasm, where it is converted to waste products that may be removed from the cell. This serves the purpose of oxidizing the electron carriers so that they can perform glycolysis again and removing the excess pyruvate. Fermentation oxidizes NADH to NAD + so it can be re-used in glycolysis. In the absence of oxygen, fermentation prevents the buildup of NADH in the cytoplasm and provides NAD + for glycolysis. This waste product varies depending on the organism. In skeletal muscles, the waste product is lactic acid. This type of fermentation is called lactic acid fermentation. In strenuous exercise, when energy demands exceed energy supply, the respiratory chain cannot process all of the hydrogen atoms joined by NADH. During anaerobic glycolysis, NAD + regenerates when pairs of hydrogen combine with pyruvate to form lactate. Lactate formation is catalyzed by lactate dehydrogenase in a reversible reaction. Lactate can also be used as an indirect precursor for liver glycogen. During recovery, when oxygen becomes available, NAD + attaches to hydrogen from lactate to form ATP. In yeast, the waste products are ethanol and carbon dioxide. This type of fermentation is known as alcoholic or ethanol fermentation. The ATP generated in this process is made by substrate-level phosphorylation, which does not require oxygen.
Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that can later be released to fuel the organism's metabolic activities via cellular respiration. This chemical energy is stored in carbohydrate molecules, such as sugars, which are synthesized from carbon dioxide and water.    In most cases, oxygen is also released as a waste product. Most plants, algae, and cyanobacteria perform photosynthesis, which is largely responsible for producing and maintaining the oxygen content of the Earth's atmosphere, and supplies most of the energy necessary for life on Earth. 
Photosynthesis has four stages: Light absorption, electron transport, ATP synthesis, and carbon fixation.  Light absorption is the initial step of photosynthesis whereby light energy is absorbed by chlorophyll pigments attached to proteins in the thylakoid membranes. The absorbed light energy is used to remove electrons from a donor (water) to a primary electron acceptor, a quinone designated as Q. In the second stage, electrons move from the quinone primary electron acceptor through a series of electron carriers until they reach a final electron acceptor, which is usually the oxidized form of NADP + , which is reduced to NADPH, a process that takes place in a protein complex called photosystem I (PSI). The transport of electrons is coupled to the movement of protons (or hydrogen) from the stroma to the thylakoid membrane, which forms a pH gradient across the membrane as hydrogen becomes more concentrated in the lumen than in the stroma. This is analogous to the proton-motive force generated across the inner mitochondrial membrane in aerobic respiration. 
During the third stage of photosynthesis, the movement of protons down their concentration gradients from the thylakoid lumen to the stroma through the ATP synthase is coupled to the synthesis of ATP by that same ATP synthase.  The NADPH and ATPs generated by the light-dependent reactions in the second and third stages, respectively, provide the energy and electrons to drive the synthesis of glucose by fixing atmospheric carbon dioxide into existing organic carbon compounds, such as ribulose bisphosphate (RuBP) in a sequence of light-independent (or dark) reactions called the Calvin cycle. 
Cell communication (or signaling) is the ability of cells to receive, process, and transmit signals with its environment and with itself.   Signals can be non-chemical such as light, electrical impulses, and heat, or chemical signals (or ligands) that interact with receptors, which can be found embedded in the cell membrane of another cell or located deep inside a cell.   There are generally four types of chemical signals: autocrine, paracrine, juxtacrine, and hormones.  In autocrine signaling, the ligand affects the same cell that releases it. Tumor cells, for example, can reproduce uncontrollably because they release signals that initiate their own self-division. In paracrine signaling, the ligand diffuses to nearby cells and affect them. For example, brain cells called neurons release ligands called neurotransmitters that diffuse across a synaptic cleft to bind with a receptor on an adjacent cell such as another neuron or muscle cell. In juxtacrine signaling, there is direct contact between the signaling and responding cells. Finally, hormones are ligands that travel through the circulatory systems of animals or vascular systems of plants to reach their target cells. Once a ligand binds with a receptor, it can influence the behavior of another cell, depending on the type of receptor. For instance, neurotransmitters that bind with an inotropic receptor can alter the excitability of a target cell. Other types of receptors include protein kinase receptors (e.g., receptor for the hormone insulin) and G protein-coupled receptors. Activation of G protein-coupled receptors can initiate second messenger cascades. The process by which a chemical or physical signal is transmitted through a cell as a series of molecular events is called signal transduction
The cell cycle is a series of events that take place in a cell that cause it to divide into two daughter cells. These events include the duplication of its DNA and some of its organelles, and the subsequent partitioning of its cytoplasm into two daughter cells in a process called cell division.  In eukaryotes (i.e., animal, plant, fungal, and protist cells), there are two distinct types of cell division: mitosis and meiosis.  Mitosis is part of the cell cycle, in which replicated chromosomes are separated into two new nuclei. Cell division gives rise to genetically identical cells in which the total number of chromosomes is maintained. In general, mitosis (division of the nucleus) is preceded by the S stage of interphase (during which the DNA is replicated) and is often followed by telophase and cytokinesis which divides the cytoplasm, organelles and cell membrane of one cell into two new cells containing roughly equal shares of these cellular components. The different stages of mitosis all together define the mitotic phase of an animal cell cycle—the division of the mother cell into two genetically identical daughter cells.  The cell cycle is a vital process by which a single-celled fertilized egg develops into a mature organism, as well as the process by which hair, skin, blood cells, and some internal organs are renewed. After cell division, each of the daughter cells begin the interphase of a new cycle. In contrast to mitosis, meiosis results in four haploid daughter cells by undergoing one round of DNA replication followed by two divisions.  Homologous chromosomes are separated in the first division (meiosis I), and sister chromatids are separated in the second division (meiosis II). Both of these cell division cycles are used in the process of sexual reproduction at some point in their life cycle. Both are believed to be present in the last eukaryotic common ancestor.
Prokaryotes (i.e., archaea and bacteria) can also undergo cell division (or binary fission). Unlike the processes of mitosis and meiosis in eukaryotes, binary fission takes in prokaryotes takes place without the formation of a spindle apparatus on the cell. Before binary fission, DNA in the bacterium is tightly coiled. After it has uncoiled and duplicated, it is pulled to the separate poles of the bacterium as it increases the size to prepare for splitting. Growth of a new cell wall begins to separate the bacterium (triggered by FtsZ polymerization and "Z-ring" formation)  The new cell wall (septum) fully develops, resulting in the complete split of the bacterium. The new daughter cells have tightly coiled DNA rods, ribosomes, and plasmids.
Genetics is the scientific study of inheritance.    Mendelian inheritance, specifically, is the process by which genes and traits are passed on from parents to offspring.  It was formulated by Gregor Mendel, based on his work with pea plants in the mid-nineteenth century. Mendel established several principles of inheritance. The first is that genetic characteristics, which are now called alleles, are discrete and have alternate forms (e.g., purple vs. white or tall vs. dwarf), each inherited from one of two parents. Based on his law of dominance and uniformity, which states that some alleles are dominant while others are recessive an organism with at least one dominant allele will display the phenotype of that dominant allele.  Exceptions to this rule include penetrance and expressivity.  Mendel noted that during gamete formation, the alleles for each gene segregate from each other so that each gamete carries only one allele for each gene, which is stated by his law of segregation. Heterozygotic individuals produce gametes with an equal frequency of two alleles. Finally, Mendel formulated the law of independent assortment, which states that genes of different traits can segregate independently during the formation of gametes, i.e., genes are unlinked. An exception to this rule would include traits that are sex-linked. Test crosses can be performed to experimentally determine the underlying genotype of an organism with a dominant phenotype.  A Punnett square can be used to predict the results of a test cross. The chromosome theory of inheritance, which states that genes are found on chromosomes, was supported by Thomas Morgans's experiments with fruit flies, which established the sex linkage between eye color and sex in these insects.  In humans and other mammals (e.g., dogs), it is not feasible or practical to conduct test cross experiments. Instead, pedigrees, which are genetic representations of family trees,  are used instead to trace the inheritance of a specific trait or disease through multiple generations. 
Deoxyribonucleic acid (DNA) is a molecule composed of two polynucleotide chains that coil around each other to form a double helix carrying genetic hereditary information. The two DNA strands are known as polynucleotides as they are composed of monomers called nucleotides.   Each nucleotide is composed of one of four nitrogenous bases (cytosine [C], guanine [G], adenine [A] or thymine [T]), a sugar called deoxyribose, and a phosphate group. The nucleotides are joined to one another in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone. It is the sequence of these four bases along the backbone that encodes genetic information. Bases of the two polynucleotide strands are bound together by hydrogen bonds, according to base pairing rules (A with T and C with G), to make double-stranded DNA. The bases are divided into two groups: pyrimidines and purines. In DNA, the pyrimidines are thymine and cytosine whereas the purines are adenine and guanine. The two strands of DNA run in opposite directions to each other and are thus antiparallel. DNA is replicated once the two strands separate.
A gene is a unit of heredity that corresponds to a region of DNA that influences the form or function of an organism in specific ways. DNA is found as linear chromosomes in eukaryotes, and circular chromosomes in prokaryotes. A chromosome is an organized structure consisting of DNA and histones. The set of chromosomes in a cell and any other hereditary information found in the mitochondria, chloroplasts, or other locations is collectively known as a cell's genome. In eukaryotes, genomic DNA is localized in the cell nucleus, or with small amounts in mitochondria and chloroplasts.  In prokaryotes, the DNA is held within an irregularly shaped body in the cytoplasm called the nucleoid.  The genetic information in a genome is held within genes, and the complete assemblage of this information in an organism is called its genotype.  Genes encode the information needed by cells for the synthesis of proteins, which in turn play a central role in influencing the final phenotype of the organism.
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect. The process is summarized in the central dogma of molecular biology first formulated by Francis Crick in 1958.    Gene expression is the most fundamental level at which a genotype gives rise to a phenotype, i.e., observable trait. The genetic information stored in DNA represents the genotype, whereas the phenotype results from the synthesis of proteins that control an organism's structure and development, or that act as enzymes catalyzing specific metabolic pathways. A large part of DNA (e.g., >98% in humans) is non-coding, meaning that these sections do not serve as patterns for protein sequences. Messenger RNA (mRNA) strands are created using DNA strands as a template in a process called transcription, where DNA bases are exchanged for their corresponding bases except in the case of thymine (T), for which RNA substitutes uracil (U).  Under the genetic code, these mRNA strands specify the sequence of amino acids within proteins in a process called translation, which occurs in ribosomes. This process is used by all life—eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea), and utilized by viruses—to generate the macromolecular machinery for life. Gene products are often proteins, but in non-protein-coding genes such as transfer RNA (tRNA) and small nuclear RNA (snRNA), the product is a functional non-coding RNA.   All steps in the gene expression process can be regulated, including the transcription, RNA splicing, translation, and post-translational modification of a protein. Regulation of gene expression gives control over the timing, location, and amount of a given gene product (protein or ncRNA) present in a cell and can have a profound effect on cellular structure and function.
A genome is an organism's complete set of DNA, including all of its genes.  Sequencing and analysis of genomes can be done using high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes.    Many genes encode more than one protein, with posttranslational modifications increasing the diversity of proteins within a cell. A cell's proteome is its entire set of proteins expressed by its genome.  The genomes of prokaryotes are small, compact, and diverse. In contrast, the genomes of eukaryotes are larger and more complex such as having more regulatory sequences and much of its genome are made up of non-coding DNA sequences for functional RNA (rRNA, tRNA, and mRNA) or regulatory sequences. The genomes of various model organisms such as arabidopsis, fruit fly, mice, nematodes, and yeast have been sequenced. The sequencing of the entire human genome has yielded practical applications such as DNA fingerprinting, which can be used for paternity testing and forensics. In medicine, sequencing of the entire human genome has allowed for the identification mutations that cause tumors as well as genes that cause a specific genetic disorder. 
Biotechnology is the use of cells or living organisms to develop products for humans.  It includes tools such as recombinant DNA, which are DNA molecules formed by laboratory methods of genetic recombination such as molecular cloning, which bring together genetic material from multiple sources, creating sequences that would otherwise not be found in a genome. Other tools include the use of genomic libraries, DNA microarrays, expression vectors, synthetic genomics, and CRISPR gene editing.   Many of these tools have wide applications such as creating medically useful proteins, or improving plant cultivation and animal husbandry.  Human insulin, for example, was the first medicine to be made using recombinant DNA technology. Other approaches such as pharming can produce large quantities of medically useful products through the use of genetically modified organisms. 
