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Are histone proteins present around DNA in the nucleus during all of interphase (including G1) or do histone proteins only form later on when chromosomes are condensing into chromatids?
Thanks in advance!
Yes, DNA is always wrapped around histones.
DNA condensation using histones is not only meant to form the chromatids for mitosis/meiosis, but also one of the factors that control gene expression. Tightly packed heterochromatin is not being expressed, whereas unpacked euchromatin is transcriptionally active. The process of condensation is controlled by enzymes such as histone actelytransferase (HAT) and deacetylase (HDAC) that change the electrostatic properties of the histone proteins. Positively charged lysine in heterochromatin histones allows condensation with negatively charged DNA. By acetylation of these lysines, they become neutral and the heterochromatin turns into euchromatin, which, provided the necessary activators etc., can now be translated. To silence gene expression, the process is reversed.
Gene expression control is very complex and histone acetylation is only one factor out of many. Nonetheless, you see that histones are a crucial part of the chromosomes and are not only formed during mitosis or meiosis.
3.0.jpg">https://en.wikipedia.org/wiki/File:Histone_acetylation_and_deacetylation.jpg">ShareImprove this answeredited May 11 '17 at 1:22answered May 10 '17 at 22:59adjanadjan2,0389 silver badges23 bronze badges
- In eukaryotic cells, DNA and RNA synthesis occur in a different location than protein synthesis in prokaryotic cells, both these processes occur together.
- DNA is &ldquosupercoiled&rdquo in prokaryotic cells, meaning that the DNA is either under-wound or over-wound from its normal relaxed state.
- In eukaryotic cells, DNA is wrapped around proteins known as histones to form structures called nucleosomes.
- nucleosomes: The fundamental subunit of chromatin, composed of a little less than two turns of DNA wrapped around a set of eight proteins called histones.
- histones: The chief protein components of chromatin, which act as spools around which DNA winds.
A eukaryote contains a well-defined nucleus, whereas in prokaryotes the chromosome lies in the cytoplasm in an area called the nucleoid. In eukaryotic cells, DNA and RNA synthesis occur in a separate compartment from protein synthesis. In prokaryotic cells, both processes occur together. What advantages might there be to separating the processes? What advantages might there be to having them occur together?
Figure (PageIndex<1>): Eukaryotic and prokaryotic cells: A eukaryote contains a well-defined nucleus, whereas in prokaryotes, the chromosome lies in the cytoplasm in an area called the nucleoid.
The size of the genome in one of the most well-studied prokaryotes, E.coli, is 4.6 million base pairs (approximately 1.1 mm, if cut and stretched out). So how does this fit inside a small bacterial cell? The DNA is twisted by what is known as supercoiling. Supercoiling means that DNA is either under-wound (less than one turn of the helix per 10 base pairs) or over-wound (more than 1 turn per 10 base pairs) from its normal relaxed state. Some proteins are known to be involved in the supercoiling other proteins and enzymes such as DNA gyrase help in maintaining the supercoiled structure.
Eukaryotes, whose chromosomes each consist of a linear DNA molecule, employ a different type of packing strategy to fit their DNA inside the nucleus. At the most basic level, DNA is wrapped around proteins known as histones to form structures called nucleosomes. The histones are evolutionarily conserved proteins that are rich in basic amino acids and form an octamer. The DNA (which is negatively charged because of the phosphate groups) is wrapped tightly around the histone core. This nucleosome is linked to the next one with the help of a linker DNA. This is also known as the &ldquobeads on a string&rdquo structure. This is further compacted into a 30 nm fiber, which is the diameter of the structure. At the metaphase stage the chromosomes are at their most compact, approximately 700 nm in width, and are found in association with scaffold proteins.
Figure (PageIndex<1>): Eukaryotic chromosomes: These figures illustrate the compaction of the eukaryotic chromosome.
In interphase, eukaryotic chromosomes have two distinct regions that can be distinguished by staining. The tightly packaged region is known as heterochromatin, and the less dense region is known as euchromatin.
Heterochromatin usually contains genes that are not expressed, and is found in the regions of the centromere and telomeres. The euchromatin usually contains genes that are transcribed, with DNA packaged around nucleosomes but not further compacted.
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. 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 (a solenoid (DNA)-like particle). 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.  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. 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). Higher-order structures include the 30 nm fiber (forming an irregular zigzag) and 100 nm fiber, these being the structures found in normal cells. During mitosis and meiosis, the condensed chromosomes are assembled through interactions between nucleosomes and other regulatory proteins.
Histones are subdivided into canonical replication-dependent histones that are expressed during the S-phase of the cell cycle and replication-independent histone variants, expressed during the whole cell cycle. In animals, genes encoding canonical histones are typically clustered along the chromosome, lack introns and use a stem loop structure at the 3' end instead of a polyA tail. Genes encoding histone variants are usually not clustered, have introns and their mRNAs are regulated with polyA tails. Complex multicellular organisms typically have a higher number of histone variants providing a variety of different functions. Recent data are accumulating about the roles of diverse histone variants highlighting the functional links between variants and the delicate regulation of organism development.  Histone variants from different organisms, their classification and variant specific features can be found in "HistoneDB 2.0 - Variants" database.
