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Stepwise de novo establishment of inactive X chromosome architecture in early development [MEF RNA-Seq]

ABSTRACT: Stepwise de novo establishment of inactive X chromosome architecture in early development [MEF RNA-Seq]

PROVIDER: PRJNA848789 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19637408_1.fastq.gz	Fastqsanger.gz
	SRR19637408_2.fastq.gz	Fastqsanger.gz
	SRR19637409_1.fastq.gz	Fastqsanger.gz
	SRR19637409_2.fastq.gz	Fastqsanger.gz

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Stepwise de novo establishment of inactive X chromosome architecture in early development [MEF ChIP]

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Stepwise de novo establishment of inactive X chromosome architecture in early development [MEF HiC]

Project description:X chromosome inactivation (XCI) triggers a drastic reprogramming of gene activities and chromosome architecture. However, how the 3D organization of the inactive X chromosome (Xi) is de novo established in vivo in mammals remains poorly understood. By comprehensive stage- and lineage- specific Hi-C mapping, we identified a unique Xist-separated megadomain structure (X-megadomains) on the Xi in mouse early embryos. X-megadomains emerge in extraembryonic lineages during imprinted XCI, in derived extraembryonic endoderm (XEN) cells, and transiently in the embryonic lineages during random XCI, before Dxz4-delineated megadomains (D-megadomains) occur at later stages in a strain-specific manner. Mechanistically, the emergence of X-megadomain boundary coincides with developmentally regulated enhancer activities and cohesin binding in a regulatory region near Xist (XRR). We pinpointed a subregion XRRa that is critical for the X-megadomain boundary. X-megadomains are impaired when XRRa is removed or cohesin is degraded in XEN cells. Importantly, this is accompanied by ectopic activation of regulatory elements and genes near Xist, suggesting that cohesin loading at regulatory elements promotes X-megadomains and confines local gene activities. Finally, the knockout of XRRa in mouse preimplantation embryos severely impairs the activation of Xist and the initiation of XCI. Hence, our data not only reveal stepwise chromosome folding during de novo XCI in vivo, but also support a model that regulatory element-dependent gene activation and cohesin loading simultaneously promote essential transcription activities and subsequent self-insulation amid global silencing during the early stage of XCI.

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Stepwise de novo establishment of inactive X chromosome architecture in early development [MEF ChIP]

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Stepwise de novo establishment of inactive X chromosome architecture in early development [MEF Cut&Run]

Project description:X chromosome inactivation (XCI) triggers drastic reorganization of chromatin architecture, which in turn facilitates XCI. However, how the 3D organization is de novo established during XCI in vivo remains poorly understood. Mouse embryos present an ideal model, as they undergo imprinted XCI, X chromosome reactivation (XCR) and subsequent random XCI. Using low-input Hi-C, we revealed a unique chromatin structure of the inactive X chromosome (Xi) during both imprinted and random XCI in early mouse embryos. A bipartite structure featured by two megadomains separated by Xist (X-megadomains), emerges in extraembryonic lineages, derived extraembryonic endoderm (XEN) cells, and also transiently in embryonic lineages. X-megadomains then diminish in adult tissues, where previously reported Dxz4-delineated megadomains (D-megadomains) appear in a strain-specific manner. Mechanistically, X-megadomains coincide with developmentally controlled activities of regulatory regions near Xist (XRRs), and loss of XRR disrupts X-megadomains. CUT&RUN revealed strong enrichment of CTCF and cohesin near Xist, despite global depletion, on Xi in embryos and XEN cells. X-megadomains are also impaired when Xist is silenced, accompanied by global cohesin restoration, or when residual cohesin is degraded, suggesting that X-megadomain formation is promoted by both global cohesin depletion and local cohesin loading. Importantly, the loss of cohesin leads to ectopic activation of regulatory elements and genes near Xist. Hence, these data reveal programming of chromatin architecture during de novo establishment of mammalian XCI in vivo, and suggest that cohesin mediates self-insulation of gene activity of essential escapees amid global silencing.

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