Balancing cohesin eviction and retention prevents aberrant chromosomal interactions, Polycomb-mediated repression, and X-inactivation
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE144834 | GEO | 2021/03/15
REPOSITORIES: GEO
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Project description:The inactive X chromosome (Xi) serves as a model to understand gene silencing on a global scale. Here, we perform identification of direct RNA interacting proteins? (iDRiP) to isolate a comprehensive protein interactome for Xist, an RNA required for Xi silencing. We discover multiple classes of interactors, including cohesins, condensins, topoisomerases, RNA helicases, chromatin remodelers and modifiers, which synergistically repress Xi transcription. Inhibiting two or three interactors destabilizes silencing. While Xist attracts some interactors, it repels architectural factors. Xist evicts cohesins from the Xi and directs an Xi-specific chromosome conformation. Upon deleting Xist, the Xi acquires the cohesin-binding and chromosomal architecture of the active X. Our study unveils many layers of Xi repression and demonstrates a central role for RNA in the topological organization of mammalian chromosomes. The RNA-seq data sets generated in this study provide a resource for examining the effects of knockdowns of various Xist-interacting proteins on gene expression. The ChIP-seq data sets provide a comprehensive set of data examining CTCF and cohesion binding the X-chromosome, and the effects of deleting Xist on CTCF and cohesion binding. The Hi-C data is an allele-specific contact map of the X-chromosome higher-order chromatin structure in mouse. RNA-seq in 3 control and 10 knockdown cell lines. ChIP-seq for CTCF, Rad21 and Smc1a in wild-type fibroblasts and Xist-deletion fibroblasts. Hi-C in wild-type and Xist-deletion fibroblasts.
2015-06-19 | E-GEOD-67516 | biostudies-arrayexpress
Project description:During X-inactivation, Xist RNA spreads along an entire chromosome to establish silencing. However, the mechanism and functional RNA elements involved in spreading remain undefined. By performing a comprehensive endogenous Xist deletion screen, we identify Repeat B as crucial for spreading Xist and maintaining Polycomb repressive complexes 1 and 2 (PRC1/PRC2) along the inactive X (Xi). Unexpectedly, spreading of these three factors is inextricably linked. Deleting Repeat B or its direct binding partner, HNRNPK, compromises recruitment of PRC1 and PRC2. In turn, ablating PRC1 or PRC2 impairs Xist spreading. Therefore, Xist and Polycomb complexes require each other to propagate along the Xi, suggesting a positive feedback mechanism between RNA initiator and protein effectors. Perturbing Xist/Polycomb spreading causes failure of de novo Xi silencing, with partial compensatory downregulation of the active X, and also disrupts topological Xi reconfiguration. Thus, Repeat B is a multifunctional element that integrates interdependent Xist/ Polycomb spreading, silencing, and changes in chromosome architecture.
2019-03-01 | GSE107217 | GEO
Project description:The inactive X chromosome (Xi) serves as a model to understand gene silencing on a global scale. Here, we perform identification of direct RNA interacting proteins? (iDRiP) to isolate a comprehensive protein interactome for Xist, an RNA required for Xi silencing. We discover multiple classes of interactors, including cohesins, condensins, topoisomerases, RNA helicases, chromatin remodelers and modifiers, which synergistically repress Xi transcription. Inhibiting two or three interactors destabilizes silencing. While Xist attracts some interactors, it repels architectural factors. Xist evicts cohesins from the Xi and directs an Xi-specific chromosome conformation. Upon deleting Xist, the Xi acquires the cohesin-binding and chromosomal architecture of the active X. Our study unveils many layers of Xi repression and demonstrates a central role for RNA in the topological organization of mammalian chromosomes. The RNA-seq data sets generated in this study provide a resource for examining the effects of knockdowns of various Xist-interacting proteins on gene expression. The ChIP-seq data sets provide a comprehensive set of data examining CTCF and cohesion binding the X-chromosome, and the effects of deleting Xist on CTCF and cohesion binding. The Hi-C data is an allele-specific contact map of the X-chromosome higher-order chromatin structure in mouse.
2015-06-19 | GSE67516 | GEO
Project description:The noncoding Xist RNA recruits silencing factors to the inactive X (Xi) and facilitates re-organization of Xi structure. Here, we examine the epigenomic landscape of the Xi and assess how Xist alters chromatin accessibility. Interestingly, Xist deletion propels selective chromatin re-accessibility on the Xi, affecting various Xi regions differentially. Re-accessibility is regulated by BRG1, an ATPase subunit of SWI/SNF chromatin remodeling complex. In vitro, RNA binding inhibits the nucleosome remodeling and ATPase activities of BRG1. In vivo, Xist directly interacts with BRG1 and expels BRG1 from the Xi. Xist ablation leads to a selective return of BRG1 in cis, emanating from pre-existing BRG1 sites that are Xist-free. BRG1's return correlates with cohesin re-binding and restoration of topologically associated domains (TADs), and results in formation of de novo Xi "superloops." Thus, Xist RNA binding inhibits BRG1's nucleosome remodeling activity and results in expulsion of the SWI/SNF complex from the Xi.