The following is a list of human histone proteins:
|Linker||H1||H1F||H1F0, H1FNT, H1FOO, H1FX|
|H1H1||HIST1H1A, HIST1H1B, HIST1H1C, HIST1H1D, HIST1H1E, HIST1H1T|
|Core||H2A||H2AF||H2AFB1, H2AFB2, H2AFB3, H2AFJ, H2AFV, H2AFX, H2AFY, H2AFY2, H2AFZ|
|H2A1||HIST1H2AA, HIST1H2AB, HIST1H2AC, HIST1H2AD, HIST1H2AE, HIST1H2AG, HIST1H2AI, HIST1H2AJ, HIST1H2AK, HIST1H2AL, HIST1H2AM|
|H2B||H2BF||H2BFM, H2BFS, H2BFWT|
|H2B1||HIST1H2BA, HIST1H2BB, HIST1H2BC, HIST1H2BD, HIST1H2BE, HIST1H2BF, HIST1H2BG, HIST1H2BH, HIST1H2BI, HIST1H2BJ, HIST1H2BK, HIST1H2BL, HIST1H2BM, HIST1H2BN, HIST1H2BO|
|H3||H3A1||HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J|
|H4||H41||HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4G, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L|
The nucleosome core is formed of two H2A-H2B dimers and a H3-H4 tetramer, forming two nearly symmetrical halves by tertiary structure (C2 symmetry one macromolecule is the mirror image of the other).  The H2A-H2B dimers and H3-H4 tetramer also show pseudodyad symmetry. The 4 'core' histones (H2A, H2B, H3 and H4) are relatively similar in structure and are highly conserved through evolution, all featuring a 'helix turn helix turn helix' motif (DNA-binding protein motif that recognize specific DNA sequence). They also share the feature of long 'tails' on one end of the amino acid structure - this being the location of post-translational modification (see below). 
Archaeal histone only contains a H3-H4 like dimeric structure made out of the same protein. Such dimeric structures can stack into a tall superhelix ("hypernucleosome") onto which DNA coils in a manner similar to nucleosome spools.  Only some archaeal histones have tails. 
The distance between the spools around which eukaryotic cells wind their DNA has been determined to range from 59 to 70 Å. 
In all, histones make five types of interactions with DNA:
- and hydrogen bonds between side chains of basic amino acids (especially lysine and arginine) and phosphate oxygens on DNA
- Helix-dipoles form alpha-helixes in H2B, H3, and H4 cause a net positive charge to accumulate at the point of interaction with negatively charged phosphate groups on DNA between the DNA backbone and the amide group on the main chain of histone proteins
- Nonpolar interactions between the histone and deoxyribose sugars on DNA
- Non-specific minor groove insertions of the H3 and H2B N-terminal tails into two minor grooves each on the DNA molecule
The highly basic nature of histones, aside from facilitating DNA-histone interactions, contributes to their water solubility.
Histones are subject to post translational modification by enzymes primarily on their N-terminal tails, but also in their globular domains.   Such modifications include methylation, citrullination, acetylation, phosphorylation, SUMOylation, ubiquitination, and ADP-ribosylation. This affects their function of gene regulation.
In general, genes that are active have less bound histone, while inactive genes are highly associated with histones during interphase.  It also appears that the structure of histones has been evolutionarily conserved, as any deleterious mutations would be severely maladaptive. All histones have a highly positively charged N-terminus with many lysine and arginine residues.
Core histones are found in the nuclei of eukaryotic cells and in most Archaeal phyla, but not in bacteria.  However the linker histones have homologs in bacteria.  The unicellular algae known as dinoflagellates were previously thought to be the only eukaryotes that completely lack histones,  however, later studies showed that their DNA still encodes histone genes.  Unlike the core histones, lysine-rich linker histone (H1) proteins are found in bacteria, otherwise known as nucleoprotein HC1/HC2. 
It has been proposed that histone proteins are evolutionarily related to the helical part of the extended AAA+ ATPase domain, the C-domain, and to the N-terminal substrate recognition domain of Clp/Hsp100 proteins. Despite the differences in their topology, these three folds share a homologous helix-strand-helix (HSH) motif. 
Archaeal histones may well resemble the evolutionary precursors to eukaryotic histones.  Furthermore, the nucleosome (core) histones may have evolved from ribosomal proteins (RPS6/RPS15) with which they share much in common, both being short and basic proteins.  Histone proteins are among the most highly conserved proteins in eukaryotes, emphasizing their important role in the biology of the nucleus.  : 939 In contrast mature sperm cells largely use protamines to package their genomic DNA, most likely because this allows them to achieve an even higher packaging ratio. 
There are some variant forms in some of the major classes. They share amino acid sequence homology and core structural similarity to a specific class of major histones but also have their own feature that is distinct from the major histones. These minor histones usually carry out specific functions of the chromatin metabolism. For example, histone H3-like CENPA is associated with only the centromere region of the chromosome. Histone H2A variant H2A.Z is associated with the promoters of actively transcribed genes and also involved in the prevention of the spread of silent heterochromatin.  Furthermore, H2A.Z has roles in chromatin for genome stability.  Another H2A variant H2A.X is phosphorylated at S139 in regions around double-strand breaks and marks the region undergoing DNA repair.  Histone H3.3 is associated with the body of actively transcribed genes. 
Compacting DNA strands Edit
Histones act as spools around which DNA winds. This enables the compaction necessary to fit the large genomes of eukaryotes inside cell nuclei: the compacted molecule is 40,000 times shorter than an unpacked molecule.
Chromatin regulation Edit
Histones undergo posttranslational modifications that alter their interaction with DNA and nuclear proteins. The H3 and H4 histones have long tails protruding from the nucleosome, which can be covalently modified at several places. Modifications of the tail include methylation, acetylation, phosphorylation, ubiquitination, SUMOylation, citrullination, and ADP-ribosylation. The core of the histones H2A and H2B can also be modified. Combinations of modifications are thought to constitute a code, the so-called "histone code".   Histone modifications act in diverse biological processes such as gene regulation, DNA repair, chromosome condensation (mitosis) and spermatogenesis (meiosis). 
