Editing Histone (section)

== Function{{anchor|Histone modifications}} ==
[[File:Basic units of chromatin structure.svg|thumb|Basic units of chromatin structure]]

=== Compacting DNA strands ===

Histones act as spools around which DNA winds. This enables the compaction necessary to fit the large [[genome]]s of eukaryotes inside cell nuclei: the compacted molecule is 40,000 times shorter than an unpacked molecule.

=== Chromatin regulation ===
[[File:Histone tails and their function in chromatin formation.svg|thumb|Histone tails and their function in chromatin formation]]

Histones undergo [[posttranslational modification]]s that alter their interaction with [[DNA]] and nuclear proteins. The H3 and H4 histones have long tails protruding from the [[nucleosome]], which can be [[covalent]]ly 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, known as ''histone marks'', are thought to constitute a code, the so-called "[[histone code]]".<ref>{{cite journal |vauthors=Strahl BD, Allis CD |date=January 2000 |title=The language of covalent histone modifications |url=https://ui.adsabs.harvard.edu/abs/2000Natur.403...41S/abstract |journal=Nature |volume=403 |issue=6765 |pages=41–5 |bibcode=2000Natur.403...41S |doi=10.1038/47412 |pmid=10638745 |s2cid=4418993}}</ref><ref>{{cite journal | vauthors = Jenuwein T, Allis CD | title = Translating the histone code | journal = Science | volume = 293 | issue = 5532 | pages = 1074–80 | date = August 2001 | pmid = 11498575 | doi = 10.1126/science.1063127 | url = http://www.gs.washington.edu/academics/courses/braun/55104/readings/jenuwein.pdf | s2cid = 1883924 | citeseerx = 10.1.1.453.900 }}</ref> Histone modifications act in diverse biological processes such as [[gene regulation]], [[DNA repair]], chromosome condensation ([[mitosis]]) and [[spermatogenesis]] ([[meiosis]]).<ref>{{cite journal | vauthors = Song N, Liu J, An S, Nishino T, Hishikawa Y, Koji T | title = Immunohistochemical Analysis of Histone H3 Modifications in Germ Cells during Mouse Spermatogenesis | journal = Acta Histochemica et Cytochemica | volume = 44 | issue = 4 | pages = 183–90 | date = August 2011 | pmid = 21927517 | pmc = 3168764 | doi = 10.1267/ahc.11027 }}</ref>

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.