2019-01-14 | GSE109395 | GEO
Project description:The Xist long noncoding RNA (lncRNA) is essential for X-chromosome inactivation (XCI), the process by which mammals compensate for unequal numbers of sex chromosomes. During XCI, Xist coats the future inactive X (Xi) and recruits Polycomb Repressive Complex 2 (PRC2) to the X-inactivation center (Xic). Currently unclear is how Xist spreads silencing on a 150 Mb scale. Here we generate high-resolution maps of Xist binding across a developmental time course using CHART-seq. In female cells undergoing XCI de novo, Xist follows a two-step mechanism in which it initially targets gene-rich islands before spreading to intervening gene-poor domains. Xist is depleted from genes that escape XCI but frequently concentrates near escapee boundaries. Xist binding was linearly proportional to PRC2 density and H3 lysine 27 trimethylation (H3K27me3), suggesting co-migration of Xist and PRC2. Interestingly, when the Xi is acutely stripped of Xist in post-XCI cells, Xist recovers quickly within both gene-rich and -poor domains on a time scale of hours instead of days, suggesting a previously primed Xi chromatin state. We conclude that Xist spreading takes on distinct stage-specific forms: During initial establishment, Xist follows a two-step mechanism, but during maintenance, Xist spreads rapidly to both gene-rich and -poor regions. Capture hybridization analysis of RNA targets (CHART) and input samples of (differentiating) mouse embryonic stem (ES) cells and immortalized mouse embryonic fibroblasts (MEF) using paired-end 75 nt reads on Illumina HiSeq2500, with 2 replicates per sample (# of samples). RNA-seq of the same cell lines with 50 nt reads on Illumina HiSeq2000, with 2 replicates per sample (2 samples, 4 datasets total). CHIP-seq: Data from GSE36905 was aligned and processed as CHART-seq samples. Resulting coverage tracks (EZH2/K27me3) are linked directly to GSE48649 (bedGraphs linked below).
2013-11-04 | E-GEOD-48649 | biostudies-arrayexpress
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.
2024-09-10 | GSE206010 | GEO
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.
2024-09-10 | GSE206178 | GEO
Project description:The Xist long noncoding RNA (lncRNA) is essential for X-chromosome inactivation (XCI), the process by which mammals compensate for unequal numbers of sex chromosomes. During XCI, Xist coats the future inactive X (Xi) and recruits Polycomb Repressive Complex 2 (PRC2) to the X-inactivation center (Xic). Currently unclear is how Xist spreads silencing on a 150 Mb scale. Here we generate high-resolution maps of Xist binding across a developmental time course using CHART-seq. In female cells undergoing XCI de novo, Xist follows a two-step mechanism in which it initially targets gene-rich islands before spreading to intervening gene-poor domains. Xist is depleted from genes that escape XCI but frequently concentrates near escapee boundaries. Xist binding was linearly proportional to PRC2 density and H3 lysine 27 trimethylation (H3K27me3), suggesting co-migration of Xist and PRC2. Interestingly, when the Xi is acutely stripped of Xist in post-XCI cells, Xist recovers quickly within both gene-rich and -poor domains on a time scale of hours instead of days, suggesting a previously primed Xi chromatin state. We conclude that Xist spreading takes on distinct stage-specific forms: During initial establishment, Xist follows a two-step mechanism, but during maintenance, Xist spreads rapidly to both gene-rich and -poor regions.
2013-11-04 | GSE48649 | GEO
Project description:HUES24 cell line was nucleofected with POU5f1 cDNA to overexpress OCT4; This leads to the formation of mesendodermal cells Short- and Long-scales intra- and inter-chromosomal interactions are linked to gene transcription, but the molecular event underlying these structures and how it affects cell fate decision during embryonic development are poorly understood. One of the first embryonic cell fate decisions (i.e mesendoderm determination) is driven by the POU factor OCT4, acting in concert with the high mobility group genes SOX-2 and SOX-17. Here, we identify novel chromatin remodelling mechanism and enhancer function driven by both OCT4 and SALL4 that mediate cell fate switching. We found that OCT4 alters the higher-order chromatin structure at both Sox-2 and Sox-17 loci. OCT4 titrates out cohesin and switches the Sox-17 enhancer from a locked (within an inter-chromosomal Sox-2 enhancer/CTCF/cohesin loop) to an active (within an intra-chromosomal Sox-17 promoter/enhancer/cohesin loop) state. SALL4 concomitantly mobilizes the polycomb complexes at the Soxs loci. Thus, OCT4/SALL4-driven cohesin-and polycombs-mediated changes in higher order chromatin structure mediate instruction of early cell fate in embryonic cells. ChIP anti-OCT4 on chip. results_v2.xls file description: Enriched binding sites. Mutant means oct4 overexpressing cells , wt GFP nucleofected cells.
2015-04-02 | E-GEOD-58125 | biostudies-arrayexpress
Project description:X-chromosome inactivation (XCI) is a global silencing mechanism by which XX and XY mammals equalize X-linked gene dosages. XCI begins with an establishment phase during which Xist RNA spreads and induces de novo heterochromatinization across a female X chromosome, and is followed by a maintenance phase when multiple epigenetic pathways lock down the inactive X (Xi) state. Involvement of Polycomb repressive complexes 1 and 2 in XCI has been intensively studied, but with conflicting conclusions regarding their recruitment and role in Xi silencing. Here we reveal that establishment of XCI has two phases and reconcile the roles that Xist Repeats A and B play in gene silencing and Polycomb recruitment. Repeat A initiates both processes, whereas Repeat B bolsters or stabilizes them thereafter. Once established, XCI no longer requires Repeat A during maintenance. These findings integrate disparate studies and present a unified view of Xist?s role in Polycomb-mediated silencing.
2020-06-15 | GSE135389 | GEO