The common nomenclature of histone modifications is:
- The name of the histone (e.g., H3)
- The single-letter amino acid abbreviation (e.g., K for Lysine) and the amino acid position in the protein
- The type of modification (Me: methyl, P: phosphate, Ac: acetyl, Ub: ubiquitin)
- The number of modifications (only Me is known to occur in more than one copy per residue. 1, 2 or 3 is mono-, di- or tri-methylation)
So H3K4me1 denotes the monomethylation of the 4th residue (a lysine) from the start (i.e., the N-terminal) of the H3 protein.
|Type of |
|mono-methylation||activation ||activation ||activation ||activation  ||activation ||activation |
|di-methylation||repression ||repression ||activation |
|tri-methylation||activation ||repression ||repression ||activation,  |
|acetylation||activation ||activation ||activation ||activation ||activation|
A huge catalogue of histone modifications have been described, but a functional understanding of most is still lacking. Collectively, it is thought that histone modifications may underlie a histone code, whereby combinations of histone modifications have specific meanings. However, most functional data concerns individual prominent histone modifications that are biochemically amenable to detailed study.
Lysine methylation Edit
The addition of one, two, or many methyl groups to lysine has little effect on the chemistry of the histone methylation leaves the charge of the lysine intact and adds a minimal number of atoms so steric interactions are mostly unaffected. However, proteins containing Tudor, chromo or PHD domains, amongst others, can recognise lysine methylation with exquisite sensitivity and differentiate mono, di and tri-methyl lysine, to the extent that, for some lysines (e.g.: H4K20) mono, di and tri-methylation appear to have different meanings. Because of this, lysine methylation tends to be a very informative mark and dominates the known histone modification functions.
Glutamine serotonylation Edit
Recently it has been shown, that the addition of a serotonin group to the position 5 glutamine of H3, happens in serotonergic cells such as neurons. This is part of the differentiation of the serotonergic cells. This post-translational modification happens in conjunction with the H3K4me3 modification. The serotonylation potentiates the binding of the general transcription factor TFIID to the TATA box. 
Arginine methylation Edit
What was said above of the chemistry of lysine methylation also applies to arginine methylation, and some protein domains—e.g., Tudor domains—can be specific for methyl arginine instead of methyl lysine. Arginine is known to be mono- or di-methylated, and methylation can be symmetric or asymmetric, potentially with different meanings.
Arginine citrullination Edit
Enzymes called peptidylarginine deiminases (PADs) hydrolyze the imine group of arginines and attach a keto group, so that there is one less positive charge on the amino acid residue. This process has been involved in the activation of gene expression by making the modified histones less tightly bound to DNA and thus making the chromatin more accessible.  PADs can also produce the opposite effect by removing or inhibiting mono-methylation of arginine residues on histones and thus antagonizing the positive effect arginine methylation has on transcriptional activity. 
Lysine acetylation Edit
Addition of an acetyl group has a major chemical effect on lysine as it neutralises the positive charge. This reduces electrostatic attraction between the histone and the negatively charged DNA backbone, loosening the chromatin structure highly acetylated histones form more accessible chromatin and tend to be associated with active transcription. Lysine acetylation appears to be less precise in meaning than methylation, in that histone acetyltransferases tend to act on more than one lysine presumably this reflects the need to alter multiple lysines to have a significant effect on chromatin structure. The modification includes H3K27ac.
Serine/threonine/tyrosine phosphorylation Edit
Addition of a negatively charged phosphate group can lead to major changes in protein structure, leading to the well-characterised role of phosphorylation in controlling protein function. It is not clear what structural implications histone phosphorylation has, but histone phosphorylation has clear functions as a post-translational modification, and binding domains such as BRCT have been characterised.
Effects on transcription Edit
Most well-studied histone modifications are involved in control of transcription.
Actively transcribed genes Edit
Two histone modifications are particularly associated with active transcription:
Trimethylation of H3 lysine 4 (H3K4me3) This trimethylation occurs at the promoter of active genes    and is performed by the COMPASS complex.    Despite the conservation of this complex and histone modification from yeast to mammals, it is not entirely clear what role this modification plays. However, it is an excellent mark of active promoters and the level of this histone modification at a gene's promoter is broadly correlated with transcriptional activity of the gene. The formation of this mark is tied to transcription in a rather convoluted manner: early in transcription of a gene, RNA polymerase II undergoes a switch from initiating' to 'elongating', marked by a change in the phosphorylation states of the RNA polymerase II C terminal domain (CTD). The same enzyme that phosphorylates the CTD also phosphorylates the Rad6 complex,   which in turn adds a ubiquitin mark to H2B K123 (K120 in mammals).  H2BK123Ub occurs throughout transcribed regions, but this mark is required for COMPASS to trimethylate H3K4 at promoters.   Trimethylation of H3 lysine 36 (H3K36me3) This trimethylation occurs in the body of active genes and is deposited by the methyltransferase Set2.  This protein associates with elongating RNA polymerase II, and H3K36Me3 is indicative of actively transcribed genes.  H3K36Me3 is recognised by the Rpd3 histone deacetylase complex, which removes acetyl modifications from surrounding histones, increasing chromatin compaction and repressing spurious transcription.    Increased chromatin compaction prevents transcription factors from accessing DNA, and reduces the likelihood of new transcription events being initiated within the body of the gene. This process therefore helps ensure that transcription is not interrupted.
Repressed genes Edit
Three histone modifications are particularly associated with repressed genes:
Trimethylation of H3 lysine 27 (H3K27me3) This histone modification is deposited by the polycomb complex PRC2.  It is a clear marker of gene repression,  and is likely bound by other proteins to exert a repressive function. Another polycomb complex, PRC1, can bind H3K27me3  and adds the histone modification H2AK119Ub which aids chromatin compaction.   Based on this data it appears that PRC1 is recruited through the action of PRC2, however, recent studies show that PRC1 is recruited to the same sites in the absence of PRC2.   Di and tri-methylation of H3 lysine 9 (H3K9me2/3) H3K9me2/3 is a well-characterised marker for heterochromatin, and is therefore strongly associated with gene repression. The formation of heterochromatin has been best studied in the yeast Schizosaccharomyces pombe, where it is initiated by recruitment of the RNA-induced transcriptional silencing (RITS) complex to double stranded RNAs produced from centromeric repeats.  RITS recruits the Clr4 histone methyltransferase which deposits H3K9me2/3.  This process is called histone methylation. H3K9Me2/3 serves as a binding site for the recruitment of Swi6 (heterochromatin protein 1 or HP1, another classic heterochromatin marker)   which in turn recruits further repressive activities including histone modifiers such as histone deacetylases and histone methyltransferases.  Trimethylation of H4 lysine 20 (H4K20me3) This modification is tightly associated with heterochromatin,   although its functional importance remains unclear. This mark is placed by the Suv4-20h methyltransferase, which is at least in part recruited by heterochromatin protein 1. 