Genes, development, and evolution
Development is the process by which a multicellular organism (plant or animal) goes through a series of a changes, starting from a single cell, and taking on various forms that are characteristic of its life cycle.  There are four key processes that underlie development: Determination, differentiation, morphogenesis, and growth. Determination sets the developmental fate of a cell, which becomes more restrictive during development. Differentiation is the process by which specialized cells from less specialized cells such as stem cells.   Stem cells are undifferentiated or partially differentiated cells that can differentiate into various types of cells and proliferate indefinitely to produce more of the same stem cell.  Cellular differentiation dramatically changes a cell's size, shape, membrane potential, metabolic activity, and responsiveness to signals, which are largely due to highly controlled modifications in gene expression and epigenetics. With a few exceptions, cellular differentiation almost never involves a change in the DNA sequence itself.  Thus, different cells can have very different physical characteristics despite having the same genome. Morphogenesis, or development of body form, is the result of spatial differences in gene expression.  Specially, the organization of differentiated tissues into specific structures such as arms or wings, which is known as pattern formation, is governed by morphogens, signaling molecules that move from one group of cells to surrounding cells, creating a morphogen gradient as described by the French flag model. Apoptosis, or programmed cell death, also occurs during morphogenesis, such as the death of cells between digits in human embryonic development, which frees up individual fingers and toes. Expression of transcription factor genes can determine organ placement in a plant and a cascade of transcription factors themselves can establish body segmentation in a fruit fly. 
A small fraction of the genes in an organism's genome called the developmental-genetic toolkit control the development of that organism. These toolkit genes are highly conserved among phyla, meaning that they are ancient and very similar in widely separated groups of animals. Differences in deployment of toolkit genes affect the body plan and the number, identity, and pattern of body parts. Among the most important toolkit genes are the Hox genes. Hox genes determine where repeating parts, such as the many vertebrae of snakes, will grow in a developing embryo or larva.  Variations in the toolkit may have produced a large part of the morphological evolution of animals. The toolkit can drive evolution in two ways. A toolkit gene can be expressed in a different pattern, as when the beak of Darwin's large ground-finch was enlarged by the BMP gene,  or when snakes lost their legs as Distal-less (Dlx) genes became under-expressed or not expressed at all in the places where other reptiles continued to form their limbs.  Or, a toolkit gene can acquire a new function, as seen in the many functions of that same gene, distal-less, which controls such diverse structures as the mandible in vertebrates,   legs and antennae in the fruit fly,  and eyespot pattern in butterfly wings.  Given that small changes in toolbox genes can cause significant changes in body structures, they have often enabled convergent or parallel evolution.
A central organizing concept in biology is that life changes and develops through evolution, which is the change in heritable characteristics of populations over successive generations.   Evolution is now used to explain the great variations of life on Earth. The term evolution was introduced into the scientific lexicon by Jean-Baptiste de Lamarck in 1809,  and fifty years later Charles Darwin and Alfred Russel Wallace formulated the theory of evolution by natural selection.     According to this theory, individuals differ from each other with respect to their heritable traits, resulting in different rates of survival and reproduction. As a results, traits that are better adapted to their environment are more likely to be passed on to subsequent generations.   Darwin was not aware of Mendel's work of inheritance and so the exact mechanism of inheritance that underlie natural selection was not well-understood  until the early 20th century when the modern synthesis reconciled Darwinian evolution with classical genetics, which established a neo-Darwinian perspective of evolution by natural selection.  This perspective holds that evolution occurs when there are changes in the allele frequencies within a population of interbreeding organisms. In the absence of any evolutionary process acting on a large random mating population, the allele frequencies will remain constant across generations as described by the Hardy–Weinberg principle. 
Another process that drives evolution is genetic drift, which is the random fluctuations of allele frequencies within a population from one generation to the next.  When selective forces are absent or relatively weak, allele frequencies are equally likely to drift upward or downward at each successive generation because the alleles are subject to sampling error.  This drift halts when an allele eventually becomes fixed, either by disappearing from the population or replacing the other alleles entirely. Genetic drift may therefore eliminate some alleles from a population due to chance alone.
Speciation is the process of splitting one lineage into two lineages that evolve independently from each other.  For speciation to occur, there has to be reproductive isolation.  Reproductive isolation can result from incompatibilities between genes as described by Bateson–Dobzhansky–Muller model. Reproductive isolation also tends to increase with genetic divergence. Speciation can occur when there are physical barriers that divide an ancestral species, a process known as allopatric speciation.  In contrast, sympatric speciation occurs in the absence of physical barriers.
Pre-zygotic isolation such as mechanical, temporal, behavioral, habitat, and gametic isolations can prevent different species from hybridizing.  Similarly, post-zygotic isolations can result in hybridization being selected against due to the lower viability of hybrids or hybrid infertility (e.g., mule). Hybrid zones can emerge if there were to be incomplete reproductive isolation between two closely related species.
A phylogeny is an evolutionary history of a specific group of organisms or their genes.  A phylogeny can be represented using a phylogenetic tree, which is a diagram showing lines of descent among organisms or their genes. Each line drawn on the time axis of a tree represents a lineage of descendents of a particular species or population. When a lineage divides into two, it is represented as a node (or split) on the phylogenetic tree. The more splits there are over time, the more branches there will be on the tree, with the common ancestor of all the organisms in that tree being represented by the root of that tree. Phylogenetic trees may portray the evolutionary history of all life forms, a major evolutionary group (e.g., insects), or an even smaller group of closely related species. Within a tree, any group of species designated by a name is a taxon (e.g., humans, primates, mammals, or vertebrates) and a taxon that consists of all its evolutionary descendants is a clade. Closely related species are referred to as sister species and closely related clades are sister clades.
Phylogenetic trees are the basis for comparing and grouping different species.  Different species that share a feature inherited from a common ancestor are described as having homologous features. Homologous features may be any heritable traits such as DNA sequence, protein structures, anatomical features, and behavior patterns. A vertebral column is an example of a homologous feature shared by all vertebrate animals. Traits that have a similar form or function but were not derived from a common ancestor are described as analogous features. Phylogenies can be reconstructed for a group of organisms of primary interests, which are called the ingroup. A species or group that is closely related to the ingroup but is phylogenetically outside of it is called the outgroup, which serves a reference point in the tree. The root of the tree is located between the ingroup and the outgroup.  When phylogenetic trees are reconstructed, multiple trees with different evolutionary histories can be generated. Based on the principle of Parsimony (or Occam's razor), the tree that is favored is the one with the fewest evolutionary changes needed to be assumed over all traits in all groups. Computational algorithms can be used to determine how a tree might have evolved given the evidence. 
Phylogeny provides the basis of biological classification, which is based on Linnaean taxonomy that was developed by Carl Linnaeus in the 18th century.  This classification system is rank-based, with the highest rank being the domain followed by kingdom, phylum, class, order, family, genus, and species.  All living organisms can be classified as belonging to one of three domains: Archaea (originally Archaebacteria) bacteria (originally eubacteria), or eukarya (includes the protist, fungi, plant, and animal kingdoms).  A binomial nomenclature is used to classify different species. Based on this system, each species is given two names, one for its genus and another for its species.  For example, humans are Homo sapiens, with Homo being the genus and sapiens being the species. By convention, the scientific names of organisms are italicized, with only the first letter of the genus capitalized.  
History of life
The history of life on Earth traces the processes by which organisms have evolved from the earliest emergence of life to present day. Earth formed about 4.5 billion years ago and all life on Earth, both living and extinct, descended from a last universal common ancestor that lived about 3.5 billion years ago.   The similarities among all known present-day species indicate that they have diverged through the process of evolution from their common ancestor.  Biologists regard the ubiquity of the genetic code as evidence of universal common descent for all bacteria, archaea, and eukaryotes.    
Microbal mats of coexisting bacteria and archaea were the dominant form of life in the early Archean Epoch and many of the major steps in early evolution are thought to have taken place in this environment.  The earliest evidence of eukaryotes dates from 1.85 billion years ago,   and while they may have been present earlier, their diversification accelerated when they started using oxygen in their metabolism. Later, around 1.7 billion years ago, multicellular organisms began to appear, with differentiated cells performing specialised functions. 
Algae-like multicellular land plants are dated back even to about 1 billion years ago,  although evidence suggests that microorganisms formed the earliest terrestrial ecosystems, at least 2.7 billion years ago.  Microorganisms are thought to have paved the way for the inception of land plants in the Ordovician period. Land plants were so successful that they are thought to have contributed to the Late Devonian extinction event. 
Ediacara biota appear during the Ediacaran period,  while vertebrates, along with most other modern phyla originated about 525 million years ago during the Cambrian explosion.  During the Permian period, synapsids, including the ancestors of mammals, dominated the land,  but most of this group became extinct in the Permian–Triassic extinction event 252 million years ago.  During the recovery from this catastrophe, archosaurs became the most abundant land vertebrates  one archosaur group, the dinosaurs, dominated the Jurassic and Cretaceous periods.  After the Cretaceous–Paleogene extinction event 66 million years ago killed off the non-avian dinosaurs,  mammals increased rapidly in size and diversity.  Such mass extinctions may have accelerated evolution by providing opportunities for new groups of organisms to diversify. 
Bacteria and Archaea
Bacteria are a type of cell that constitute a large domain of prokaryotic microorganisms. Typically a few micrometers in length, bacteria have a number of shapes, ranging from spheres to rods and spirals. Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste,  and the deep biosphere of the earth's crust. Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only about 27 percent of the bacterial phyla have species that can be grown in the laboratory. 
Archaea constitute the other domain of prokaryotic cells and were initially classified as bacteria, receiving the name archaebacteria (in the Archaebacteria kingdom), a term that has fallen out of use.  Archaeal cells have unique properties separating them from the other two domains, Bacteria and Eukaryota. Archaea are further divided into multiple recognized phyla. Archaea and bacteria are generally similar in size and shape, although a few archaea have very different shapes, such as the flat and square cells of Haloquadratum walsbyi.  Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably for the enzymes involved in transcription and translation. Other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes,  including archaeols. Archaea use more energy sources than eukaryotes: these range from organic compounds, such as sugars, to ammonia, metal ions or even hydrogen gas. Salt-tolerant archaea (the Haloarchaea) use sunlight as an energy source, and other species of archaea fix carbon, but unlike plants and cyanobacteria, no known species of archaea does both. Archaea reproduce asexually by binary fission, fragmentation, or budding unlike bacteria, no known species of Archaea form endospores.
The first observed archaea were extremophiles, living in extreme environments, such as hot springs and salt lakes with no other organisms. Improved molecular detection tools led to the discovery of archaea in almost every habitat, including soil, oceans, and marshlands. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet.
Archaea are a major part of Earth's life. They are part of the microbiota of all organisms. In the human microbiome, they are important in the gut, mouth, and on the skin.  Their morphological, metabolic, and geographical diversity permits them to play multiple ecological roles: carbon fixation nitrogen cycling organic compound turnover and maintaining microbial symbiotic and syntrophic communities, for example. 
Protists are eukaryotic organism that is not an animal, plant, or fungus. While it is likely that protists share a common ancestor (the last eukaryotic common ancestor),  the exclusion of other eukaryotes means that protists do not form a natural group, or clade. [a] So some protists may be more closely related to animals, plants, or fungi than they are to other protists however, like algae, invertebrates, or protozoans, the grouping is used for convenience. 
The taxonomy of protists is still changing. Newer classifications attempt to present monophyletic groups based on morphological (especially ultrastructural),    biochemical (chemotaxonomy)   and DNA sequence (molecular research) information.   Because protists as a whole are paraphyletic, new systems often split up or abandon the kingdom, instead treating the protist groups as separate lines of eukaryotes.
Plants are mainly multicellular organisms, predominantly photosynthetic eukaryotes of the kingdom Plantae. Botany is the study of plant life, which would exclude fungi and some algae. Botanists have studied approximately 410,000 species of land plants of which some 391,000 species are vascular plants (including approximately 369,000 species of flowering plants),  and approximately 20,000 are bryophytes. 
Algae is a large and diverse group of photosynthetic eukaryotic organisms. Included organisms range from unicellular microalgae, such as Chlorella, Prototheca and the diatoms, to multicellular forms, such as the giant kelp, a large brown alga. Most are aquatic and autotrophic and lack many of the distinct cell and tissue types, such as stomata, xylem and phloem, which are found in land plants. The largest and most complex marine algae are called seaweeds, while the most complex freshwater forms are the Charophyta.
