Abstract
Nucleosome turnover concomitant with incorporation of the replication-independent histone variant H3.3 is a hallmark of regulatory regions in the animal genome. Nucleosome turnover is known to be universally linked to DNA accessibility and histone acetylation. In mouse embryonic stem cells, H3.3 is also highly enriched at interstitial heterochromatin, most prominently at intracisternal A-particle endogenous retroviral elements. Interstitial heterochromatin is established over confined domains by the TRIM28-KAP1/SETDB1 corepressor complex and has stereotypical features of repressive chromatin, such as H3K9me3 and recruitment of all HP1 isoforms. Here, we demonstrate that fast histone turnover and H3.3 incorporation is compatible with these hallmarks of heterochromatin. Further, we find that Smarcad1 chromatin remodeler evicts nucleosomes generating accessible DNA. Free DNA is repackaged via DAXX-mediated nucleosome assembly with histone variant H3.3 in this dynamic heterochromatin state. Loss of H3.3 in mouse embryonic stem cells elicits a highly specific opening of interstitial heterochromatin with minimal effects on other silent or active regions of the genome.
Highlights
Nucleosome turnover concomitant with incorporation of the replication-independent histone variant H3.3 is a hallmark of regulatory regions in the animal genome
Enrichment of H3.3 at H3K9me[3] heterochromatin regions, so far uniquely observed in mouse embryonic stem cells (ESC), poses a conundrum: do these regions show fast nucleosome turnover as known for euchromatic H3.3-enriched regions? Does the presence of H3.3 coincide with DNA accessibility, and how would such dynamic properties be reconciled with a silent, condensed heterochromatin structure? Here, we reveal surprisingly dynamic properties of interstitial heterochromatin in ESC and find well-known hallmarks of heterochromatin are compatible with rapid exchange of core histones while maintaining DNA in an inaccessible state
Several studies have assessed genome-wide H3.3 dynamics in ESC, either measuring incorporation or turnover of ectopically tagged H3.35,8,9,34, albeit exclusively looking at dynamics related to enhancers and transcription
Summary
Nucleosome turnover concomitant with incorporation of the replication-independent histone variant H3.3 is a hallmark of regulatory regions in the animal genome. A multitude of genome-wide studies have identified such dynamic chromatin at promoters, enhancers, gene bodies and origins of replication[4,5,6,7,8,9,10,11,12,13] In these instances, nucleosome turnover is thought to be a consequence of chromatin remodeling, transcriptional activity, nucleosome-destabilizing DNA sequences, competition with other chromatin binding factors, or a combination thereof. Interstitial heterochromatin in mouse ESC spreads over relatively small genomic distance (~10 kb), is established by a Tripartite motif-containing 28 (TRIM28 known as KAP1, TIF1b) co-repressor/SETDB1 histone methyltransferase complex and includes a subset of endogenous retroviral elements (ERVs), most prominently intracisternal A-type particle (IAP), and imprinted genes[22,23,24,25,26,27]. Enrichment of H3.3 at H3K9me[3] heterochromatin regions, so far uniquely observed in mouse ESC, poses a conundrum: do these regions show fast nucleosome turnover as known for euchromatic H3.3-enriched regions? Does the presence of H3.3 coincide with DNA accessibility, and how would such dynamic properties be reconciled with a silent, condensed heterochromatin structure? Here, we reveal surprisingly dynamic properties of interstitial heterochromatin in ESC and find well-known hallmarks of heterochromatin are compatible with rapid exchange of core histones while maintaining DNA in an inaccessible state
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
