{"id":139,"date":"2017-01-13T11:20:33","date_gmt":"2017-01-13T18:20:33","guid":{"rendered":"https:\/\/blogs.ubc.ca\/cdrohanbiol463\/?p=139"},"modified":"2017-01-13T11:20:38","modified_gmt":"2017-01-13T18:20:38","slug":"chromatin-remodeling-and-bivalent-histone-modification-in-escs","status":"publish","type":"post","link":"https:\/\/blogs.ubc.ca\/cdrohanbiol463\/2017\/01\/13\/chromatin-remodeling-and-bivalent-histone-modification-in-escs\/","title":{"rendered":"Chromatin remodeling and bivalent histone modification in ESCs"},"content":{"rendered":"<div>\n<ul>\n<li><b>Chromatin remodelling: <\/b>any change or modification to the chromatin\n<ul>\n<li>In the paper, authors\u00a0used term to describe ATP-dependent remodelling factors<\/li>\n<\/ul>\n<\/li>\n<li>Epigenetic modification of histones makes different transcription patterns possible with the same genome\n<ul>\n<li>Includes acetylation, methylation, ubiquitinylation, phosphorylation, sumoylation, ADP ribosylation, and many other modifications<\/li>\n<\/ul>\n<\/li>\n<li>Histone modifications can assist with activation and repression of transcription\n<ul>\n<li>H3K4me3: trimethylated lysine-4 of histone 3, activating histone mark<\/li>\n<li>H3K27me3: trimethylated lysine-27 on histone 3, repressive histone mark<\/li>\n<li>These two can be found in combination on certain promoters, called bivalent modifications<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/div>\n<div><b>Bivalent modifications<\/b><\/div>\n<div>\n<ul>\n<li>HCNE: highly conserved non-coding elements, tend to be enrichev d with these bivalent marks\n<ul>\n<li>Upon depletion of PRC2 subunit, there was a loss of H3K27me3, which led to an upregulation of the genes<\/li>\n<li>Under wild-type conditions, bivalent genes showed little to no activation, suggesting genes are poised for activation in mouse ESCs<\/li>\n<\/ul>\n<\/li>\n<li>In human ESCs and iPSCs, bivalent domains were often identified, on developmentally regulated genes<\/li>\n<li>H3K4me3 and H3K27me3 were found together on regulators of development that were expressed at low levels\n<ul>\n<li>Also seen in other stem cell types, e.g. hematopoietic stem cells<\/li>\n<li>Some promoters still had bivalent promoters, even when they were terminally differentiated, suggesting that maybe bivalent marks are present at a low level in all cell types<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/div>\n<div>\n<ul>\n<li>\n<ul>\n<li>Trithorax group (TrxG) deposits the H3K4me3 mark<\/li>\n<li>Polycomb group (PcG) proteins deposit the H3K27me3 (repressive) mark on histones<\/li>\n<li>Bivalent domains are mainly associated with CpG islands in ESCs<\/li>\n<\/ul>\n<\/li>\n<li>H3K4me3 is deposited by the SETD1A, SETD1B, and MLL complexes\n<ul>\n<li>Globally, the mark is deposited by the SETE1A and SET1B complexes<\/li>\n<li>MLL1 through MLL4 appear to carry out more specific functions<\/li>\n<li>MLL2: main methyltransferase at bivalent promoters<\/li>\n<li>MLL1\/2: contain CXXC or zinc-finger CXXC (ZF-CXXC) domains, which specifically recognize unmethylated CpGs<\/li>\n<\/ul>\n<\/li>\n<li>H3K27me3 is deposited by the PRC2 complex at bivalent promoters\n<ul>\n<li>The core PRC2 complex is made up of EZH2 or EZH1, EED, SUZ12<\/li>\n<li>EZH2: enhancer of zeste homologue 2, catalytic subunit of the PRC2, methyltransferase<\/li>\n<li>H3K27 is recognized by chromodomain-containing proteins such as CBX<\/li>\n<li>many developmentally regulated genes are marked by bivalent domains bound by PRC and PRC2, though some exclusively by PRC2<\/li>\n<li>PRC2-specific bivalent domains are usually found on the promoters of genes that are not true developmentally active genes<\/li>\n<\/ul>\n<\/li>\n<li>key pluripotent genes are shown to interact with MLL and PRC proteins\n<ul>\n<li>Depletion of Oct4 in ESCs leads to selective depletion of H2K4me3 levels<\/li>\n<li>When ESCs are undifferentiated, those deficient of PRC2 show aberrant differentiated potential<\/li>\n<li>PcG proteins are therefore vital for embryonic stem cell differentiation<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<div><\/div>\n<\/div>\n<div>Chromatin remodelling and bivalency<\/div>\n<div><\/div>\n<div><\/div>\n","protected":false},"excerpt":{"rendered":"<p>Chromatin remodelling: any change or modification to the chromatin In the paper, authors\u00a0used term to describe ATP-dependent remodelling factors Epigenetic modification of histones makes different transcription patterns possible with the same genome Includes acetylation, methylation, ubiquitinylation, phosphorylation, sumoylation, ADP ribosylation, and many other modifications Histone modifications can assist with activation and repression of transcription H3K4me3: [&hellip;]<\/p>\n","protected":false},"author":8192,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1788162],"tags":[],"class_list":["post-139","post","type-post","status-publish","format-standard","hentry","category-paper-summaries"],"_links":{"self":[{"href":"https:\/\/blogs.ubc.ca\/cdrohanbiol463\/wp-json\/wp\/v2\/posts\/139","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.ubc.ca\/cdrohanbiol463\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.ubc.ca\/cdrohanbiol463\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.ubc.ca\/cdrohanbiol463\/wp-json\/wp\/v2\/users\/8192"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.ubc.ca\/cdrohanbiol463\/wp-json\/wp\/v2\/comments?post=139"}],"version-history":[{"count":1,"href":"https:\/\/blogs.ubc.ca\/cdrohanbiol463\/wp-json\/wp\/v2\/posts\/139\/revisions"}],"predecessor-version":[{"id":140,"href":"https:\/\/blogs.ubc.ca\/cdrohanbiol463\/wp-json\/wp\/v2\/posts\/139\/revisions\/140"}],"wp:attachment":[{"href":"https:\/\/blogs.ubc.ca\/cdrohanbiol463\/wp-json\/wp\/v2\/media?parent=139"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.ubc.ca\/cdrohanbiol463\/wp-json\/wp\/v2\/categories?post=139"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.ubc.ca\/cdrohanbiol463\/wp-json\/wp\/v2\/tags?post=139"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}