Abstract
IntroductionDespite 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.ResultHere, 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.ConclusionsThese results reveal the role of H3K9me3 in genome organization could be partially separated from its function in gene repression.
Highlights
Despite the long-observed correlation between H3K9me3, chromatin architecture, and transcriptional repression, how H3K9me3 regulates genome higherorder organization and transcriptional activity in living cells remains unclear
These results reveal the role of H3K9me3 in genome organization could be partially separated from its function in gene repression
Establishment of EpiGo-KRAB To investigate how H3K9me3 regulates genome architecture and gene expression in living cells, here we developed a CRISPR-based system, namely EpiGo (Epigenetic perturbation induced Genome organization)-KRAB (Fig. 1a)
Summary
Despite the long-observed correlation between H3K9me, chromatin architecture, and transcriptional repression, how H3K9me regulates genome higherorder organization and transcriptional activity in living cells remains unclear. Human genome is organized in a hierarchy manner from kilobase to megabase scales such as nucleosome, loops, topologically associated domains (TADs), and A/B compartments [1,2,3,4]. It has been proposed that the loop extrusion drives TAD formation [5]. Liquid-liquid phase separation is suggested to mediate genome compartmentalization [5, 6]. Heterochromatin protein HP1α undergoes liquid-liquid demixing suggesting a role of phase separation in heterochromatin domain formation [7,8,9]. Heterochromatin drives compartmentalization in the inverted nuclei of rods in nocturnal mammals [10].
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