Histone code: Difference between revisions

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Revision as of 21:40, 3 January 2017

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!style="background: #dedefa;" | activation<ref>{{cite journal|last1=Creyghton|first1=MP|title=Histone H3K27ac separates active from poised enhancers and predicts developmental state|journal=Proc Natl Acad Sci USA|date=Dec 2010|volume=107|issue=50|pages=21931–6|doi=10.1073/pnas.1016071107|pmid=21106759|pmc=3003124}}</ref>

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!style="background: #dedefa;" |activation<ref>{{Cite journal|last=Pradeepa|first=Madapura M.|last2=Grimes|first2=Graeme R.|last3=Kumar|first3=Yatendra|last4=Olley|first4=Gabrielle|last5=Taylor|first5=Gillian C. A.|last6=Schneider|first6=Robert|last7=Bickmore|first7=Wendy A.|date=2016-04-18|title=Histone H3 globular ___domain acetylation identifies a new class of enhancers|url=http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3550.html|journal=Nature Genetics|language=en|volume=advance online publication48|doi=10.1038/ng.3550|issn=1546-1718|pages=681–686}}</ref>

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Unlike this simplified model, any real histone code has the potential to be massively complex; each of the four standard histones can be simultaneously modified at multiple different sites with multiple different modifications. To give an idea of this complexity, [[histone H3]] contains nineteen lysines known to be methylated — each can be un-, mono-, di- or tri-methylated. If modifications are independent, this allows a potential 4¹⁹ or 280 billion different lysine methylation patterns, far more than the maximum number of histones in a human genome (6.4&nbsp;Gb / ~150&nbsp;bp = ~44 million histones if they are very tightly packed). And this does not include lysine acetylation (known for H3 at nine residues), arginine methylation (known for H3 at three residues) or threonine/serine/tyrosine phosphorylation (known for H3 at eight residues), not to mention modifications of other histones.

Every [[nucleosome]] in a cell can therefore have a different set of modifications, raising the question of whether common patterns of histone modifications exist. A recent study of about 40 histone modifications across human gene promoters found over 4000 different combinations used, over 3000 occurring at only a single promoter. However, patterns were discovered including a set of 17 histone modifications that are present together at over 3000 genes.<ref name="pmid18552846">{{cite journal |vauthors=Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, etal | title=Combinatorial patterns of histone acetylations and methylations in the human genome. | journal=Nat Genet | year= 2008 | volume= 40 | issue= 7 | pages= 897–903 | pmid=18552846 | doi=10.1038/ng.154 | pmc=2769248 | url=http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&tool=sumsearch.org/cite&retmode=ref&cmd=prlinks&id=18552846 }}</ref> Therefore, patterns of histone modifications do occur but they are very intricate, and we currently have detailed biochemical understanding of the importance of a relatively small number of modifications.

Structural determinants of histone recognition by readers, writers and erasers of the histone code are revealed by a growing body of experimental data.<ref name="Wang">{{cite journal |vauthors=Wang M, Mok MW, Harper H, Lee WH, Min J, Knapp S, Oppermann U, Marsden B, Schapira M |title=Structural Genomics of Histone Tail Recognition |journal=Bioinformatics |volume=26|issue=20 |pages=2629–2630 |date=24 Aug 2010 |pmid=20739309 |pmc=2951094 |doi=10.1093/bioinformatics/btq491}}</ref>