Bivalent promoters Edit
Analysis of histone modifications in embryonic stem cells (and other stem cells) revealed many gene promoters carrying both H3K4Me3 and H3K27Me3, in other words these promoters display both activating and repressing marks simultaneously. This peculiar combination of modifications marks genes that are poised for transcription they are not required in stem cells, but are rapidly required after differentiation into some lineages. Once the cell starts to differentiate, these bivalent promoters are resolved to either active or repressive states depending on the chosen lineage. 
Other functions Edit
DNA damage Edit
Marking sites of DNA damage is an important function for histone modifications. It also protects DNA from getting destroyed by ultraviolet radiation of sun.
Phosphorylation of H2AX at serine 139 (γH2AX) Phosphorylated H2AX (also known as gamma H2AX) is a marker for DNA double strand breaks,  and forms part of the response to DNA damage.   H2AX is phosphorylated early after detection of DNA double strand break, and forms a domain extending many kilobases either side of the damage.    Gamma H2AX acts as a binding site for the protein MDC1, which in turn recruits key DNA repair proteins  (this complex topic is well reviewed in  ) and as such, gamma H2AX forms a vital part of the machinery that ensures genome stability. Acetylation of H3 lysine 56 (H3K56Ac) H3K56Acx is required for genome stability.   H3K56 is acetylated by the p300/Rtt109 complex,    but is rapidly deacetylated around sites of DNA damage. H3K56 acetylation is also required to stabilise stalled replication forks, preventing dangerous replication fork collapses.   Although in general mammals make far greater use of histone modifications than microorganisms, a major role of H3K56Ac in DNA replication exists only in fungi, and this has become a target for antibiotic development. 
DNA repair Edit
H3K36me3 has the ability to recruit the MSH2-MSH6 (hMutSα) complex of the DNA mismatch repair pathway.  Consistently, regions of the human genome with high levels of H3K36me3 accumulate less somatic mutations due to mismatch repair activity. 
Chromosome condensation Edit
Epigenetic modifications of histone tails in specific regions of the brain are of central importance in addictions.    Once particular epigenetic alterations occur, they appear to be long lasting "molecular scars" that may account for the persistence of addictions. 
Cigarette smokers (about 15% of the US population) are usually addicted to nicotine.  After 7 days of nicotine treatment of mice, acetylation of both histone H3 and histone H4 was increased at the FosB promoter in the nucleus accumbens of the brain, causing 61% increase in FosB expression.  This would also increase expression of the splice variant Delta FosB. In the nucleus accumbens of the brain, Delta FosB functions as a "sustained molecular switch" and "master control protein" in the development of an addiction.  
About 7% of the US population is addicted to alcohol. In rats exposed to alcohol for up to 5 days, there was an increase in histone 3 lysine 9 acetylation in the pronociceptin promoter in the brain amygdala complex. This acetylation is an activating mark for pronociceptin. The nociceptin/nociceptin opioid receptor system is involved in the reinforcing or conditioning effects of alcohol. 
Methamphetamine addiction occurs in about 0.2% of the US population.  Chronic methamphetamine use causes methylation of the lysine in position 4 of histone 3 located at the promoters of the c-fos and the C-C chemokine receptor 2 (ccr2) genes, activating those genes in the nucleus accumbens (NAc).  c-fos is well known to be important in addiction.  The ccr2 gene is also important in addiction, since mutational inactivation of this gene impairs addiction. 
The first step of chromatin structure duplication is the synthesis of histone proteins: H1, H2A, H2B, H3, H4. These proteins are synthesized during S phase of the cell cycle. There are different mechanisms which contribute to the increase of histone synthesis.
Yeast carry one or two copies of each histone gene, which are not clustered but rather scattered throughout chromosomes. Histone gene transcription is controlled by multiple gene regulatory proteins such as transcription factors which bind to histone promoter regions. In budding yeast, the candidate gene for activation of histone gene expression is SBF. SBF is a transcription factor that is activated in late G1 phase, when it dissociates from its repressor Whi5. This occurs when Whi5 is phosphorylated by Cdc8 which is a G1/S Cdk.  Suppression of histone gene expression outside of S phases is dependent on Hir proteins which form inactive chromatin structure at the locus of histone genes, causing transcriptional activators to be blocked.  
In metazoans the increase in the rate of histone synthesis is due to the increase in processing of pre-mRNA to its mature form as well as decrease in mRNA degradation this results in an increase of active mRNA for translation of histone proteins. The mechanism for mRNA activation has been found to be the removal of a segment of the 3' end of the mRNA strand, and is dependent on association with stem-loop binding protein (SLBP).  SLBP also stabilizes histone mRNAs during S phase by blocking degradation by the 3'hExo nuclease.  SLBP levels are controlled by cell-cycle proteins, causing SLBP to accumulate as cells enter S phase and degrade as cells leave S phase. SLBP are marked for degradation by phosphorylation at two threonine residues by cyclin dependent kinases, possibly cyclin A/ cdk2, at the end of S phase.  Metazoans also have multiple copies of histone genes clustered on chromosomes which are localized in structures called Cajal bodies as determined by genome-wide chromosome conformation capture analysis (4C-Seq). 
