Insulator-based loops mediate the spreading of H3K27me3 over distant micro-domains repressing euchromatin genes

Abstract

Background: Chromosomes are subdivided spatially to delimit long-range interactions into topologically associating domains (TADs). TADs are often flanked by chromatin insulators and transcription units that may participate in such demarcation. Remarkably, single-cell Drosophila TAD units correspond to dynamic heterochromatin nanocompartments that can self-assemble. The influence of insulators on such dynamic compartmentalization remains unclear. Moreover, to what extent heterochromatin domains are fully compartmentalized away from active genes remains unclear from Drosophila to human. Results: Here, we identify H3K27me3 micro-domains genome-wide in Drosophila, which are attributed to the three-dimensional spreading of heterochromatin marks into euchromatin. Whereas depletion of insulator proteins increases H3K27me3 spreading locally, across heterochromatin borders, it concomitantly decreases H3K27me3 levels at distant micro-domains discrete sites. Quantifying long-range interactions suggests that random interactions between heterochromatin TADs and neighbor euchromatin cannot predict the presence of micro-domains, arguing against the hypothesis that they reflect defects in self-folding or in insulating repressive TADs. Rather, microdomains are predicted by specific long-range interactions with the TAD borders bound by insulator proteins and co-factors required for looping. Accordingly, H3K27me3 spreading to distant sites is impaired by insulator mutants that compromise recruitment of looping co-factors. Both depletions and insulator mutants significantly reduce H3K27me3 micro-domains, deregulating the flanking genes. Conclusions: Our data highlight a new regulatory mode of H3K27me3 by insulatorbased long-range interactions controlling distant euchromatic genes.

Three classes of epigenomic regulators converge to hyperactivate the essential maternal gene deadhead within a heterochromatin mini-domain

“…This would be notably consistent with the previously described role of Mod(mdg4) in organizing 3D contacts between regulatory elements and promoters [36]. It would also be consistent with recent findings that H3K27me3 micro-domains may reflect such contacts [53].…”

“…This would be notably consistent with the previously described role of Mod(mdg4) in organizing 3D contacts between regulatory elements and promoters [36]. It would also be consistent with recent findings that H3K27me3 micro-domains may reflect such contacts [53]. However, no interaction between dhd and any other locus can be found in Hi-C data, and our rescue transgene experiments show that a small (4kb), ectopic genomic segment encapsulates the elements required for ovary-specific hyperactivation, arguing against a critical role of the genomic and epigenomic environment in the dhd locus.…”

“…Another recent study reported the existence of H3K27me3 micro-domains (typically 2-8 nucleosomes wide) that depend on 3D contacts with larger H3K27me3 domains, mediated, in particular, by BEAF-32 and CP190 [53]. The dhd mini-domain is wider and much more strongly enriched in H3K27me3 than typical micro-domains.…”

Chromatin-associated MRN complex protects highly transcribing genes from genomic instability

“…Heatmaps on genomic features were created using genomation’s ( 41 ) gridHeat function, using the profile matrices generated by DeepTools. GSEA was performed using fgsea as described previously ( 42 ), and all enrichment plots were created using the plotEnrichment function of the package. Decile matrices were created using color2D matplot from the plotrix package.…”

The chromatin factor ROW cooperates with BEAF-32 in regulating long-range inducible genes

“…A previous study showed that HP1c and HP1b form heterodimers in vitro and in vivo 42 . (D) Previously published studies showed that BEAF-32 regulates the expression of genes not directly bound by BEAF-32 through long-range contacts that depend on the interaction of BEAF-32 with CP190 10,43 .…”