X-chromosome inactivation involves chromosome-wide gene silencing accompanied by extensive chromatin changes, as well the loss of topologically associating domains. Yet discrete regions of the inactive X chromosome retain activity within localised 3D domains, which contain active genes that variably escape from X inactivation. The transcription factor and architectural protein CTCF has been proposed to be implicated in escape by insulating escape domains or sustaining their topology via cohesin-mediated loop extrusion. Here, we test the role of CTCF and cohesin in escape using acute degron-mediated depletion of CTCF and RAD21 in neural progenitor cells with established escape profiles. Although CTCF occupancy correlates with escape status on the inactive X chromosome, its removal - together with loss of loop extrusion - does not disrupt escapee gene expression, or domain organization, nor does it result in spreading of silencing or activation of genes in cis. Rather, we show that facultative escape regions are self-sustaining compartments of active chromatin enriched in H3K27 acetylation and depleted in H3K27 methylation, with the magnitude of compartment strength scaling up with the degree of transcriptional activity on the inactive X chromosome. These active escapee compartments are propagated independently of CTCF and RAD21-dependent 3D architecture. Our findings identify chromatin compartmentalization as the primary feature of facultative escapee domains.
Antonia Hauth, A. Loda, Nikolai S. Bykov et al.· bioRxiv· 0 citations
The lack of temporal resolution in transcriptomic data during mammalian embryonic genome activation (EGA) has precluded the comprehensive understanding of the functional relationships between the various gene regulatory mechanisms governing this process. Here, we finely dissect the transcriptional dynamics of mouse EGA using precision in vitro fertilization (IVF) coupled with single-embryo RNA sequencing. Our highly temporally resolved dataset uncovers an extensive, step-wise remodeling of the embryonic messenger RNA landscape, affecting ∼30% of the total detectable transcripts over a 9-hour time frame. We capture the gradual shift from maternal to embryonic messenger RNAs, successfully identify ribosome biogenesis and translation as hallmarks of EGA, and find previously unidentified gene expression dynamics. We further uncover a set of eight histone demethylating enzymes among the earliest up-regulated EGA genes and leverage our precision-IVF to dissect the transcriptional versus developmental impact of histone H3 lysine-4 trimethylation (H3K4me3) remodeling after fertilization. Our results indicate that precocious removal of H3K4me3 from embryonic chromatin only modestly affects embryonic transcription without perturbing EGA timing, arguing against a major instructive role of precocious remodeling of maternally inherited H3K4me3 after fertilization on genome activation. High-resolution transcriptome mapping coupled with functional perturbations allows us to distinguish direct gene expression effects from general impacts on developmental timing, opening avenues for further quantitative characterization of the impact of epigenome remodeling on embryonic transcription.
Jasmina Al-Mousawi, L. Michetti, Laura Castaldi et al.· Science Advances· 0 citations
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