Link between cell-cycle control and synthesis Edit
Nuclear protein Ataxia-Telangiectasia (NPAT), also known as nuclear protein coactivator of histone transcription, is a transcription factor which activates histone gene transcription on chromosomes 1 and 6 of human cells. NPAT is also a substrate of cyclin E-Cdk2, which is required for the transition between G1 phase and S phase. NPAT activates histone gene expression only after it has been phosphorylated by the G1/S-Cdk cyclin E-Cdk2 in early S phase.  This shows an important regulatory link between cell-cycle control and histone synthesis.
Histones were discovered in 1884 by Albrecht Kossel.  The word "histone" dates from the late 19th century and is derived from the German word "Histon", a word itself of uncertain origin - perhaps from the Greek histanai or histos.
In the early 1960s, before the types of histones were known and before histones were known to be highly conserved across taxonomically diverse organisms, James F. Bonner and his collaborators began a study of these proteins that were known to be tightly associated with the DNA in the nucleus of higher organisms.  Bonner and his postdoctoral fellow Ru Chih C. Huang showed that isolated chromatin would not support RNA transcription in the test tube, but if the histones were extracted from the chromatin, RNA could be transcribed from the remaining DNA.  Their paper became a citation classic.  Paul T'so and James Bonner had called together a World Congress on Histone Chemistry and Biology in 1964, in which it became clear that there was no consensus on the number of kinds of histone and that no one knew how they would compare when isolated from different organisms.   Bonner and his collaborators then developed methods to separate each type of histone, purified individual histones, compared amino acid compositions in the same histone from different organisms, and compared amino acid sequences of the same histone from different organisms in collaboration with Emil Smith from UCLA.  For example, they found Histone IV sequence to be highly conserved between peas and calf thymus.  However, their work on the biochemical characteristics of individual histones did not reveal how the histones interacted with each other or with DNA to which they were tightly bound. 
Also in the 1960s, Vincent Allfrey and Alfred Mirsky had suggested, based on their analyses of histones, that acetylation and methylation of histones could provide a transcriptional control mechanism, but did not have available the kind of detailed analysis that later investigators were able to conduct to show how such regulation could be gene-specific.  Until the early 1990s, histones were dismissed by most as inert packing material for eukaryotic nuclear DNA, a view based in part on the models of Mark Ptashne and others, who believed that transcription was activated by protein-DNA and protein-protein interactions on largely naked DNA templates, as is the case in bacteria.
During the 1980s, Yahli Lorch and Roger Kornberg  showed that a nucleosome on a core promoter prevents the initiation of transcription in vitro, and Michael Grunstein  demonstrated that histones repress transcription in vivo, leading to the idea of the nucleosome as a general gene repressor. Relief from repression is believed to involve both histone modification and the action of chromatin-remodeling complexes. Vincent Allfrey and Alfred Mirsky had earlier proposed a role of histone modification in transcriptional activation,  regarded as a molecular manifestation of epigenetics. Michael Grunstein  and David Allis  found support for this proposal, in the importance of histone acetylation for transcription in yeast and the activity of the transcriptional activator Gcn5 as a histone acetyltransferase.
The discovery of the H5 histone appears to date back to the 1970s,  and it is now considered an isoform of Histone H1.    
8.2 Binary Fission
The process of binary fission in bacteria involves the following steps. First, the cell’s DNA is replicated. The replicated DNA copies then move to opposite poles of the cell in an energy-dependent process. The cell lengthens. Then, the equatorial plane of the cell constricts and separates the plasma membrane such that each new cell has exactly the same genetic material.
More specifically, the following steps occur:
- The DNA is tightly coiled.
- The DNA is unwound and duplicated.
- The DNA is pulled to the separate poles of the bacterium as it increases the size to prepare for splitting.
- The growth of a new cell wall begins to separate the bacterium
- The new cell wall fully develops, resulting in the complete split of the bacterium.
- The new daughter cells have tightly coiled DNA rods, ribosomes, and plasmids these are now brand-new organisms.
Binary fission is generally rapid though its speed varies between species. Under optimal conditions, E. coli, cells divide about every 20 minutes at 37 °C. Because the new cells will, in turn, undergo binary fission, the time binary fission requires is also the time the bacterial culture requires to double in the number of cells it contains. This time period is, therefore, be referred to as the doubling time. Some strains of Mycobacterium tuberculosis have doubling times of nearly 100 hours. Bacterial growth is limited by nutrient availability and density, so binary fission occurs at much lower rates in bacterial cultures once they enter the stationary phase of growth.
Some organelles in eukaryotic cells reproduce using binary fission. Mitochondrial fission occurs frequently within the cell, even when the cell is not actively undergoing mitosis, and is necessary to regulate the cell’s metabolism. All chloroplasts and some mitochrondria (not in animals), both organelles derived from endosymbiosis of bacteria, also use FtsZ in a bacteria-like fashion. The cell-division 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. Although the various stages of interphase are not usually morphologically distinguishable, each phase of the cell cycle has a distinct set of specialized biochemical processes that prepare the cell for initiation of the cell division.
Which of the following does cytosine pair with?
[reveal-answer q=″]Show Answer[/reveal-answer]
Prokaryotes contain a ________chromosome, and eukaryotes contain ________ chromosomes.
- single-stranded circular single-stranded linear
- single-stranded linear single-stranded circular
- double-stranded circular double-stranded linear
- double-stranded linear double-stranded circular
[reveal-answer q=″]Show Answer[/reveal-answer]
The transcriptional regulation of the genome is controlled primarily at the preinitiation stage by binding of the core transcriptional machinery proteins (namely, RNA polymerase, transcription factors, and activators and repressors) to the core promoter sequence on the coding region of the DNA. However, DNA is tightly packaged in the nucleus with the help of packaging proteins, chiefly histone proteins to form repeating units of nucleosomes which further bundle together to form condensed chromatin structure. Such condensed structure occludes many DNA regulatory regions, not allowing them to interact with transcriptional machinery proteins and regulate gene expression. To overcome this issue and allow dynamic access to condensed DNA, a process known as chromatin remodeling alters nucleosome architecture to expose or hide regions of DNA for transcriptional regulation.
