Editing Epigenetics (section)

===Histone modifications===
Histones H3 and H4 can also be manipulated through demethylation using [[histone lysine demethylase]] (KDM). This recently identified enzyme has a catalytically active site called the Jumonji domain (JmjC). The demethylation occurs when JmjC utilizes multiple cofactors to hydroxylate the methyl group, thereby removing it. JmjC is capable of demethylating mono-, di-, and tri-methylated substrates.<ref name="pmid19234061">{{cite journal | vauthors = Nottke A, Colaiácovo MP, Shi Y | title = Developmental roles of the histone lysine demethylases | journal = Development | volume = 136 | issue = 6 | pages = 879–89 | date = March 2009 | pmid = 19234061 | pmc = 2692332 | doi = 10.1242/dev.020966 }}</ref>

Chromosomal regions can adopt stable and heritable alternative states resulting in bistable gene expression without changes to the DNA sequence. Epigenetic control is often associated with alternative [[covalent modification]]s of histones.<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> The stability and heritability of states of larger chromosomal regions are suggested to involve positive feedback where modified [[nucleosome]]s recruit enzymes that similarly modify nearby nucleosomes.<ref>{{cite journal | vauthors = Sneppen K, Micheelsen MA, Dodd IB | title = Ultrasensitive gene regulation by positive feedback loops in nucleosome modification | journal = Molecular Systems Biology | volume = 4 | issue = 1 | pages = 182 | date = 15 April 2008 | pmid = 18414483 | pmc = 2387233 | doi = 10.1038/msb.2008.21 }}</ref> A simplified stochastic model for this type of epigenetics is found here.<ref>{{cite web |url=http://cmol.nbi.dk/models/epigen/Epigen.html |title=Epigenetic cell memory |publisher=Cmol.nbi.dk |access-date=26 July 2012 |archive-url=https://web.archive.org/web/20110930093915/http://cmol.nbi.dk/models/epigen/Epigen.html |archive-date=30 September 2011 |url-status=dead }}</ref><ref name="pmid17512413">{{cite journal | vauthors = Dodd IB, Micheelsen MA, Sneppen K, Thon G | title = Theoretical analysis of epigenetic cell memory by nucleosome modification | journal = Cell | volume = 129 | issue = 4 | pages = 813–22 | date = May 2007 | pmid = 17512413 | doi = 10.1016/j.cell.2007.02.053 | s2cid = 16091877 | doi-access = free }}</ref>

It has been suggested that chromatin-based transcriptional regulation could be mediated by the effect of small RNAs. [[Small interfering RNA]]s can modulate transcriptional gene expression via epigenetic modulation of targeted [[Promoter (biology)|promoters]].<ref name="Morris">{{cite book | vauthors = Morris KL | title=RNA and the Regulation of Gene Expression: A Hidden Layer of Complexity | chapter=Epigenetic Regulation of Gene Expression | publisher=Caister Academic Press | location=Norfolk, England | year=2008 | isbn=978-1-904455-25-7 }}{{page needed|date=August 2013}}</ref>