Nonvascular plants are plants without a vascular system consisting of xylem and phloem. Instead, they may possess simpler tissues that have specialized functions for the internal transport of water. Vascular plants, on the other hand, are a large group of plants (c. 300,000 accepted known species)  that are defined as land plants with lignified tissues (the xylem) for conducting water and minerals throughout the plant.  They also have a specialized non-lignified tissue (the phloem) to conduct products of photosynthesis. Vascular plants include the clubmosses, horsetails, ferns, gymnosperms (including conifers) and angiosperms (flowering plants).
Seed plants (or spermatophyte) comprise five divisions, four of which are grouped as gymnosperms and one is angiosperms. Gymnosperms includes conifers, cycads, Ginkgo, and gnetophytes. Gymnosperm seeds develop either on the surface of scales or leaves, which are often modified to form cones, or solitary as in yew, Torreya, Ginkgo.  Angiosperms are the most diverse group of land plants, with 64 orders, 416 families, approximately 13,000 known genera and 300,000 known species.  Like gymnosperms, angiosperms are seed-producing plants. They are distinguished from gymnosperms by having characteristics such as flowers, endosperm within their seeds, and production of fruits that contain the seeds.
Fungi are eukaryotic organisms that include microorganisms such as yeasts and molds, as well as the more familiar mushrooms. A characteristic that places fungi in a different kingdom from plants, bacteria, and some protists is chitin in their cell walls. Fungi, like animals, are heterotrophs they acquire their food by absorbing dissolved molecules, typically by secreting digestive enzymes into their environment. Fungi do not photosynthesize. Growth is their means of mobility, except for spores (a few of which are flagellated), which may travel through the air or water. Fungi are the principal decomposers in ecological systems. These and other differences place fungi in a single group of related organisms, named the Eumycota (true fungi or Eumycetes), which share a common ancestor (from a monophyletic group). This fungal group is distinct from the structurally similar myxomycetes (slime molds) and oomycetes (water molds).
Most fungi are inconspicuous because of the small size of their structures, and their cryptic lifestyles in soil or on dead matter. Fungi include symbionts of plants, animals, or other fungi and also parasites. They may become noticeable when fruiting, either as mushrooms or as molds. Fungi perform an essential role in the decomposition of organic matter and have fundamental roles in nutrient cycling and exchange in the environment.
The fungus kingdom encompasses an enormous diversity of taxa with varied ecologies, life cycle strategies, and morphologies ranging from unicellular aquatic chytrids to large mushrooms. However, little is known of the true biodiversity of Kingdom Fungi, which has been estimated at 2.2 million to 3.8 million species.  Of these, only about 148,000 have been described,  with over 8,000 species known to be detrimental to plants and at least 300 that can be pathogenic to humans. 
Animals are multicellular eukaryotic organisms that form the kingdom Animalia. With few exceptions, animals consume organic material, breathe oxygen, are able to move, can reproduce sexually, and grow from a hollow sphere of cells, the blastula, during embryonic development. Over 1.5 million living animal species have been described—of which around 1 million are insects—but it has been estimated there are over 7 million animal species in total. They have complex interactions with each other and their environments, forming intricate food webs.
Sponges, the members of the phylum Porifera, are a basal Metazoa (animal) clade as a sister of the Diploblasts.      They are multicellular organisms that have bodies full of pores and channels allowing water to circulate through them, consisting of jelly-like mesohyl sandwiched between two thin layers of cells.
97%) of animal species are invertebrates,  which are animals that neither possess nor develop a vertebral column (commonly known as a backbone or spine), derived from the notochord. This includes all animals apart from the subphylum Vertebrata. Familiar examples of invertebrates include arthropods (insects, arachnids, crustaceans, and myriapods), mollusks (chitons, snail, bivalves, squids, and octopuses), annelid (earthworms and leeches), and cnidarians (hydras, jellyfishes, sea anemones, and corals). Many invertebrate taxa have a greater number and variety of species than the entire subphylum of Vertebrata. 
In contrast, vertebrates comprise all species of animals within the subphylum Vertebrata (chordates with backbones). Vertebrates represent the overwhelming majority of the phylum Chordata, with currently about 69,963 species described.  Vertebrates include such groups as jawless fishes, jawed vertebrates such as cartilaginous fishes (sharks, rays, and ratfish), bony fishes, tetrapods such as amphibians, reptiles, birds and mammals.
Viruses are submicroscopic infectious agents that replicate inside the living cells of organisms.  Viruses infect all types of life forms, from animals and plants to microorganisms, including bacteria and archaea.   More than 6,000 virus species have been described in detail.  Viruses are found in almost every ecosystem on Earth and are the most numerous type of biological entity.  
When infected, a host cell is forced to rapidly produce thousands of identical copies of the original virus. When not inside an infected cell or in the process of infecting a cell, viruses exist in the form of independent particles, or virions, consisting of the genetic material (DNA or RNA), a protein coat called capsid, and in some cases an outside envelope of lipids. The shapes of these virus particles range from simple helical and icosahedral forms to more complex structures. Most virus species have virions too small to be seen with an optical microscope, as they are one-hundredth the size of most bacteria.
The origins of viruses in the evolutionary history of life are unclear: some may have evolved from plasmids—pieces of DNA that can move between cells—while others may have evolved from bacteria. In evolution, viruses are an important means of horizontal gene transfer, which increases genetic diversity in a way analogous to sexual reproduction.  Because viruses possess some but not all characteristics of life, they have been described as "organisms at the edge of life",  and as self-replicators. 
Viruses can spread in many ways. One transmission pathway is through disease-bearing organisms known as vectors: for example, viruses are often transmitted from plant to plant by insects that feed on plant sap, such as aphids and viruses in animals can be carried by blood-sucking insects. Influenza viruses are spread by coughing and sneezing. Norovirus and rotavirus, common causes of viral gastroenteritis, are transmitted by the faecal–oral route, passed by hand-to-mouth contact or in food or water. Viral infections in animals provoke an immune response that usually eliminates the infecting virus. Immune responses can also be produced by vaccines, which confer an artificially acquired immunity to the specific viral infection.
Plant form and function
The plant body is made up of organs that can be organized into two major organ systems: a root system and a shoot system.  The root system anchors the plants into place. The roots themselves absorb water and minerals and store photosynthetic products. The shoot system is composed of stem, leaves, and flowers. The stems hold and orient the leaves to the sun, which allow the leaves to conduct photosynthesis. The flowers are shoots that have been modified for reproduction. Shoots are composed of phytomers, which are functional units that consist of a node carrying one or more leaves, internode, and one or more buds.
A plant body has two basic patterns (apical–basal and radial axes) that been established during embryogenesis.  Cells and tissues are arranged along the apical-basal axis from root to shoot whereas the three tissue systems (dermal, ground, and vascular) that make up a plant's body are arranged concentrically around its radial axis.  The dermal tissue system forms the epidermis (or outer covering) of a plant, which is usually a single cell layer that consists of cells that have differentiated into three specialized structures: stomata for gas exchange in leaves, trichomes (or leaf hair) for protection against insects and solar radiation, and root hairs for increased surface areas and absorption of water and nutrients. The ground tissue makes up virtually all the tissue that lies between the dermal and vascular tissues in the shoots and roots. It consists of three cell types: Parenchyma, collenchyma, and sclerenchyma cells. Finally, the vascular tissues are made up of two constituent tissues: xylem and phloem. The xylem is made up two of conducting cells called tracheids and vessel elements whereas the phloem is characterized by the presence of sieve tube elements and companion cells. 
Plant nutrition and transport
Like all other organisms, plants are primarily made up of water and other molecules containing elements that are essential to life.  The absence of specific nutrients (or essential elements), many of which have been identified in hydroponic experiments, can disrupt plant growth and reproduction. The majority of plants are able to obtain these nutrients from solutions that surrounds their roots in the soil.  Continuous leaching and harvesting of crops can deplete the soil of its nutrients, which can be restored with the use of fertilizers. Carnivorous plants such as Venus flytraps are able to obtain nutrients by digesting other arthropods whereas parasitic plants such as mistletoes can parasitize other plants for water and nutrients.
Plants need water to conduct photosynthesis, transport solutes between organs, cool their leaves by evaporation, and maintain internal pressures that support their bodies.  Water is able to diffuse in and out of plant cells by osmosis. The direction of water movement across a semipermeable membrane is determined by the water potential across that membrane.  Water is able to diffuse across a root cell's membrane through aquaporins whereas solutes are transported across by the membrane by ion channels and pumps. In vascular plants, water and solutes are able to enter the xylem, a vascular tissue, by way of an apoplast and symplast. Once in the xylem, the water and minerals are distributed upward by transpiration from the soil to the aerial parts of the plant.   In contrast, the phloem, another vascular tissue, distributes carbohydrates (e.g., sucrose) and other solutes such as hormones by translocation from a source (e.g., mature leaf or root) in which they were produced to a sink (e.g., root, flower, or developing fruit) in which they will be used and stored.  Sources and sinks can switch roles, depending on the amount of carbohydrates accumulated or mobilized for the nourishment of other organs.
Plant development is regulated by environmental cues and the plant's own receptors, hormones, and genome.  Morever, they have several characteristics that allow them to obtain resources for growth and reproduction such as meristems, post-embryonic organ formation, and differential growth.
Development begins with a seed, which is an embryonic plant enclosed in a protective outer covering. Most plant seeds are usually dormant, a condition in which the seed's normal activity is suspended.  Seed dormancy may last may last weeks, months, years, and even centuries. Dormancy is broken once conditions are favorable for growth, and the seed will begin to sprout, a process called germination. Imbibition is the first step in germination, whereby water is absorbed by the seed. Once water is absorbed, the seed undergoes metabolic changes whereby enzymes are activated and RNA and proteins are synthesized. Once the seed germinates, it obtains carbohydrates, amino acids, and small lipids that serve as building blocks for its development. These monomers are obtained from the hydrolysis of starch, proteins, and lipids that are stored in either the cotyledons or endosperm. Germination is completed once embryonic roots called radicle have emerged from the seed coat. At this point, the developing plant is called a seedling and its growth is regulated by its own photoreceptor proteins and hormones. 
Unlike animals in which growth is determinate, i.e., ceases when the adult state is reached, plant growth is indeterminate as it is an open-ended process that could potentially be lifelong.  Plants grow in two ways: primary and secondary. In primary growth, the shoots and roots are formed and lengthened. The apical meristem produces the primary plant body, which can be found in all seed plants. During secondary growth, the thickness of the plant increases as the lateral meristem produces the secondary plant body, which can be found in woody eudicots such as trees and shrubs. Monocots do not go through secondary growth.  The plant body is generated by a hierarchy of meristems. The apical meristems in the root and shoot systems give rise to primary meristems (protoderm, ground meristem, and procambium), which in turn, give rise to the three tissue systems (dermal, ground, and vascular).
Most angiosperms (or flowering plants) engage in sexual reproduction.  Their flowers are organs that facilitate reproduction, usually by providing a mechanism for the union of sperm with eggs. Flowers may facilitate two types of pollination: self-pollination and cross-pollination. Self-pollination occurs when the pollen from the anther is deposited on the stigma of the same flower, or another flower on the same plant. Cross-pollination is the transfer of pollen from the anther of one flower to the stigma of another flower on a different individual of the same species. Self-pollination happened in flowers where the stamen and carpel mature at the same time, and are positioned so that the pollen can land on the flower’s stigma. This pollination does not require an investment from the plant to provide nectar and pollen as food for pollinators. 
Like animals, plants produce hormones in one part of its body to signal cells in another part to respond. The ripening of fruit and loss of leaves in the winter are controlled in part by the production of the gas ethylene by the plant. Stress from water loss, changes in air chemistry, or crowding by other plants can lead to changes in the way a plant functions. These changes may be affected by genetic, chemical, and physical factors.
To function and survive, plants produce a wide array of chemical compounds not found in other organisms. Because they cannot move, plants must also defend themselves chemically from herbivores, pathogens and competition from other plants. They do this by producing toxins and foul-tasting or smelling chemicals. Other compounds defend plants against disease, permit survival during drought, and prepare plants for dormancy, while other compounds are used to attract pollinators or herbivores to spread ripe seeds.