By definition, chromatin remodeling is the enzyme-assisted process to facilitate access of nucleosomal DNA by remodeling the structure, composition and positioning of nucleosomes.
Access to nucleosomal DNA is governed by two major classes of protein complexes:
Covalent histone-modifying complexes Edit
Specific protein complexes, known as histone-modifying complexes catalyze addition or removal of various chemical elements on histones. These enzymatic modifications include acetylation, methylation, phosphorylation, and ubiquitination and primarily occur at N-terminal histone tails. Such modifications affect the binding affinity between histones and DNA, and thus loosening or tightening the condensed DNA wrapped around histones, e.g., Methylation of specific lysine residues in H3 and H4 causes further condensation of DNA around histones, and thereby prevents binding of transcription factors to the DNA that lead to gene repression. On the contrary, histone acetylation relaxes chromatin condensation and exposes DNA for TF binding, leading to increased gene expression. 
Known modifications Edit
Well characterized modifications to histones include: 
Both lysine and arginine residues are known to be methylated. Methylated lysines are the best understood marks of the histone code, as specific methylated lysine match well with gene expression states. Methylation of lysines H3K4 and H3K36 is correlated with transcriptional activation while demethylation of H3K4 is correlated with silencing of the genomic region. Methylation of lysines H3K9 and H3K27 is correlated with transcriptional repression.  Particularly, H3K9me3 is highly correlated with constitutive heterochromatin. 
Acetylation tends to define the ‘openness’ of chromatin as acetylated histones cannot pack as well together as deacetylated histones.
However, there are many more histone modifications, and sensitive mass spectrometry approaches have recently greatly expanded the catalog. 
Histone code hypothesis Edit
The histone code is a hypothesis that the transcription of genetic information encoded in DNA is in part regulated by chemical modifications to histone proteins, primarily on their unstructured ends. Together with similar modifications such as DNA methylation it is part of the epigenetic code.
Cumulative evidence suggests that such code is written by specific enzymes which can (for example) methylate or acetylate DNA ('writers'), removed by other enzymes having demethylase or deacetylase activity ('erasers'), and finally readily identified by proteins (‘readers’) that are recruited to such histone modifications and bind via specific domains, e.g., bromodomain, chromodomain. These triple action of ‘writing’, ‘reading’ and ‘erasing’ establish the favorable local environment for transcriptional regulation, DNA-damage repair, etc. 
The critical concept of the histone code hypothesis is that the histone modifications serve to recruit other proteins by specific recognition of the modified histone via protein domains specialized for such purposes, rather than through simply stabilizing or destabilizing the interaction between histone and the underlying DNA. These recruited proteins then act to alter chromatin structure actively or to promote transcription.
A very basic summary of the histone code for gene expression status is given below (histone nomenclature is described here):
|Type of |
|mono-methylation||activation ||activation ||activation ||activation  ||activation ||activation |
|di-methylation||repression ||repression ||activation |
|tri-methylation||activation ||repression ||repression ||activation,  |
|acetylation||activation ||activation |
ATP-dependent chromatin remodeling Edit
ATP-dependent chromatin-remodeling complexes regulate gene expression by either moving, ejecting or restructuring nucleosomes. These protein complexes have a common ATPase domain and energy from the hydrolysis of ATP allows these remodeling complexes to reposition nucleosomes (often referred to as "nucleosome sliding") along the DNA, eject or assemble histones on/off of DNA or facilitate exchange of histone variants, and thus creating nucleosome-free regions of DNA for gene activation.  Also, several remodelers have DNA-translocation activity to carry out specific remodeling tasks. 
All ATP-dependent chromatin-remodeling complexes possess a sub unit of ATPase that belongs to the SNF2 superfamily of proteins. In association to the sub unit's identity, two main groups have been classified for these proteins. These are known as the SWI2/SNF2 group and the imitation SWI (ISWI) group. The third class of ATP-dependent complexes that has been recently described contains a Snf2-like ATPase and also demonstrates deacetylase activity. 
Known chromatin remodeling complexes Edit
There are at least five families of chromatin remodelers in eukaryotes: SWI/SNF, ISWI, NuRD/Mi-2/CHD, INO80 and SWR1 with first two remodelers being very well studied so far, especially in the yeast model. Although all of remodelers share common ATPase domain, their functions are specific based on several biological processes (DNA repair, apoptosis, etc.). This is due to the fact that each remodeler complex has unique protein domains (Helicase, bromodomain, etc.) in their catalytic ATPase region and also has different recruited subunits.
Specific functions Edit
- Several in-vitro experiments suggest that ISWI remodelers organize nucleosome into proper bundle form and create equal spacing between nucleosomes, whereas SWI/SNF remodelers disorder nucleosomes.
- The ISWI-family remodelers have been shown to play central roles in chromatin assembly after DNA replication and maintenance of higher-order chromatin structures.
- INO80 and SWI/SNF-family remodelers participate in DNA double-strand break (DSB) repair and nucleotide-excision repair (NER) and thereby plays crucial role in TP53 mediated DNA-damage response.
- NuRD/Mi-2/CHD remodeling complexes primarily mediate transcriptional repression in the nucleus and are required for the maintenance of pluripotency of embryonic stem cells. 
In normal biological processes Edit
Chromatin remodeling plays a central role in the regulation of gene expression by providing the transcription machinery with dynamic access to an otherwise tightly packaged genome. Further, nucleosome movement by chromatin remodelers is essential to several important biological processes, including chromosome assembly and segregation, DNA replication and repair, embryonic development and pluripotency, and cell-cycle progression. Deregulation of chromatin remodeling causes loss of transcriptional regulation at these critical check-points required for proper cellular functions, and thus causes various disease syndromes, including cancer.