{| class="wikitable" style="text-align:center"
|+ Examples of histone modifications in transcriptional regulation
|-
! rowspan="2" | Type of<br/>modification
! colspan="9" | Histone
|-
! H3K4
! H3K9
! H3K14
! H3K27
! H3K79
! H3K36
! H4K20
! H2BK5
! H2BK20
|-
| mono-[[methylation]]
| [[H3K4me1|activation]]<ref>{{cite journal |vauthors=Benevolenskaya EV |date=August 2007 |title=Histone H3K4 demethylases are essential in development and differentiation |url=https://cdnsciencepub.com/doi/10.1139/O07-057 |journal=Biochemistry and Cell Biology |volume=85 |issue=4 |pages=435–43 |doi=10.1139/o07-057 |pmid=17713579}}</ref>
| activation<ref name="Barski_2007">{{cite journal | vauthors = Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K | title = High-resolution profiling of histone methylations in the human genome | journal = Cell | volume = 129 | issue = 4 | pages = 823–37 | date = May 2007 | pmid = 17512414 | doi = 10.1016/j.cell.2007.05.009 | doi-access = free }}</ref>
|
| activation<ref name="Barski_2007"/>
| activation<ref name="Barski_2007"/><ref name="Steger_2008">{{cite journal | vauthors = Steger DJ, Lefterova MI, Ying L, Stonestrom AJ, Schupp M, Zhuo D, Vakoc AL, Kim JE, Chen J, Lazar MA, Blobel GA, Vakoc CR | title = DOT1L/KMT4 recruitment and H3K79 methylation are ubiquitously coupled with gene transcription in mammalian cells | journal = Molecular and Cellular Biology | volume = 28 | issue = 8 | pages = 2825–39 | date = April 2008 | pmid = 18285465 | pmc = 2293113 | doi = 10.1128/MCB.02076-07 }}</ref>
|
|[[H4K20me|activation]]<ref name="Barski_2007"/>
| activation<ref name="Barski_2007"/>
|
|-
| di-methylation
| 
|[[H3K9me2|repression]]<ref name="Rosenfeld_2009">{{cite journal | vauthors = Rosenfeld JA, Wang Z, Schones DE, Zhao K, DeSalle R, Zhang MQ | title = Determination of enriched histone modifications in non-genic portions of the human genome | journal = BMC Genomics | volume = 10 | pages = 143 | date = March 2009 | pmid = 19335899 | pmc = 2667539 | doi = 10.1186/1471-2164-10-143 | doi-access = free }}</ref>
| 
| repression<ref name = "Rosenfeld_2009"/>
|[[H3K79me2|activation]]<ref name="Steger_2008"/>
|
|
|
| 
|-
| tri-methylation
| [[H3K4me3|activation]]<ref name="Koch_2007">{{cite journal | vauthors = Koch CM, Andrews RM, Flicek P, Dillon SC, Karaöz U, Clelland GK, Wilcox S, Beare DM, Fowler JC, Couttet P, James KD, Lefebvre GC, Bruce AW, Dovey OM, Ellis PD, Dhami P, Langford CF, Weng Z, Birney E, Carter NP, Vetrie D, Dunham I | title = The landscape of histone modifications across 1% of the human genome in five human cell lines | journal = Genome Research | volume = 17 | issue = 6 | pages = 691–707 | date = June 2007 | pmid = 17567990 | pmc = 1891331 | doi = 10.1101/gr.5704207 }}</ref>
|[[H3K9me3|repression]]<ref name="Barski_2007"/>
|
| [[H3K27me3|repression]]<ref name="Barski_2007"/>
| activation,<ref name="Steger_2008"/><br/>repression<ref name="Barski_2007"/>
|[[H3K36me3|activation]]
| repression<ref>{{cite journal | vauthors = Xu J, Kidder BL | title = H4K20me3 co-localizes with activating histone modifications at transcriptionally dynamic regions in embryonic stem cells | journal = BMC Genomics | volume = 19 | issue = 1 | pages = 514 | date = July 2018 | pmid = 29969988 | pmc = 6029396 | doi = 10.1186/s12864-018-4886-4 | doi-access = free }}</ref>
|
|
|-
| [[acetylation]]
| activation<ref>{{cite journal | vauthors = Guillemette B, Drogaris P, Lin HH, Armstrong H, Hiragami-Hamada K, Imhof A, Bonneil E, Thibault P, Verreault A, Festenstein RJ | title = H3 lysine 4 is acetylated at active gene promoters and is regulated by H3 lysine 4 methylation | journal = PLOS Genetics | volume = 7 | issue = 3 | pages = e1001354 | date = March 2011 | pmid = 21483810 | pmc = 3069113 | doi = 10.1371/journal.pgen.1001354 | doi-access = free }}</ref>
|[[H3K9ac|activation]]<ref name="Koch_2007"/>
| activation<ref name="Koch_2007"/>
| [[H3K27ac|activation]]<ref>{{cite journal | vauthors = Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA, Boyer LA, Young RA, Jaenisch R | title = Histone H3K27ac separates active from poised enhancers and predicts developmental state | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 107 | issue = 50 | pages = 21931–6 | date = December 2010 | pmid = 21106759 | pmc = 3003124 | doi = 10.1073/pnas.1016071107 | doi-access = free }}</ref>
| 
|
| 
| 
|activation
|}