Many plant organs contain different types of photoreceptor proteins, each of which reacts very specifically to certain wavelengths of light.  The photoreceptor proteins relay information such as whether it is day or night, duration of the day, intensity of light available, and the source of light. Shoots generally grow towards light, while roots grow away from it, responses known as phototropism and skototropism, respectively. They are brought about by light-sensitive pigments like phototropins and phytochromes and the plant hormone auxin.  Many flowering plants bloom at the appropriate time because of light-sensitive compounds that respond to the length of the night, a phenomenon known as photoperiodism.
In addition to light, plants can respond to other types of stimuli. For instance, plants can sense the direction of gravity to orient themselves correctly. They can respond to mechanical stimulation. 
Animal form and function
The cells in each animal body are bathed in interstitial fluid, which make up the cell's environment. This fluid and all its characteristics (e.g., temperature, ionic composition) can be described as the animal's internal environment, which is in contrast to the external environment that encompasses the animal's outside world.  Animals can be classified as either regulators or conformers. Animals such as mammals and birds are regulators as they are able to maintain a constant internal environment such as body temperature despite their environments changing. These animals are also described as homeotherms as they exhibit thermoregulation by keeping their internal body temperature constant. In contrast, animals such as fishes and frogs are conformers as they adapt their internal environment (e.g., body temperature) to match their external environments. These animals are also described as poikilotherms or ectotherms as they allow their body temperatures to match their external environments. In terms of energy, regulation is more costly than conformity as an animal expands more energy to maintain a constant internal environment such as increasing its basal metabolic rate, which is the rate of energy consumption.  Similarly, homeothermy is more costly than poikilothermy. Homeostasis is the stability of an animal's internal environment, which is maintained by negative feedback loops.  
The body size of terrestrial animals vary across different species but their use of energy does not scale linearly according to their size.  Mice, for example, are able to consume three times more food than rabbits in proportion to their weights as the basal metabolic rate per unit weight in mice is greater than in rabbits.  Physical activity can also increase an animal's metabolic rate. When an animal runs, its metabolic rate increases linearly with speed.  However, the relationship is non-linear in animals that swim or fly. When a fish swims faster, it encounters greater water resistance and so its metabolic rates increases exponential.  Alternatively, the relationship of flight speeds and metabolic rates is U-shaped in birds.  At low flight speeds, a bird must maintain a high metabolic rates to remain airborne. As it speeds up its flight, its metabolic rate decreases with the aid of air rapidly flows over its wings. However, as it increases in its speed even further, its high metabolic rates rises again due to the increased effort associated with rapid flight speeds. Basal metabolic rates can be measured based on an animal's rate of heat production.
Water and salt balance
An animal's body fluids have three properties: osmotic pressure, ionic composition, and volume.  Osmotic pressures determine the direction of the diffusion of water (or osmosis), which moves from a region where osmotic pressure (total solute concentration) is low to a region where osmotic pressure (total solute concentration) is high. Aquatic animals are diverse with respect to their body fluid compositions and their environments. For example, most invertebrate animals in the ocean have body fluids that are isosmotic with seawater. In contrast, ocean bony fishes have body fluids that are hyposmotic to seawater. Finally, freshwater animals have body fluids that are hyperosmotic to fresh water. Typical ions that can be found in an animal's body fluids are sodium, potassium, calcium, and chloride. The volume of body fluids can be regulated by excretion. Vertebrate animals have kidneys, which are excretory organs made up of tiny tubular structures called nephrons, which make urine from blood plasma. The kidneys' primary function is to regulate the composition and volume of blood plasma by selectively removing material from the blood plasma itself. The ability of xeric animals such as kangaroo rats to minimize water loss by producing urine that is 10-20 times concentrated than their blood plasma allows them to adapt in desert environments that receive very little precipitation. 
Nutrition and digestion
Animals are heterotrophs as they feed on other living organisms to obtain energy and organic compounds.  They are able to obtain food in three major ways such as targeting visible food objects, collecting tiny food particles, or depending on microbes for critical food needs. The amount of energy stored in food can be quantified based on the amount of heat (measured in calories or kilojoules) emitted when the food is burnt in the presence of oxygen. If an animal were to consume food that contains an excess amount of chemical energy, it will store most of that energy in the form of lipids for future use and some of that energy as glycogen for more immediate use (e.g., meeting the brain's energy needs).  The molecules in food are chemical building blocks that are needed for growth and development. These molecules include nutrients such as carbohydrates, fats, and proteins. Vitamins and minerals (e.g., calcium, magnesium, sodium, and phosphorus) are also essential. The digestive system, which typically consist of a tubular tract that extends from the mouth to the anus, is involved in the breakdown (or digestion) of food into small molecules as it travels down peristaltically through the gut lumen shortly after it has been ingested. These small food molecules are then absorbed into the blood from the lumen, where they are then distributed to the rest of the body as building blocks (e.g., amino acids) or sources of energy (e.g., glucose). 
In addition to their digestive tracts, vertebrate animals have accessory glands such as a liver and pancreas as part of their digestive systems.  The processing of food in these animals begins in the foregut, which includes the mouth, esophagus, and stomach. Mechanical digestion of food starts in the mouth with the esophagus serving as a passageway for food to reach the stomach, where it is stored and disintegrated (by the stomach's acid) for further processing. Upon leaving the stomach, food enters into the midgut, which is the first part of the intestine (or small intestine in mammals) and is the principal site of digestion and absorption. Food that does not get absorbed are stored as indigestible waste (or feces) in the hindgut, which is the second part of the intestine (or large intestine in mammals). The hindgut then completes the reabsorption of needed water and salt prior to eliminating the feces from the rectum. 
The respiratory system consists of specific organs and structures used for gas exchange in animals and plants. The anatomy and physiology that make this happen varies greatly, depending on the size of the organism, the environment in which it lives and its evolutionary history. In land animals the respiratory surface is internalized as linings of the lungs.  Gas exchange in the lungs occurs in millions of small air sacs in mammals and reptiles these are called alveoli, and in birds they are known as atria. These microscopic air sacs have a very rich blood supply, thus bringing the air into close contact with the blood.  These air sacs communicate with the external environment via a system of airways, or hollow tubes, of which the largest is the trachea, which branches in the middle of the chest into the two main bronchi. These enter the lungs where they branch into progressively narrower secondary and tertiary bronchi that branch into numerous smaller tubes, the bronchioles. In birds the bronchioles are termed parabronchi. It is the bronchioles, or parabronchi that generally open into the microscopic alveoli in mammals and atria in birds. Air has to be pumped from the environment into the alveoli or atria by the process of breathing which involves the muscles of respiration.
A circulatory system usually consists of a muscular pump such as a heart, a fluid (blood), and system of blood vessels that deliver it.   Its principal function is to transport blood and other substances to and from cell (biology)s and tissues. There are two types of circulatory systems: open and closed. In open circulatory systems, blood exits blood vessels as it circulates throughout the body whereas in closed circulatory system, blood is contained within the blood vessels as it circulates. Open circulatory systems can be observed in invertebrate animals such as arthropods (e.g., insects, spiders, and lobsters) whereas closed circulatory systems can be found in vertebrate animals such as fishes, amphibians, and mammals. Circulation in animals occur between two types of tissues: systemic tissues and breathing (or pulmonary) organs.  Systemic tissues are all the tissues and organs that make up an animal's body other than its breathing organs. Systemic tissues take up oxygen but adds carbon dioxide to the blood whereas a breathing organs takes up carbon dioxide but add oxygen to the blood.  In birds and mammals, the systemic and pulmonary systems are connected in series.
In the circulatory system, blood is important because it is the means by which oxygen, carbon dioxide, nutrients, hormones, agents of immune system, heat, wastes, and other commodities are transported.  In annelids such as earthworms and leeches, blood is propelled by peristaltic waves of contractions of the heart muscles that make up the blood vessels. Other animals such as crustaceans (e.g., crayfish and lobsters), have more than one heart to propel blood throughout their bodies. Vertebrate hearts are multichambered and are able to pump blood when their ventricles contract at each cardiac cycle, which propels blood through the blood vessels.  Although vertebrate hearts are myogenic, their rate of contraction (or heart rate) can be modulated by neural input from the body's autonomic nervous system.
Muscle and movement
In vertebrates, the muscular system consists of skeletal, smooth and cardiac muscles. It permits movement of the body, maintains posture and circulates blood throughout the body.  Together with the skeletal system, it forms the musculoskeletal system, which is responsible for the movement of vertebrate animals.  Skeletal muscle contractions are neurogenic as they require synaptic input from motor neurons. A single motor neuron is able to innervate multiple muscle fibers, thereby causing the fibers to contract at the same time. Once innervated, the protein filaments within each skeletal muscle fiber slide past each other to produce a contraction, which is explained by the sliding filament theory. The contraction produced can be described as a twitch, summation, or tetanus, depending on the frequency of action potentials. Unlike skeletal muscles, contractions of smooth and cardiac muscles are myogenic as they are initiated by the smooth or heart muscle cells themselves instead of a motor neuron. Nevertheless, the strength of their contractions can be modulated by input from the autonomic nervous system. The mechanisms of contraction are similar in all three muscle tissues.
In invertebrates such as earthworms and leeches, circular and longitudinal muscles cells form the body wall of these animals and are responsible for their movement.  In an earthworm that is moving through a soil, for example, contractions of circular and longitudinal muscles occur reciprocally while the coelomic fluid serves as a hydroskeleton by maintaining turgidity of the earthworm.  Other animals such as mollusks, and nematodes, possess obliquely striated muscles, which contain bands of thick and thin filaments that are arranged helically rather than transversely, like in vertebrate skeletal or cardiac muscles.  Advanced insects such as wasps, flies, bees, and beetles possess asynchronous muscles that constitute the flight muscles in these animals.  These flight muscles are often called fibrillar muscles because they contain myofibrils that are thick and conspicuous. 
The nervous system is a network of cells that processes sensory information and generates behaviors. At the cellular level, the nervous system is defined by the presence of neurons, which are cells specialized to handle information.  They can transmit or receive information at sites of contacts called synapses.  More specifically, neurons can conduct nerve impulses (or action potentials) that travel along their thin fibers called axons, which can then be transmitted directly to a neighboring cell through electrical synapses or cause chemicals called neurotransmitters to be released at chemical synapses. According to the sodium theory, these action potentials can be generated by the increased permeability of the neuron's cell membrane to sodium ions.  Cells such as neurons or muscle cells may be excited or inhibited upon receiving a signal from another neuron. The connections between neurons can form neural pathways, neural circuits, and larger networks that generate an organism's perception of the world and determine its behavior. Along with neurons, the nervous system contains other specialized cells called glia or glial cells, which provide structural and metabolic support.
Nervous systems are found in most multicellular animals, but vary greatly in complexity.  In vertebrates, the nervous system consists of the central nervous system (CNS), which includes the brain and spinal cord, and the peripheral nervous system (PNS), which consists of nerves that connect the CNS to every other part of the body. Nerves that transmit signals from the CNS are called motor nerves or efferent nerves, while those nerves that transmit information from the body to the CNS are called sensory nerves or afferent nerves. Spinal nerves are mixed nerves that serve both functions. The PNS is divided into three separate subsystems, the somatic, autonomic, and enteric nervous systems. Somatic nerves mediate voluntary movement. The autonomic nervous system is further subdivided into the sympathetic and the parasympathetic nervous systems. The sympathetic nervous system is activated in cases of emergencies to mobilize energy, while the parasympathetic nervous system is activated when organisms are in a relaxed state. The enteric nervous system functions to control the gastrointestinal system. Both autonomic and enteric nervous systems function involuntarily. Nerves that exit directly from the brain are called cranial nerves while those exiting from the spinal cord are called spinal nerves.
Many animals have sense organs that can detect their environment. These sense organs contain sensory receptors, which are sensory neurons that convert stimuli into electrical signals.  Mechanoreceptors, for example, which can be found in skin, muscle, and hearing organs, generate action potentials in response to changes in pressures.   Photoreceptor cells such as rods and cones, which are part of the vertebrate retina, can respond to specific wavelengths of light.   Chemoreceptors detect chemicals in the mouth (taste) or in the air (smell). 
Hormones are signaling molecules transported in the blood to distant organs to regulate their function.   Hormones are secreted by internal glands that are part of an animal's endocrine system. In vertebrates, the hypothalamus is the neural control center for all endocrine systems. In humans specifically, the major endocrine glands are the thyroid gland and the adrenal glands. Many other organs that are part of other body systems have secondary endocrine functions, including bone, kidneys, liver, heart and gonads. For example, kidneys secrete the endocrine hormone erythropoietin. Hormones can be amino acid complexes, steroids, eicosanoids, leukotrienes, or prostaglandins.  The endocrine system can be contrasted to both exocrine glands, which secrete hormones to the outside of the body, and paracrine signaling between cells over a relatively short distance. Endocrine glands have no ducts, are vascular, and commonly have intracellular vacuoles or granules that store their hormones. In contrast, exocrine glands, such as salivary glands, sweat glands, and glands within the gastrointestinal tract, tend to be much less vascular and have ducts or a hollow lumen.
