Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription

Abstract

Introduction Despite the long-observed correlation between H3K9me3, chromatin architecture, and transcriptional repression, how H3K9me3 regulates genome higher-order organization and transcriptional activity in living cells remains unclear. Result Here, we develop EpiGo (Epigenetic perturbation induced Genome organization)-KRAB to introduce H3K9me3 at hundreds of loci spanning megabases on human chromosome 19 and simultaneously track genome organization. EpiGo-KRAB is sufficient to induce genomic clustering and de novo heterochromatin-like domain formation, which requires SETDB1, a methyltransferase of H3K9me3. Unexpectedly, EpiGo-KRAB-induced heterochromatin-like domain does not result in widespread gene repression except a small set of genes with concurrent loss of H3K4me3 and H3K27ac. Ectopic H3K9me3 appears to spread in inactive regions but is largely restricted from transcriptional initiation sites in active regions. Finally, Hi-C analysis showed that EpiGo-KRAB reshapes existing compartments mainly at compartment boundaries. Conclusions These results reveal the role of H3K9me3 in genome organization could be partially separated from its function in gene repression.

Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair

“…5f, Additional file 1: Figure S15). This is consistent with previous suggestions that H3K9me3 play a limited role in gene repression [44][45][46] and the likely presence of other epigenetic modifications regulating the expression of the genes in the PCH.…”

Programmed suppression of oxidative phosphorylation and mitochondrial function by gestational alcohol exposure correlate with widespread increases in H3K9me2 that do not suppress transcription

“…Importantly, if a gene locus that becomes relocated to the nuclear periphery and silenced during differentiation is artificially moved to the nuclear periphery outside of a differentiation context, it does not become silenced [ 72 , 74 ]. Similarly, although CAS9-mediated increases in H3K9 methylation across a large region of human chromosome 19 can induce the formation of heterochromatin-like domains, this large-scale change in chromatin structure did not result in widespread gene repression [ 20 ]. From these various studies, it appears that although increased H3K9 methylation may associate with transcriptional suppression, direct regulation of gene expression falls to protein factors (activators/repressors) located in the various nuclear compartments during specific developmental windows; not by a change in histone methylation.…”

“…Although H3K9me2-enriched regions of the genome associate with gene silencing, heterochromatin also protects chromosome integrity during cellular stress [ 19 ]. Further, recent studies indicate that increased H3K9 methylation and formation of heterochromatin-like domains do not necessarily result in widespread gene repression [ 20 ]. Work in multiple organisms, including C. elegans , have demonstrated that the effects of early-life mitochondrial dysfunction and oxidative stress persist throughout the lifespan [ 21 , 22 ].…”

Simulating the chromatin mediated phase separation of model proteins with multiple domains

“…(35) also showed that removal of the H3K9me3 histone modification leads to loss of HP1 co-localisation, but the heterochromatin foci remain intact (inconsistent with HP1 begin a driver of heterochromatin body formation). Other work (40) has suggested that while HP1 may not be necessary to compact large satellite repeat heterochromatin regions, it is required to compact and silence smaller H3K9me3 marked segments within otherwise active regions. The function of HP1 clearly still not well understood.…”