Response to DNA damage Edit
Chromatin relaxation is one of the earliest cellular responses to DNA damage.  The relaxation appears to be initiated by PARP1, whose accumulation at DNA damage is half complete by 1.6 seconds after DNA damage occurs.  This is quickly followed by accumulation of chromatin remodeler Alc1, which has an ADP-ribose–binding domain, allowing it to be quickly attracted to the product of PARP1. The maximum recruitment of Alc1 occurs within 10 seconds of DNA damage.  About half of the maximum chromatin relaxation, presumably due to action of Alc1, occurs by 10 seconds.  PARP1 action at the site of a double-strand break allows recruitment of the two DNA repair enzymes MRE11 and NBS1. Half maximum recruitment of these two DNA repair enzymes takes 13 seconds for MRE11 and 28 seconds for NBS1. 
Another process of chromatin relaxation, after formation of a DNA double-strand break, employs γH2AX, the phosphorylated form of the H2AX protein. The histone variant H2AX constitutes about 10% of the H2A histones in human chromatin.  γH2AX (phosphorylated on serine 139 of H2AX) was detected at 20 seconds after irradiation of cells (with DNA double-strand break formation), and half maximum accumulation of γH2AX occurred in one minute.  The extent of chromatin with phosphorylated γH2AX is about two million base pairs at the site of a DNA double-strand break. 
γH2AX does not, by itself, cause chromatin decondensation, but within seconds of irradiation the protein “Mediator of the DNA damage checkpoint 1” (MDC1) specifically attaches to γH2AX.   This is accompanied by simultaneous accumulation of RNF8 protein and the DNA repair protein NBS1 which bind to MDC1 as MDC1 attaches to γH2AX.  RNF8 mediates extensive chromatin decondensation, through its subsequent interaction with CHD4 protein,  a component of the nucleosome remodeling and deacetylase complex NuRD. CHD4 accumulation at the site of the double-strand break is rapid, with half-maximum accumulation occurring by 40 seconds after irradiation. 
The fast initial chromatin relaxation upon DNA damage (with rapid initiation of DNA repair) is followed by a slow recondensation, with chromatin recovering a compaction state close to its predamage level in ∼ 20 min. 
Chromatin remodeling provides fine-tuning at crucial cell growth and division steps, like cell-cycle progression, DNA repair and chromosome segregation, and therefore exerts tumor-suppressor function. Mutations in such chromatin remodelers and deregulated covalent histone modifications potentially favor self-sufficiency in cell growth and escape from growth-regulatory cell signals - two important hallmarks of cancer. 
- Inactivating mutations in SMARCB1, formerly known as hSNF5/INI1 and a component of the human SWI/SNF remodeling complex have been found in large number of rhabdoid tumors, commonly affecting pediatric population.  Similar mutations are also present in other childhood cancers, such as choroid plexus carcinoma, medulloblastoma and in some acute leukemias. Further, mouse knock-out studies strongly support SMARCB1 as a tumor suppressor protein. Since the original observation of SMARCB1 mutations in rhabdoid tumors, several more subunits of the human SWI/SNF chromatin remodeling complex have been found mutated in a wide range of neoplasms. 
- The SWI/SNF ATPase BRG1 (or SMARCA4) is the most frequently mutated chromatin remodeling ATPase in cancer.  Mutations in this gene were first recognized in human cancer cell lines derived from adrenal gland  and lung.  In cancer, mutations in BRG1 show an unusually high preference for missense mutations that target the ATPase domain.  Mutations are enriched at highly conserved ATPase sequences,  which lie on important functional surfaces such as the ATP pocket or DNA-binding surface.  These mutations act in a genetically dominant manner to alter chromatin regulatory function at enhancers  and promoters. 
- PML-RAR fusion protein in acute myeloid leukemia recruits histone deacetylases. This leads to repression of gene responsible for myelocytes to differentiate, leading to leukemia.
- Tumor suppressor Rb protein functions by the recruitment of the human homologs of the SWI/SNF enzymes BRG1, histone deacetylase and DNA methyltransferase. Mutations in BRG1 are reported in several cancers causing loss of tumor suppressor action of Rb. 
- Recent reports indicate DNA hypermethylation in the promoter region of major tumor suppressor genes in several cancers. Although few mutations are reported in histone methyltransferases yet, correlation of DNA hypermethylation and histone H3 lysine-9 methylation has been reported in several cancers, mainly in colorectal and breast cancers.
- Mutations in Histone Acetyl Transferases (HAT) p300 (missense and truncating type) are most commonly reported in colorectal, pancreatic, breast and gastric carcinomas. Loss of heterozygosity in coding region of p300 (chromosome 22q13) is present in large number of glioblastomas.
- Further, HATs have diverse role as transcription factors beside having histone acetylase activity, e.g., HAT subunit, hADA3 may act as an adaptor protein linking transcription factors with other HAT complexes. In the absence of hADA3, TP53 transcriptional activity is significantly reduced, suggesting role of hADA3 in activating TP53 function in response to DNA-damage.
- Similarly, TRRAP, the human homolog to yeast Tra1, has been shown to directly interact with c-Myc and E2F1 - known oncoproteins.
Cancer genomics Edit
Rapid advance in cancer genomics and high-throughput ChIP-chip, ChIP-Seq and Bisulfite sequencing methods are providing more insight into role of chromatin remodeling in transcriptional regulation and role in cancer.