Animals can reproduce in one of two ways: asexual and sexual. Nearly all animals engage in some form of sexual reproduction.  They produce haploid gametes by meiosis. The smaller, motile gametes are spermatozoa and the larger, non-motile gametes are ova.  These fuse to form zygotes,  which develop via mitosis into a hollow sphere, called a blastula. In sponges, blastula larvae swim to a new location, attach to the seabed, and develop into a new sponge.  In most other groups, the blastula undergoes more complicated rearrangement.  It first invaginates to form a gastrula with a digestive chamber and two separate germ layers, an external ectoderm and an internal endoderm.  In most cases, a third germ layer, the mesoderm, also develops between them.  These germ layers then differentiate to form tissues and organs.  Some animals are capable of asexual reproduction, which often results in a genetic clone of the parent. This may take place through fragmentation budding, such as in Hydra and other cnidarians or parthenogenesis, where fertile eggs are produced without mating, such as in aphids.  
Animal development begins with the formation of a zygote that results from the fusion of a sperm and egg during fertilization.  The zygote undergoes a rapid multiple rounds of mitotic cell period of cell divisions called cleavage, which forms a ball of similar cells called a blastula. Gastrulation occurs, whereby morphogenetic movements convert the cell mass into a three germ layers that comprise the ectoderm, mesoderm and endoderm.
The end of gastrulation signals the beginning of organogenesis, whereby the three germ layers form the internal organs of the organism.  The cells of each of the three germ layers undergo differentiation, a process where less-specialized cells become more-specialized through the expression of a specific set of genes. Cellular differentiation is influenced by extracellular signals such as growth factors that are exchanged to adjacent cells, which is called juxtracrine signaling, or to neighboring cells over short distances, which is called paracrine signaling.   Intracellular signals consist of a cell signaling itself (autocrine signaling), also play a role in organ formation. These signaling pathways allows for cell rearrangement and ensures that organs form at specific sites within the organism.  
The immune system is a network of biological processes that detects and responds to a wide variety of pathogens. Many species have two major subsystems of the immune system. The innate immune system provides a preconfigured response to broad groups of situations and stimuli. The adaptive immune system provides a tailored response to each stimulus by learning to recognize molecules it has previously encountered. Both use molecules and cells to perform their functions.
Nearly all organisms have some kind of immune system. Bacteria have a rudimentary immune system in the form of enzymes that protect against virus infections. Other basic immune mechanisms evolved in ancient plants and animals and remain in their modern descendants. These mechanisms include phagocytosis, antimicrobial peptides called defensins, and the complement system. Jawed vertebrates, including humans, have even more sophisticated defense mechanisms, including the ability to adapt to recognize pathogens more efficiently. Adaptive (or acquired) immunity creates an immunological memory leading to an enhanced response to subsequent encounters with that same pathogen. This process of acquired immunity is the basis of vaccination.
Behaviors play a central a role in animals' interaction with each other and with their environment.  They are able to use their muscles to approach one another, vocalize, seek shelter, and migrate. An animal's nervous system activates and coordinates its behaviors. Fixed action patterns, for instance, are genetically determined and stereotyped behaviors that occur without learning.   These behaviors are under the control of the nervous system and can be quite elaborate.  Examples include the pecking of kelp gull chicks at the red dot on their mother's beak. Other behaviors that have emerged as a result of natural selection include foraging, mating, and altruism.  In addition to evolved behavior, animals have evolved the ability to learn by modifying their behaviors as a result of early individual experiences. 
Ecology is the study of the distribution and abundance of living organisms, the interaction between them and their environment.  The community of living (biotic) organisms in conjunction with the nonliving (abiotic) components (e.g., water, light, radiation, temperature, humidity, atmosphere, acidity, and soil) of their environment is called an ecosystem.    These biotic and abiotic components are linked together through nutrient cycles and energy flows.  Energy from the sun enters the system through photosynthesis and is incorporated into plant tissue. By feeding on plants and on one another, animals play an important role in the movement of matter and energy through the system. They also influence the quantity of plant and microbial biomass present. By breaking down dead organic matter, decomposers release carbon back to the atmosphere and facilitate nutrient cycling by converting nutrients stored in dead biomass back to a form that can be readily used by plants and other microbes. 
The Earth's physical environment is shaped by solar energy and topography.  The amount of solar energy input varies in space and time due to the spherical shape of the Earth and its axial tilt. Variation in solar energy input drives weather and climate patterns. Weather is the day-to-day temperature and precipitation activity, whereas climate is the long-term average of weather, typically averaged over a period of 30 years.   Variation in topography also produces environmental heterogeneity. On the windward side of a mountain, for example, air rises and cools, with water changing from gaseous to liquid or solid form, resulting in precipitation such as rain or snow.  As a result, wet environments allow for lush vegetation to grow. In contrast, conditions tend to be dry on the leeward side of a mountain due to the lack of precipitation as air descends and warms, and moisture remains as water vapor in the atmosphere. Temperature and precipitation are the main factors that shape terrestrial biomes.
A population is the number of organisms of the same species that occupy an area and reproduce from generation to generation.      Its abundance can be measured using population density, which is the number of individuals per unit area (e.g., land or tree) or volume (e.g., sea or air).  Given that it is usually impractical to count every individual within a large population to determine its size, population size can be estimated by multiplying population density by the area or volume. Population growth during short-term intervals can be determined using the population growth rate equation, which takes into consideration birth, death, and immigration rates. In the longer term, the exponential growth of a population tends to slow down as it reaches its carrying capacity, which can be modeled using the logistic equation.  The carrying capacity of an environment is the maximum population size of a species that can be sustained by that specific environment, given the food, habitat, water, and other resources that are available.  The carrying capacity of a population can be affected by changing environmental conditions such as changes in the availability resources and the cost of maintaining them. In human populations, new technologies such as the Green revolution have helped increase the Earth's carrying capacity for humans over time, which has stymied the attempted predictions of impending population decline, the famous of which was by Thomas Malthus in the 18th century. 
A community is a group of populations of two or more different species occupying the same geographical area at the same time. A biological interaction is the effect that a pair of organisms living together in a community have on each other. They can be either of the same species (intraspecific interactions), or of different species (interspecific interactions). These effects may be short-term, like pollination and predation, or long-term both often strongly influence the evolution of the species involved. A long-term interaction is called a symbiosis. Symbioses range from mutualism, beneficial to both partners, to competition, harmful to both partners. 
Every species participates as a consumer, resource, or both in consumer–resource interactions, which form the core of food chains or food webs.  There are different trophic levels within any food web, with the lowest level being the primary producers (or autotrophs) such as plants and algae that convert energy and inorganic material into organic compounds, which can then be used by the rest of the community.    At the next level are the heterotrophs, which are the species that obtain energy by breaking apart organic compounds from other organisms.  Heterotrophs that consume plants are primary consumers (or herbivores) whereas heterotrophs that consume herbivores are secondary consumers (or carnivores). And those that eat secondary consumers are tertiary consumers and so on. Omnivorous heterotrophs are able to consume at multiple levels. Finally, there are decomposers that feed on the waste products or dead bodies of organisms. 
On average, the total amount of energy incorporated into the biomass of a trophic level per unit of time is about one-tenth of the energy of the trophic level that it consumes. Waste and dead material used by decomposers as well as heat lost from metabolism make up the other ninety percent of energy that is not consumed by the next trophic level. 
In the global ecosystem (or biosphere), matter exist as different interacting compartments, which can be biotic or abiotic as well as accessible or inaccessible, depending on their forms and locations.  For example, matter from terrestrial autotrophs are both biotic and accessible to other living organisms whereas the matter in rocks and minerals are abiotic and inaccessible to living organisms. A biogeochemical cycle is a pathway by which specific elements of matter are turned over or moved through the biotic (biosphere) and the abiotic (lithosphere, atmosphere, and hydrosphere) compartments of Earth. There are biogeochemical cycles for nitrogen, carbon, and water. In some cycles there are reservoirs where a substance remains or is sequestered for a long period of time.
Climate change includes both global warming driven by human-induced emissions of greenhouse gases and the resulting large-scale shifts in weather patterns. Though there have been previous periods of climatic change, since the mid-20th century humans have had an unprecedented impact on Earth's climate system and caused change on a global scale.  The largest driver of warming is the emission of greenhouse gases, of which more than 90% are carbon dioxide and methane.  Fossil fuel burning (coal, oil, and natural gas) for energy consumption is the main source of these emissions, with additional contributions from agriculture, deforestation, and manufacturing.  Temperature rise is accelerated or tempered by climate feedbacks, such as loss of sunlight-reflecting snow and ice cover, increased water vapor (a greenhouse gas itself), and changes to land and ocean carbon sinks.
Conservation biology is the study of the conservation of Earth's biodiversity with the aim of protecting species, their habitats, and ecosystems from excessive rates of extinction and the erosion of biotic interactions.    It is concerned with factors that influence the maintenance, loss, and restoration of biodiversity and the science of sustaining evolutionary processes that engender genetic, population, species, and ecosystem diversity.     The concern stems from estimates suggesting that up to 50% of all species on the planet will disappear within the next 50 years,  which has contributed to poverty, starvation, and will reset the course of evolution on this planet.   Biodiversity affects the functioning of ecosystems, which provide a variety of services upon which people depend.
Conservation biologists research and educate on the trends of biodiversity loss, species extinctions, and the negative effect these are having on our capabilities to sustain the well-being of human society. Organizations and citizens are responding to the current biodiversity crisis through conservation action plans that direct research, monitoring, and education programs that engage concerns at local through global scales.    
Part 3: Spreading the Silence
00:00:15.08 Hello, everyone.
00:00:16.16 Welcome to Lecture 3.
00:00:18.08 And again, I'm Jeanie Lee.
00:00:19.25 I'm a Professor of Genetics at Harvard Medical School.
00:00:22.07 I'm also a faculty member in the Department of Molecular Biology
00:00:25.00 at the Massachusetts General Hospital.
00:00:30.05 So, we talked about the different steps of X chromosome inactivation,
00:00:34.06 and in Lecture 2, we covered, in some detail,
00:00:36.27 the molecular mechanisms behind X chromosome
00:00:39.29 counting and allelic choice.
00:00:41.25 And what I'd like to do in this last lecture
00:00:44.25 is to talk about the step of nucleation,
00:00:48.11 followed by the spreading of silencing
00:00:51.02 across the rest of the X chromosome.
00:00:53.10 And recall that the problem is that.
00:00:56.18 here we have Xist RNA,
00:00:58.07 which is shown in red.
00:01:00.04 It coats the inactive X chromosome in cis.
00:01:02.17 And it does so without spilling over
00:01:05.01 into any of the other X chromosomes.
00:01:07.26 into any of the other X chromosomes in the cell,
00:01:10.04 or to any autosomes for that matter.
00:01:13.08 And so a question is,
00:01:14.29 how does this RNA stay put on that chromosome?
00:01:18.06 And we know that this property belongs to
00:01:21.12 the small piece of DNA called the X inactivation center,
00:01:24.13 because when we place the inactivation center
00:01:27.09 on an autosome -- so, a non-sex chromosome --
00:01:30.01 we see that Xist can also coat that chromosome,
00:01:32.28 in cis,
00:01:34.12 without spilling over into any of the other chromosomes,
00:01:36.17 including the X chromosome
00:01:39.03 where it normally would be produced and would be spread.
00:01:43.24 So, we're gonna start with this concept of nucleation.
00:01:47.03 Now, this is something that we stumbled upon sort of by accident.
00:01:51.16 So, recall this experiment,
00:01:53.17 which we had done back in the 1990s,
00:01:55.23 that sort of led to this dogma that Xist RNA
00:01:59.08 is strictly cis-acting.
00:02:01.11 So, the idea here was to place an inactivation center,
00:02:04.18 or Xist,
00:02:06.13 onto an autosome in a male cell,
00:02:08.06 and we could observe that Xist
00:02:10.28 is produced from this ectopic inactivation center,
00:02:13.29 and that that RNA spreads strictly in cis
00:02:17.27 across the autosome, without ever diffusing,
00:02:22.19 or so we thought, to the natural X chromosome,
00:02:26.27 which is located in a different place in the genome,
00:02:29.07 or in the nucleus.
