Editing Histone (section)

== Evolution and species distribution ==

Core histones are found in the [[nucleus (biology)|nuclei]] of [[eukaryote|eukaryotic]] [[cell (biology)|cells]] and in most [[Archaea]]l phyla, but not in [[bacteria]].<ref name=pmid30212449/> The unicellular algae known as [[dinoflagellate]]s were previously thought to be the only eukaryotes that completely lack histones,<ref>{{cite journal | vauthors = Rizzo PJ | title = Those amazing dinoflagellate chromosomes | journal = Cell Research | volume = 13 | issue = 4 | pages = 215–7 | date = August 2003 | pmid = 12974611 | doi = 10.1038/sj.cr.7290166 | doi-access = free }}</ref> but later studies showed that their DNA still encodes histone genes.<ref>{{cite journal | vauthors = Talbert PB, Henikoff S | title = Chromatin: packaging without nucleosomes | journal = Current Biology | volume = 22 | issue = 24 | pages = R1040-3 | date = December 2012 | pmid = 23257187 | doi = 10.1016/j.cub.2012.10.052 | doi-access = free | bibcode = 2012CBio...22R1040T }}</ref> Unlike the core histones, homologs of the lysine-rich linker histone (H1) proteins are found in bacteria, otherwise known as nucleoprotein HC1/HC2.<ref>{{cite journal |vauthors=Kasinsky HE, Lewis JD, Dacks JB, Ausió J |date=January 2001 |title=Origin of H1 linker histones |journal=FASEB Journal |volume=15 |issue=1 |pages=34–42 |doi=10.1096/fj.00-0237rev |doi-access=free |pmid=11149891 |s2cid=10089116}}</ref>

It has been proposed that core 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.<ref name=HSH>{{cite journal | vauthors = Alva V, Ammelburg M, Söding J, Lupas AN | title = On the origin of the histone fold | journal = BMC Structural Biology | volume = 7 | pages = 17 | date = March 2007 | pmid = 17391511 | pmc = 1847821 | doi = 10.1186/1472-6807-7-17 | doi-access = free }}</ref> It's also proposed that they may have evolved from ribosomal proteins ([[RPS6]]/[[RPS15]]), both being short and basic proteins.<ref>{{cite journal |vauthors=Bozorgmehr JH |date=February 2020 |title=The origin of chromosomal histones in a 30S ribosomal protein |url=https://www.sciencedirect.com/science/article/abs/pii/S0378111919308145 |journal=Gene |volume=726 |pages=144155 |doi=10.1016/j.gene.2019.144155 |pmid=31629821|s2cid=204813634 }}</ref>

Archaeal histones may well resemble the evolutionary precursors to eukaryotic histones.<ref name=pmid30212449>{{cite journal | vauthors = Henneman B, van Emmerik C, van Ingen H, Dame RT | title = Structure and function of archaeal histones | journal = PLOS Genetics | volume = 14 | issue = 9 | pages = e1007582 | date = September 2018 | pmid = 30212449 | pmc = 6136690 | doi = 10.1371/journal.pgen.1007582 | bibcode = 2018BpJ...114..446H | doi-access = free }}</ref> Histone proteins are among the most highly conserved proteins in eukaryotes, emphasizing their important role in the biology of the nucleus.<ref name="Nelson&Cox"/>{{rp|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.<ref>{{cite journal |vauthors=Clarke HJ |year=1992 |title=Nuclear and chromatin composition of mammalian gametes and early embryos |url=https://cdnsciencepub.com/doi/10.1139/o92-134 |journal=Biochemistry and Cell Biology |volume=70 |issue=10–11 |pages=856–66 |doi=10.1139/o92-134 |pmid=1297351}}</ref>

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]].<ref>{{cite journal | vauthors = Guillemette B, Bataille AR, Gévry N, Adam M, Blanchette M, Robert F, Gaudreau L | title = Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning | journal = PLOS Biology | volume = 3 | issue = 12 | pages = e384 | date = December 2005 | pmid = 16248679 | pmc = 1275524 | doi = 10.1371/journal.pbio.0030384 | doi-access = free }}</ref> Furthermore, H2A.Z has roles in chromatin for genome stability.<ref>{{cite journal |vauthors=Billon P, Côté J |date=October 2011 |title=Precise deposition of histone H2A.Z in chromatin for genome expression and maintenance |url=https://www.sciencedirect.com/science/article/abs/pii/S1874939911001805 |journal=Biochim Biophys Acta |volume=1819 |issue=3–4 |pages=290–302 |doi=10.1016/j.bbagrm.2011.10.004 |pmid=22027408}}</ref> Another H2A variant H2A.X is phosphorylated at S139 in regions around [[DNA repair#Double-strand breaks|double-strand breaks]] and marks the region undergoing [[DNA repair]].<ref name="pmid10959836">{{cite journal | vauthors = Paull TT, Rogakou EP, Yamazaki V, Kirchgessner CU, Gellert M, Bonner WM | title = A critical role for histone H2AX in recruitment of repair factors to nuclear foci after DNA damage | journal = Current Biology | volume = 10 | issue = 15 | pages = 886–95 | year = 2000 | pmid = 10959836 | doi = 10.1016/S0960-9822(00)00610-2 | doi-access = free | bibcode = 2000CBio...10..886P }}</ref> Histone H3.3 is associated with the body of actively transcribed genes.<ref>{{cite journal | vauthors = Ahmad K, Henikoff S | title = The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly | journal = Molecular Cell | volume = 9 | issue = 6 | pages = 1191–200 | date = June 2002 | pmid = 12086617 | doi = 10.1016/S1097-2765(02)00542-7 | doi-access = free }}</ref>