Therapeutic intervention Edit
Epigenetic instability caused by deregulation in chromatin remodeling is studied in several cancers, including breast cancer, colorectal cancer, pancreatic cancer. Such instability largely cause widespread silencing of genes with primary impact on tumor-suppressor genes. Hence, strategies are now being tried to overcome epigenetic silencing with synergistic combination of HDAC inhibitors or HDI and DNA-demethylating agents. HDIs are primarily used as adjunct therapy in several cancer types.   HDAC inhibitors can induce p21 (WAF1) expression, a regulator of p53's tumor suppressoractivity. HDACs are involved in the pathway by which the retinoblastoma protein (pRb) suppresses cell proliferation.  Estrogen is well-established as a mitogenic factor implicated in the tumorigenesis and progression of breast cancer via its binding to the estrogen receptor alpha (ERα). Recent data indicate that chromatin inactivation mediated by HDAC and DNA methylation is a critical component of ERα silencing in human breast cancer cells. 
- Approved usage:
- was licensed by the U.S. FDA in October 2006 for the treatment of cutaneous T cell lymphoma (CTCL). (trade name Istodax) was licensed by the US FDA in Nov 2009 for cutaneous T-cell lymphoma (CTCL).
- (LBH589) is in clinical trials for various cancers including a phase III trial for cutaneous T cell lymphoma (CTCL). (as Mg valproate) in phase III trials for cervical cancer and ovarian cancer.
- (PXD101) has had a phase II trial for relapsed ovarian cancer, and reported good results for T cell lymphoma.
Current front-runner candidates for new drug targets are Histone Lysine Methyltransferases (KMT) and Protein Arginine Methyltransferases (PRMT). 
Other disease syndromes Edit
- (α-thalassemia X-linked mental retardation) and α-thalassemia myelodysplasia syndrome are caused by mutations in ATRX, a SNF2-related ATPase with a PHD. , an autosomal dominant disorder, has been linked recently to haploinsufficiency of CHD7, which encodes the CHD family ATPase CHD7. 
Chromatin architectural remodeling is implicated in the process of cellular senescence, which is related to, and yet distinct from, organismal aging. Replicative cellular senescence refers to a permanent cell cycle arrest where post-mitotic cells continue to exist as metabolically active cells but fail to proliferate.   Senescence can arise due to age associated degradation, telomere attrition, progerias, pre-malignancies, and other forms of damage or disease. Senescent cells undergo distinct repressive phenotypic changes, potentially to prevent the proliferation of damaged or cancerous cells, with modified chromatin organization, fluctuations in remodeler abundance, and changes in epigenetic modifications.    Senescent cells undergo chromatin landscape modifications as constitutive heterochromatin migrates to the center of the nucleus and displaces euchromatin and facultative heterochromatin to regions at the edge of the nucleus. This disrupts chromatin-lamin interactions and inverts of the pattern typically seen in a mitotically active cell.   Individual Lamin-Associated Domains (LADs) and Topologically Associating Domains (TADs) are disrupted by this migration which can affect cis interactions across the genome.  Additionally, there is a general pattern of canonical histone loss, particularly in terms of the nucleosome histones H3 and H4 and the linker histone H1.  Histone variants with two exons are upregulated in senescent cells to produce modified nucleosome assembly which contributes to chromatin permissiveness to senescent changes.  Although transcription of variant histone proteins may be elevated, canonical histone proteins are not expressed as they are only made during the S phase of the cell cycle and senescent cells are post-mitotic.  During senescence, portions of chromosomes can be exported from the nucleus for lysosomal degradation which results in greater organizational disarray and disruption of chromatin interactions. 
Chromatin remodeler abundance may be implicated in cellular senescence as knockdown or knockout of ATP-dependent remodelers such as NuRD, ACF1, and SWI/SNP can result in DNA damage and senescent phenotypes in yeast, C. elegans, mice, and human cell cultures.    ACF1 and NuRD are downregulated in senescent cells which suggests that chromatin remodeling is essential for maintaining a mitotic phenotype.   Genes involved in signaling for senescence can be silenced by chromatin confirmation and polycomb repressive complexes as seen in PRC1/PCR2 silencing of p16.   Specific remodeler depletion results in activation of proliferative genes through a failure to maintain silencing.  Some remodelers act on enhancer regions of genes rather than the specific loci to prevent re-entry into the cell cycle by forming regions of dense heterochromatin around regulatory regions. 
Senescent cells undergo widespread fluctuations in epigenetic modifications in specific chromatin regions compared to mitotic cells. Human and murine cells undergoing replicative senescence experience a general global decrease in methylation however, specific loci can differ from the general trend.     Specific chromatin regions, especially those around the promoters or enhancers of proliferative loci, may exhibit elevated methylation states with an overall imbalance of repressive and activating histone modifications.  Proliferative genes may show increases in the repressive mark H3K27me3 while genes involved in silencing or aberrant histone products may be enriched with the activating modification H3K4me3.  Additionally, upregulating histone deacetylases, such as members of the sirtuin family, can delay senescence by removing acetyl groups that contribute to greater chromatin accessibility.  General loss of methylation, combined with the addition of acetyl groups results in a more accessible chromatin conformation with a propensity towards disorganization when compared to mitotically active cells.  General loss of histones precludes addition of histone modifications and contributes changes in enrichment in some chromatin regions during senescence. 
How are histones important to the expression of genes?
Thus, acetylation of histones is known to increase the expression of genes through transcription activation. By deacetylating the histone tails, the DNA becomes more tightly wrapped around the histone cores, making it harder for transcription factors to bind to the DNA.
Beside above, what is a histone gene? Gene group hierarchy map. Histone In biology, 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 play a role in gene regulation.
Subsequently, one may also ask, why are histones important to DNA?
Histones are proteins that are critical in the packing of DNA into the cell and into chromatin and chromosomes. They're also very important for regulation of genes. So they turn out to have very important functions, not only structurally, but also in the regulation of gene function in expression.
How does histones affect DNA yield?
In eukaryotes, multiple genes encode histone proteins that package genomic deoxyribonucleic acid (DNA) and regulate its accessibility. Because of their positive charge, 'free' (non-chromatin associated) histones can bind non-specifically to the negatively charged DNA and affect its metabolism, including DNA repair.