00:02:32.19 So, that has been recapitulated
00:02:35.11 many times by various studies.
00:02:37.27 But then, many years later,
00:02:39.20 when we repeated the same experiment
00:02:42.00 -- except this time we did it in female cells --
00:02:45.00 and in the post-inactivation state,
00:02:49.02 we got a very surprising finding.
00:02:52.16 So, now here are two X chromosomes.
00:02:54.29 One is inactive and being coated by Xist RNA.
00:02:58.11 We place an inactivation center, or Xist,
00:03:01.20 on an autosome.
00:03:03.03 And we saw, as we expected,
00:03:05.09 that Xist would be upregulated and would coat and silence
00:03:09.10 that chromosome in cis.
00:03:12.05 However, what we didn't anticipate was that
00:03:15.15 within 24 to 48 hours of doing this
00:03:19.19 Xist RNA started to fade away from the inactive X.
00:03:24.20 Now, upon probing deeper,
00:03:26.26 we realized that Xist wasn't actually going away or disappearing.
00:03:30.29 In fact, what was happening to it was that it was
00:03:33.27 being pulled away onto the autosome,
00:03:37.20 which had this multimerized X inactivation center.
00:03:42.22 So, that was extremely puzzling.
00:03:45.17 And here's the actual experiment,
00:03:47.10 where you can see the autosome
00:03:50.06 very nicely producing Xist and the X chromosome, down here,
00:03:53.25 which is starting to fade away,
00:03:56.04 at least with respect to Xist RNA.
00:03:58.13 And within 24 hours,
00:04:00.15 we see the transgenic Xist spot,
00:04:02.24 but the X chromosome spot was nowhere to be found.
00:04:06.26 So, that was indeed very surprising.
00:04:09.06 And what we learned from these experiments
00:04:11.16 is that, in fact, contrary to what we were expecting,
00:04:15.11 Xist RNA can diffuse in the nucleus.
00:04:19.02 But we normally see it.
00:04:21.02 see it localizing in cis,
00:04:23.13 because there isn't another site in the nucleus
00:04:27.16 that would be receptive to Xist.
00:04:32.01 So, Xist can diffuse in trans
00:04:34.01 and act on a different chromosome.
00:04:35.20 So, this led to a revelation
00:04:39.12 that there has to be a sort of a nucleation center
00:04:42.07 within the Xist gene itself,
00:04:45.02 and that these autosomal transgenes
00:04:47.16 must somehow contain such a nucleation site.
00:04:51.24 And so we went ahead and dug around
00:04:55.25 to try to pinpoint this nucleation site,
00:04:59.03 and identified three binding sites
00:05:02.02 for a transcription factor called YY1
00:05:05.09 that was immensely important to this process of nucleation.
00:05:10.27 And so, what we showed is that YY1 protein
00:05:13.20 binds to these three sites
00:05:16.10 and serves as a tether for Xist RNA
00:05:19.03 to anchor to the inactive X chromosome.
00:05:22.03 And when we mutated these three YY1 binding sites,
00:05:25.12 look what happens to Xist.
00:05:27.21 It disperses across almost the entire nucleus.
00:05:32.00 So, the RNA detaches from the X chromosome
00:05:34.22 and floats away into the nucleus.
00:05:39.10 So, we could recapitulate that finding
00:05:42.13 by depleting the cells of this critical anchor,
00:05:44.29 the YY1 protein.
00:05:46.19 You see how recapitulates the loss of this Xist focus
00:05:51.11 within these female cells.
00:05:53.23 And it wasn't because Xist was no longer being produced.
00:05:56.26 Xist was still produced,
00:05:59.11 but it could no longer attach to this nucleation center.
00:06:05.12 So, we conclude that YY1 is a tether for Xist RNA
00:06:08.16 at the nucleation site.
00:06:10.14 So, this nucleation allows Xist to attach
00:06:15.01 prior to the process of spreading.
00:06:17.05 It's an absolutely critical initial step
00:06:20.02 to X chromosome spreading.
00:06:23.07 So, what we observed is that the nucleation site
00:06:26.00 is located within or very close to this repeat sequence
00:06:29.27 we called repeat F,
00:06:31.27 near the 5' end of Xist
00:06:34.04 that it contains a trio of YY1 binding sites
00:06:36.25 the YY1 protein is very important in tethering Xist RNA
00:06:42.05 to this nucleation center.
00:06:44.02 And so what we imagine is that Xist RNA
00:06:46.14 gets produced from this genetic locus
00:06:48.24 and it co-transcriptionally loads onto the nucleation site.
00:06:53.27 And what we mean by co-transcriptional is,
00:06:56.04 as it's getting synthesized,
00:06:57.28 when this piece of the RNA gets exposed,
00:07:00.29 it detaches.
00:07:03.25 attaches to the inactivation center
00:07:07.02 before the transcription is complete.
00:07:12.16 And then from the nucleation site,
00:07:14.20 Xist spreads in three dimensions
00:07:17.01 across the rest of the X chromosome.
00:07:21.26 So, now let's talk about this concept of spreading itself.
00:07:25.06 How does that actually happen?
00:07:30.00 So, what happens from here,
00:07:31.27 which is the synthesis of Xist
00:07:34.01 and attachment to the nucleation site,
00:07:36.15 all the way down to here,
00:07:38.01 which is a chromosome condensation
00:07:41.16 and a lockdown of gene expression from that chromosome,
00:07:43.08 remains largely unknown.
00:07:44.29 However, we do know that several things
00:07:47.19 have to happen in between.
00:07:49.23 One of which is that Xist has to
00:07:52.29 push away these factors that normally give rise to gene expression
00:07:56.13 -- so, the activating factors --
00:07:58.16 and at the same time it has to
00:08:01.16 recruit repressive factors to the X chromosome
00:08:05.14 to start the process of silencing.
00:08:08.13 And then, probably at the same time,
00:08:12.01 it is generating a new kind of topology
00:08:14.15 on the X chromosome.
00:08:17.28 So, how does all of this work.
00:08:19.23 Well, we know that Xist is multifunctional.
00:08:22.03 And to identify important domains
00:08:24.22 that are essential for spreading,
00:08:27.02 we have performed a systematic deletional analysis of Xist
00:08:31.10 -- so, here again is Xist --
00:08:33.06 and what we've done is use the CRISPR/Cas9 gene editing technology
00:08:37.26 to remove, sequentially,
00:08:40.12 1-2 kilobase regions from Xist RNA.
00:08:44.12 And we do this at the endogenous Xist locus
00:08:47.25 in female cells,
00:08:49.21 so that we can observe everything happening in the normal physiological state.
00:08:54.23 And what we found was.
00:08:57.14 are two repeats that are very important to this process of spreading.
00:09:03.13 So, there's repeat B, shown right there,
00:09:05.11 and repeat E, which is in the last exon of Xist.
00:09:10.29 So normally, as you know by now,
00:09:12.27 Xist forms this very tight focus
00:09:15.28 over the inactive X chromosome.
00:09:18.06 But when we deleted either repeat B or repeat E,
00:09:22.21 what you see is a dispersal of the Xist RNA cloud,
00:09:27.21 sort of across the nucleus.
00:09:30.13 Okay, so I think that's very nicely illustrated here
00:09:32.29 and here,
00:09:34.13 relative to the wildtype Xist RNA.
00:09:38.07 So, to get a better understanding of
00:09:41.18 what's happening at the molecular level,
00:09:43.11 we performed an epigenetic method called CHART-seq,
00:09:48.03 and this allows us to map RNA binding sites on chromatin.
00:09:51.18 In this case, we were interested in Xist RNA.
00:09:54.27 So, here I'm showing you a time course analysis
00:09:57.19 of Xist binding during X inactivation.
00:10:00.16 And in this top row, here,
00:10:02.12 you can see that Xist is
00:10:05.04 initially expressed from the X inactivation center.
00:10:07.06 It's nucleating there.
00:10:08.28 But then it spreads sort of all at once
00:10:11.08 to the rest of the X chromosome.
00:10:14.04 In other words, it's not spreading sort of.
00:10:18.04 sort of locus by locus,
00:10:20.10 in two dimensions down the chromosome.
00:10:21.26 But instead, it's spreading
00:10:24.01 all at once in three dimensions,
00:10:25.22 because you're seeing that the RNA
00:10:28.00 is piling up across the X chromosome
00:10:29.24 more or less at the same time.
00:10:31.14 And the other thing we found out
00:10:33.29 from this experiment is that Xist is
00:10:37.14 first going to gene-rich regions,
00:10:39.03 and in particular it's going to active genes,
00:10:41.19 exactly the genes that it ought to be attacking first
00:10:45.26 if we're talking about silencing of an entire chromosome.
00:10:49.20 And then, eventually,
00:10:52.00 Xist spreads over the entire X chromosome,
00:10:54.11 until it essentially covers
00:10:57.12 the entire 166 megabase chromosome.
00:11:02.10 So, we believe that Xist RNA spreads in three dimensions
00:11:05.09 across the inactive X chromosome.
00:11:06.27 It first nucleates here, at the X inactivation center,
00:11:10.02 and then the RNA is transferred through proximity
00:11:13.25 to various secondary sites,
00:11:16.24 of which there are probably about 100 or so,
00:11:20.24 first targeting the gene-rich,
00:11:23.06 or the active gene regions,
00:11:25.04 before spreading to the rest of the X chromosome.
00:11:29.22 So, what happens when we delete this critical repeat B,
00:11:32.16 which is important for spreading?
00:11:35.07 So, again, here in the top row,
00:11:37.06 we can see the wildtype spreading pattern
00:11:39.05 that's covering essentially the entire chromosome.
00:11:41.29 But when we delete repeat B,
00:11:43.19 you see that there is a diminution of binding
00:11:47.07 across the entire X.
00:11:49.21 And it appears as though
00:11:54.01 the ends of the X chromosome are being more affected.
00:11:57.05 are more affected than the middle region,
00:12:00.16 consistent with this idea of a spreading defect
00:12:03.22 in three dimensions.
00:12:08.21 And as you would expect of an RNA
00:12:11.07 that can no longer spread efficiently on the X chromosome,
00:12:14.14 gene silencing is severely compromised.
00:12:17.21 So here, by RNA sequencing,
00:12:20.02 you can see lots of activity still
00:12:22.29 across these two representative genes.
00:12:24.24 And the activity is shown here
00:12:26.16 as these little red tick marks.
00:12:28.09 And there is almost as much activity on the inactive X chromosome
00:12:31.24 as on the active X chromosome.
00:12:36.24 So now, we've also come to understand,
00:12:39.07 in spite of what I just showed you by CHART-sequencing,
00:12:42.26 that Xist covers the whole chromosome.
00:12:45.19 when we looked at individual cells,
00:12:49.16 by super-resolution imaging with a resolution of 20 nanometers,
00:12:53.08 we see that Xist isn't actually plastered
00:12:56.24 on the entire chromosome.
00:12:58.06 It's not really a coat.
00:12:59.26 It's actually a cluster of about 100 dots,
00:13:03.23 with each dot representing 1-2 Xist transcripts,
00:13:08.22 or 1-2 Xist molecules.
00:13:12.16 So then, with only 100-200 Xist particles
00:13:15.09 on the inactive X chromosome,
00:13:17.09 if we were to place the Xist particles end-on-end
00:13:21.03 there would only be enough Xist
00:13:23.09 to cover about 1% of this 160 megabase chromosome.
00:13:27.20 Or put differently,
00:13:30.07 there's only one Xist molecule for every 10-20 genes.
00:13:34.08 So, that raises this question,
00:13:36.11 because Xist is at a stoichiometric disadvantage,
00:13:39.06 how does it actually silence an entire chromosome?
00:13:43.01 And with respect to that,
00:13:45.14 you see that there's sort of a discrepancy
00:13:48.05 between what we're seeing at the single cell level
00:13:50.23 by super-resolution imaging
00:13:52.20 and what we're seeing by CHART-sequencing,
00:13:54.27 which really is measuring a population average
00:13:58.10 across millions of cells.
00:14:00.14 And so, between what we're seeing
00:14:02.11 in a single snapshot in time,
00:14:04.11 by CHART,
00:14:05.23 and what we're seeing at the single cell level,
00:14:08.02 we can deduce that Xist is actively moving around,
00:14:11.22 very dynamically moving around the X chromosome.
00:14:15.08 So, that relates to its question of stoichiometry.
00:14:20.02 So, it turns out that Xist
00:14:23.08 overcomes this unfavorable stoichiometry
00:14:25.26 by recruiting catalytic factors.
00:14:28.21 And these are factors that can amplify the work of Xist.
00:14:32.27 So, for example,
00:14:35.00 here I'm showing four different catalytic factors
00:14:38.06 that Xist is directly interacting with,
00:14:41.19 including chromosome architectural factors,
00:14:44.02 the cohesins,
00:14:45.21 the SWI/SNF factors,
00:14:47.24 polycomb repressive complexes,
00:14:50.02 as well as this non-canonical SMC protein
00:14:53.29 called SMCHD1.
00:14:57.04 And you'll note from this list of interacting proteins
00:14:59.19 that Xist is both coming in contact
00:15:03.07 with activators as well as repressors.
00:15:06.17 And that is because, in fact,
00:15:08.21 during the process of spreading
00:15:10.28 it is interacting with both the activating factors
00:15:14.27 as well as the repressing factors.
00:15:18.11 So, we now turn our attention
00:15:20.22 to the first function of Xist,
00:15:22.10 which is the recruitment of repressive factors.
00:15:25.12 And one of the factors that it recruits
00:15:28.07 is this PRC2, or polycomb repressive complex 2.
00:15:32.05 This is an epigenetic complex
00:15:34.28 that trimethylates histone H3 at lysine 27.
00:15:39.23 And it's a very important enzyme that represses gene expression.
00:15:44.03 And it's important throughout development,
00:15:46.11 as well as during the etiology of disease.
00:15:50.10 However, there has been a long-standing question in the field
00:15:54.03 -- not just about polycomb complexes
00:15:56.29 but about many, many other epigenetic complexes --
00:16:00.08 about how they can be targeted to specific locations in our genome
00:16:07.06 when these complexes are largely devoid
00:16:10.24 of a sequence-specific DNA binding subunit.
00:16:14.20 So, how do they know where to go?
00:16:16.17 Now, the answer to this question is going to be multifaceted, of course.
00:16:19.15 There are gonna be many different recruiting mechanisms,
00:16:21.17 including transcription factors,
00:16:23.06 including specific motifs in DNA and whatnot.
00:16:28.05 But we believe that a major piece of the puzzle
00:16:31.27 lies in the non-coding RNA,
00:16:34.19 and sometimes even coding RNA,
00:16:36.25 dating back to an experiment that we did 10 years ago,
00:16:40.22 in which we demonstrated that
00:16:43.12 PRC2 can directly interact with RNA,
00:16:47.13 in this case Xist,
00:16:49.13 and recruit PRC2 to the X chromosome.
00:16:53.29 And it's doing so through a motif
00:16:56.28 at the very 5' prime end of Xist called repeat A.
00:17:01.14 So, this is a biochemical analysis
00:17:03.23 that shows that PRC2 interacts with Xist RNA
00:17:07.09 with high affinity,
00:17:09.02 with a dissociation constant of 20-80 nanomolar,
00:17:12.11 which is a very good dissociation constant
00:17:14.16 for an RNA binding protein.
00:17:16.11 And it contrasts with the affinities.
00:17:19.00 some very low affinities for these nonspecific RNAs
00:17:22.06 from various other species, like Tetrahymena and bacteria.
00:17:28.01 So, now in this slide
00:17:30.07 I will attempt to convey the complex dynamics
00:17:33.16 that occur between the RNA and PRC2.
00:17:37.24 So, as we envision it.
00:17:40.10 now, initially, the RNA that contains this repeat A motif
00:17:44.13 will attract polycomb repressive complexes
00:17:47.24 to the X inactivation center.
00:17:51.07 Now, very importantly,
00:17:53.03 our genetic and biochemical experiments
00:17:55.06 show that even though the long non-coding RNA
00:17:58.15 is recruiting PRC2 in a site-specific manner,
00:18:03.10 that does not mean that it is
00:18:07.03 automatically going to load that complex onto chromatin,
00:18:10.23 or that it will induce the catalysis on H3K27.
00:18:17.02 So, in fact, these steps are biochemically
00:18:19.14 and genetically separable.
00:18:20.27 So, for example,
00:18:22.26 as long as the antisense repressor, Tsix,
00:18:25.14 is expressed from the inactivation center,
00:18:28.06 we see that this complex
00:18:30.19 does not load onto chromatin.
00:18:32.14 So, at this time we can see a RIP,
00:18:35.10 RNA immunoprecipitation,
00:18:37.13 between PRC2 and repeat A RNA.
00:18:40.02 But we do not see them ChIPing
00:18:42.20 onto the 5' end of Xist.
00:18:47.00 And it is only when the antisense RNA disappears
00:18:50.15 that we see that complex load onto the X chromosome.
00:18:54.09 But even so, that does not by itself
00:18:57.20 unleash the methyltransferase activity
00:19:00.08 of the catalytic subunit, EZH2.
00:19:02.27 However, when this complex comes into contact
00:19:06.02 with this accessory subunit,
00:19:07.26 called JARID2,
00:19:09.19 we see that the affinity of the RNA
00:19:13.22 for the catalytic subunit, EZH2,
00:19:18.06 So, the affinity goes down.
00:19:20.07 And that loss of binding of the RNA to EZH2
00:19:24.23 is associated with unleashing of
00:19:28.23 the histone methyltransferase activity.
00:19:30.26 So, again, this principle illustrates
00:19:33.21 how we can separate polycomb recruitment
00:19:37.14 from its loading onto chromatin
00:19:39.19 to its catalysis on H3K27.
00:19:45.08 So, the take-home message.
00:19:47.13 long non-coding RNAs can recruit PRC2,
00:19:49.29 but hold their activity.
00:19:52.15 or, hold the activity of PRC2 in check
00:19:54.28 until a developmental signal is received,
00:19:58.01 at which time PRC2 and JARID2
00:20:02.12 interact to trimethylate histone H3 at lysine 27.
00:20:08.02 Xist overcomes its unfavorable stoichiometry
00:20:10.29 by recruiting these catalytic factors.
00:20:13.20 And we envision that these factors
00:20:16.13 use a hit and run mechanism
00:20:18.24 to silence the entire chromosome in an efficient manner.
00:20:22.10 So, again, Xist first binds to the inactivation center,
00:20:26.19 nucleates at that site,
00:20:28.16 recruits all these factors,
00:20:30.08 and then spreads in three dimensions
00:20:32.27 to about 100 sites located across the chromosome.
00:20:35.28 And then, at these secondary sites,
00:20:38.08 and we're taking as an example, here, PRC2,
00:20:40.25 but there are many other catalytic factors.
00:20:42.19 so, PRC2 lands,
00:20:45.18 and it processively methylates successive nucleosomes
00:20:50.11 until it covers about 1 or 2 megabases of chromatin.
00:20:53.28 And imagine that this happens
00:20:56.25 100 times over across the X chromosome,
00:20:59.07 more or less at the same time,
00:21:00.29 and then you can see how this process of silencing
00:21:03.24 can be amplified
00:21:06.05 and can take place in a very efficient manner.
00:21:09.17 So, now I'd like to turn your attention
00:21:11.28 to the second aspect of Xist function,
00:21:14.10 and that is its antagonization or its repulsion
00:21:17.27 of the activating factors.
00:21:19.29 And we're going to use as an example
00:21:22.13 this epigenetic factor called SWI/SNF.
00:21:27.28 So, SWI/SNF is an ATP-dependent
00:21:31.16 chromatin remodeling enzyme.
00:21:33.09 And central to its activity
00:21:35.23 is the catalytic subunit, BRG1.
00:21:38.19 So, SWI/SNF is normally associated
00:21:41.03 with open chromatin.
00:21:43.07 Indeed, it makes chromatin accessible,
00:21:46.13 poising it for gene activation.
00:21:49.12 And so, normally you would find SWI/SNF
00:21:51.29 on the active X chromosome
00:21:53.16 but not on the inactive X chromosome.
00:21:56.11 As Xist RNA spreads over the inactive X chromosome,
00:21:59.14 the RNA comes into contact with BRG1
00:22:02.13 and inhibits the ATP.
00:22:05.12 ATPase activity of BRG1,
00:22:08.09 just as it inhibits the methyltransferase activity
00:22:11.19 of PRC2.
00:22:13.28 So, this is an immunofluorescence experiment,
00:22:16.03 and you can see that BRG1
00:22:18.18 is normally present throughout the nucleus.
00:22:21.03 But where there is Xist RNA,
00:22:23.02 shown here in red,
00:22:24.21 you can see that there is a depletion of BRG1
00:22:28.14 over that same chromosome territory,
00:22:32.02 suggesting that Xist RNA evicts BRG.
00:22:36.10 BRG1 from the inactive X chromosome.
00:22:40.20 So then, we'll now turn to
00:22:43.05 the third and final function of Xist,
00:22:45.21 and that is its role in directing changes
00:22:49.09 in three-dimensional chromosome architecture.
00:22:52.07 So, our RNA proteomic analysis
00:22:55.19 also showed that Xist is interacting with
00:22:59.05 a number of chromosome architectural factors.
00:23:01.25 So, you can see here various cohesions,
00:23:04.07 as well as CTCF.
00:23:06.24 These are two architectural factors
00:23:09.00 that go to construct 3D chromatin.
00:23:11.04 So, we've already talked extensively about CTCF,
00:23:13.13 a zinc finger protein that brings together distant genetic elements
00:23:17.04 that form these chromatin loops.
00:23:19.01 And then we have cohesins,
00:23:20.20 which are this multi-subunit complex
00:23:22.26 that forms a ring around the base of the loops
00:23:25.12 to lock in that architectural structure.
00:23:29.09 So, it's. it is known that
00:23:32.21 mammalian chromosomes are organized into two distinct entities,
00:23:36.27 one called the topologically associating domain,
00:23:39.08 or the TAD,
00:23:41.01 and the other the compartment.
00:23:43.11 So, TADs are these large loops of chromatin
00:23:46.07 of around 1-2 megabases in size,
00:23:49.01 within which genes can be,
00:23:51.09 though they don't have to be,
00:23:53.07 coordinately regulated.
00:23:54.25 And then the active TADs,
00:23:56.23 or those active loops,
00:23:58.29 coalesce and form a separate compartment
00:24:02.11 called the A compartment,
00:24:04.16 whereas the inactive or the less active genes
00:24:08.28 form another type of compartment
00:24:11.13 that's called a B compartment.
00:24:13.11 So, as you might imagine,
00:24:15.12 the inactive X chromosome is organized completely differently
00:24:19.18 from all other chromosomes.
00:24:21.01 So now, here's an inactive X chromosome.
00:24:23.06 The entire chromosome is shown across the top.
00:24:25.22 And what I've done here is
00:24:27.22 magnified the two ends of the chromosome.
00:24:30.04 And you can see from this contact heat map
00:24:32.25 that these TADs,
00:24:34.17 which are these triangular structures,
00:24:36.20 can be seen essentially all across the chromosome.
00:24:39.27 So, the active X chromosome
00:24:42.16 looks a lot like any other chromosome,
00:24:44.15 like all autosomes.
00:24:46.15 On the X chromosome, there are about 110
00:24:48.22 of these topologically associating domains.
00:24:52.16 Now, contrast that with the inactive X chromosome,
00:24:55.21 where, yes, you might still be able to
00:24:59.17 envision a formation of these topologically associating domains,
00:25:04.05 but they are much, much weakened.
00:25:06.15 And so, one of the things that Xist has to do
00:25:10.01 as it's spreading across the chromosome
00:25:11.22 is to attenuate the formation.
00:25:14.03 although not abolish.
00:25:15.28 attenuate the formation of these so-called TADs.
00:25:19.24 When we mutate repeat B
00:25:23.00 -- so, that's the critical domain for X.
00:25:26.08 for Xist spreading --
00:25:27.24 we see that nothing happens to the active X chromosome.
00:25:31.04 The active X chromosome still has
00:25:33.07 110 or so TADs.
00:25:35.21 But on the other hand,
00:25:37.24 when we do the same thing to the inactive X chromosome,
00:25:40.17 you start to see that these TADs
00:25:43.07 persist on that chromosome,
00:25:45.01 or that maybe they're even coming back.
00:25:47.06 They either persist or come back,
00:25:49.03 suggesting that Xist is very important
00:25:51.25 to the attenuation of these topologically associating domains.
00:25:56.07 So, how does Xist do this?
00:25:58.02 Well, it's probably doing a number of different things,
00:26:01.07 one of which is that it is also evicting cohesins
00:26:04.23 from that chromosome.
00:26:07.00 So, this is one of the subunits of cohesin.
00:26:09.11 It's an immunofluorescence
00:26:11.17 that shows that cohesins are normally widely distributed
00:26:13.29 throughout the nucleus.
00:26:15.13 But again, where there is Xist,
00:26:18.10 shown here in red,
00:26:20.13 you see a depletion of cohesins next to this arrow.
00:26:25.27 And the same is true of CTCF.
00:26:30.17 Now, when we delete Xist,
00:26:31.29 the cohesins come back,
00:26:33.19 as shown here by this red peak of cohesins here and here.
00:26:38.17 And you can see that in the wildtype chromosome,
00:26:40.29 those two red peaks are not present.
00:26:43.23 Xist this not only attenuating TADs,
00:26:46.19 but it's also directing the formation of these inactive X-specific compartments.
00:26:51.14 So, SMD. SMCHD1 is very important
00:26:54.24 in the formation of these XI-specific compartments.
00:26:59.01 And it was Emma Whitelaw who observed, many years ago,
00:27:02.23 that embryos lacking SMCHD1
00:27:05.19 would die in mid-gestation
00:27:08.08 due to dysfunctional X inactivation.
00:27:10.17 So, SMCHD1 is a non-canonical SMC protein
00:27:14.03 that's like the cohesins and condensins,
00:27:16.10 except that it has a very different function.
00:27:19.07 So, here you can see that
00:27:21.24 Xist plays a very active role in the recruitment
00:27:24.21 and the enrichment of SMCHD1
00:27:26.13 along the inactive X chromosome.
00:27:30.00 And it's in fact one of the proteins
00:27:32.23 that we identified when we performed the Xist proteomic analysis,
00:27:36.09 as a factor that directly interacts with Xist.
00:27:39.19 So, it turns out that SMCHD1
00:27:42.21 plays at least two important roles
00:27:45.14 during X inactivation.
00:27:47.00 So, in the first, it's aiding the local spreading
00:27:49.25 of Xist-PRC2 complexes.
00:27:51.19 And in the second,
00:27:53.18 it's merging these inactive X-specific compartments.
00:27:59.22 So, here's the first role.
00:28:01.15 SMCHD1 is important for the regional spreading of Xist.
00:28:05.04 And you can see in this epigenomic analysis,
00:28:08.09 in the first track,
00:28:10.00 that Xist spreads along the.
00:28:12.16 this region of the X chromosome
00:28:14.23 -- it's about 1 megabase --
00:28:17.04 more or less evenly.
00:28:19.09 But in the SMCHD1 knockout,
00:28:21.10 which is shown in the second track,
00:28:23.04 you can see that there is a depletion of Xist
00:28:25.19 across this 1 megabase domain,
00:28:28.20 which is also green shaded.
00:28:31.02 And associated with that
00:28:34.16 is a defect in polycomb spreading and H3K27 methylation
00:28:38.07 across that same domain.
00:28:41.13 So, SMCHD1 is very important
00:28:44.19 for regional spreading of Xist.
00:28:46.03 And the loss of SM.
00:28:47.25 of SMCHD1 results in a defect of spreading,
00:28:51.28 as well as a focal loss of H3K27 methylation.
00:28:57.21 Now, the other thing that SMCHD1 does
00:29:00.14 is that it merges these inactive X-specific compartments.
00:29:04.24 So, shown here are Hi-C experiments,
00:29:08.23 and what I'm showing is a contact heat map
00:29:12.01 for the active X chromosome
00:29:14.11 in the wildtype state,
00:29:16.15 with the active X chromosome shown here
00:29:18.28 along the diagonal.
00:29:20.23 And what you probably cannot see at this magnification
00:29:24.28 is that there are about 110 topologically associated domains
00:29:28.24 on that active chromosome.
00:29:30.21 Whereas on the inactive chromosome,
00:29:32.24 those TADs are significantly weakened.
00:29:36.15 And instead of TADs,
00:29:38.23 this X chromosome shows
00:29:41.07 two large so-called mega domains.
00:29:43.26 So, here's one mega domain,
00:29:46.28 and here's another mega domain.
00:29:48.28 Now, contrast that with what happens
00:29:50.29 when we remove SMCHD1.
00:29:53.10 And on the active X chromosome,
00:29:54.29 nothing happens.
00:29:56.21 But on the inactive X chromosome,
00:29:59.02 you see that these two mega domains
00:30:01.17 start to break up.
00:30:03.15 And that can be much better visualized
00:30:05.18 by going to the bottom set of panels.
00:30:08.11 These are heat maps of
00:30:10.20 Pearson correlation coefficients.
00:30:13.12 And what you can see is that in the wildtype inactive X chromosome,
00:30:19.13 these two mega domains really pop out, as shown in red.
00:30:25.15 But when SMCHD1 is removed,
00:30:29.15 those two mega domains adopt a checkerboard pattern.
00:30:34.28 And the checkerboard pattern that you see on the mutant inactive X
00:30:37.29 is distinctly different from what you see
00:30:41.04 on the active X chromosome,
00:30:43.03 which shows a much finer checkerboarding pattern.
00:30:46.08 That's consistent with the A/B compartments
00:30:49.06 that we talked about a few slides ago.
00:30:52.24 So, we can better visualize this
00:30:55.03 by going to a principal component analysis.
00:30:57.21 And in the first principal component,
00:30:59.19 you can see these red/blue structures
00:31:02.21 on the active X chromosome,
00:31:04.25 which are the A/B compartments.
00:31:08.19 And when we remove SMCHD1,
00:31:11.10 nothing happens to the active X chromosome.
00:31:14.20 It's impervious to there being a loss of SMCHD1.
00:31:19.08 But then here's the act.
00:31:21.04 the inactive X chromosome.
00:31:23.09 And you can see that in the wildtype state
00:31:25.29 there are these two megadomains,
00:31:27.20 one in blue and one in red.
00:31:29.23 But when we remove SMCHD1,
00:31:32.02 those two megadomains break up
00:31:35.07 into these finer structures that we call
00:31:38.01 S1 and S2 compartments,
00:31:40.22 referring to the fact that they appear only when we remove SMCHD1.
00:31:46.00 But also appreciate that these finer structure.
00:31:49.02 these finer structures are not the A/B compartments
00:31:53.22 that you see on the active X chromosome.
00:31:57.08 So, it turns out that these S1/S2 compartments
00:32:00.18 are intermediate structures
00:32:03.01 during the formation of the inactive X.
00:32:06.04 So, prior to X inactivation,
00:32:08.12 we see these A/B compartments,
00:32:10.09 like we see on all chromosomes.
00:32:12.28 But then at the onset of X inactivation,
00:32:15.25 as Xist spreads over the X chromosome,
00:32:18.12 it merges.
00:32:22.09 it being Xist.
00:32:24.03 merges the red and blue compartments
00:32:27.11 to form these S1/S2 structures,
00:32:30.18 these larger S1/S2 structures.
00:32:34.10 And that's. as X inactivation proceeds,
00:32:36.27 Xist recruits SMCHD1,
00:32:40.08 and SMCHD1 in turn
00:32:43.20 merges the S1/S2 compartments
00:32:47.09 into these two megadomains
00:32:50.05 to form a compartment-less chromosome.
00:32:54.12 So, in these three lectures
00:32:56.05 I've thrown a lot of information at you.
00:32:57.24 And I what I'm going to attempt to do in this final slide
00:33:00.08 is to integrate some of that information.
00:33:03.27 So, we envision that at the onset of X inactivation
00:33:09.22 this RNA with the repeat A motif
00:33:12.02 recruits PRC2 to the X inactivation center.
00:33:16.29 But as I mentioned, the recruitment process.
00:33:21.00 the RNA isn't very important for the recruitment process,
00:33:23.15 but it also holds the activity of PRC2 in check.
00:33:28.22 So, recruitment is not the same thing as loading,
00:33:31.10 which is not the same thing as catalysis.
00:33:33.24 Because as long as the antisense RNA is expressed,
00:33:36.23 PRC2 is prevented from loading onto chromatin.
00:33:42.01 And I also mentioned, in Lecture 2,
00:33:44.27 that at this time one of the very first things
00:33:48.12 that we see during cell differentiation
00:33:50.27 is a pairing of the two X chromosomes.
00:33:53.01 And as a result of this pairing process,
00:33:55.13 there's a mutually exclusive determination
00:33:58.02 of the active and the inactive X chromosome,
00:34:01.05 presumably through an asymmetric expression pattern
00:34:06.25 of the antisense RNA, Tsix.
00:34:10.05 So, from the future inactive X chromosome,
00:34:13.27 the antisense RNA disappears,
00:34:16.06 while the antisense RNA
00:34:19.06 persists on the future active X chromosome.
00:34:24.14 So, then on the future inactive X chromosome,
00:34:26.07 the disappearance of the antisense RNA
00:34:29.01 allows PRC2 to load onto chromatin.
00:34:31.29 But again, that is the not.
00:34:34.12 not enough to unleash the methyltransferase activity of EZH2.
00:34:40.10 When the RNA comes into contact with the accessory subunit JARID2,
00:34:44.15 the affinity of the RNA for PRC2 decreases,
00:34:49.20 the RNA is at least partially dislodged,
00:34:53.17 and that unleashes the methyltransferase activity of EZH2.
00:35:00.17 So, while all of this is happening,
00:35:03.25 at the same time we see that the Jpx RNA
00:35:07.09 -- this RNA which is just upstream of Xist --
00:35:09.16 is transcriptionally upregulated tenfold.
00:35:13.23 And when it crosses a certain threshold,
00:35:16.11 as it will do only in the female cell,
00:35:19.05 because the female has two copies of Jpx,
00:35:21.16 Jpx evicts CTCF from the 5' end of Xist.
00:35:30.11 And at probably around the same time,
00:35:33.24 the Gribnau lab has shown that this transcriptional repressor, REXI,
00:35:38.06 is degraded by an E3-ubiquitin ligase called Rnf12.
00:35:43.26 And it's really the combination of all of these events
00:35:49.10 -- in particular the downregulation of the antisense RNA,
00:35:54.04 the upregulation of Jpx RNA,
00:35:56.02 and the eviction of CTC.
00:35:57.19 CTCF and REXI --
00:35:59.27 that allows full-length Xist to be expressed
00:36:04.20 for the first time.
00:36:06.11 So, Xist of course
00:36:08.29 also has a binding site for PRC2.
00:36:11.03 And we now know from RNA proteomic analysis
00:36:14.01 that Xist probably binds to about
00:36:16.11 100 other proteins.
00:36:18.11 Now, this RNA protein complex
00:36:20.10 has to first attach, or load,
00:36:24.09 onto a single nucleation site
00:36:28.21 through YY1, the transcription factor YY1.
00:36:31.22 Now, without attaching to YY1
00:36:33.25 this RNA-protein complex will diffuse
00:36:36.29 through the rest of the nucleus.
00:36:39.13 So, from this single nucleation center,
00:36:42.01 the RNA-protein complex then spreads in three dimensions
00:36:46.03 across the rest of the X chromosome.
00:36:48.16 And again, it does three things.
00:36:51.02 It's not only recruiting silencing factors
00:36:53.13 to the rest of the X chromosome,
00:36:55.07 but it's also evicting activating factors
00:36:58.06 like cohesins and BRG1,
00:37:00.24 or the SWI/SNF factors,
00:37:02.25 from that X chromosome.
00:37:05.04 So, that, in a nutshell,
00:37:07.10 is how we're viewing the initiation and spreading
00:37:10.08 of X inactivation.
00:37:11.22 And I should say, by way of conclusion,
00:37:14.02 that this is a model.
00:37:16.07 So, it is a facsimile of what we can't actually directly visualize
00:37:20.28 in the natural world.
00:37:23.04 And scientists use these models as basic frameworks,
00:37:27.01 within which we can design additional experiments
00:37:29.22 to probe, to refute,
00:37:32.21 or to accept a hypothesis.
00:37:34.03 And of course, scientists disagree all the time with each other
00:37:37.07 about exactly how things are working in nature.
00:37:39.25 And so, we hope that additional data
00:37:42.07 that we will generate in the coming years
00:37:44.17 will allow us to continually refine this model.
00:37:48.08 And I hope that I'll be able to share
00:37:50.24 some of those new ideas with you
00:37:53.01 in the coming years.
- Part 1: Making and Breaking the Silence