Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Xist Deletional Analysis Reveals an Interdependency between Xist RNA and Polycomb Complexes for Spreading along the Inactive X

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE107217 | GEO | 2019/03/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

4sU-seq analysis of Xist-mediated chromosomal silencing

Project description:The Polycomb repressive complexes PRC1 and PRC2 play a key role in chromosome silencing by Xist RNA. Previously we have shown that initation of Polycomb recruitment is mediated by the PCGF3/5-PRC1 complex, which catalyses chromosome-wide H2A ubiquitylation (H2AK119u1), signalling recruitment of other PRC1 complexes, and PRC2. However, the molecular basis for PCGF3/5-PRC1 recruitment by Xist RNA remains unknown. Here we define the Xist RNA Polycomb Interaction Domain (XR-PID), a 600 nt element encompassing the Xist B-repeat element. XR-PID is required for Polycomb recruitment by Xist RNA, Xist-mediated chromosome silencing. We identify the RNA-binding protein hnRNPK as the principal XR-PID binding factor required to recruit PCGF3/5-PRC1. Accordingly, synthetically tethering hnRNPK to Xist RNA lacking the B-repeat is sufficient for Xist-dependent Polycomb recruitment. Our findings resolve the molecular mechanism for Polycomb recruitment by Xist RNA, providing key insights into chromatin modification by non-coding RNA.

2017-12-08 | GSE99924 | GEO

High-resolution chromosomal maps of Xist RNA reveal a two-step spreading mechanism during X-inactivation

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

High-resolution chromosomal maps of Xist RNA reveal a two-step spreading mechanism during X-inactivation

2013-11-04 | GSE48649 | GEO

Calibrated ChIP-seq for Xist-mediated polycomb recruitment

Project description:Calibrated ChIP-seq was employed to quantitatively address the questions of how and where Xist recruits polycomb modifications (H2AK119ub and H3K27me3) to the inactive chromosome. 'Dox' samples were performed after 24 hours of induced Xist expression. Suz12 is the core enzymatic component of PRC2 while Pcgf3/5 are non-canonical PRC1 components which initiate the polycomb cascade in Xist-mediated chromosome inactivation. Xist PID region, encompassing the B-repeat and part of C-repeat, was characterized to bind hnRNPK directly, then recruit the Pcgf3/5. Notably, Suz12 KO does not affect Xist-dependent H2AK119ub deposition too much in a 24hour Xist induction.

2019-06-17 | GSE119599 | GEO

Xist Repeats A and B account for two distinct phases of X-inactivation establishment

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

An Xist-dependent protein assembly mediates Xist localization and gene silencing

Project description:Nuclear compartments play diverse roles in regulating gene expression, yet the molecular forces and components driving compartment formation are not well understood. Studying how the lncRNA Xist establishes the inactive-X-chromosome (Xi)-compartment, we found that the Xist RNA-binding-proteins PTBP1, MATR3, TDP43, and CELF1 form a condensate to create an Xi-domain that can be sustained in the absence of Xist. The E-repeat-sequence of Xist serves a multivalent binding-platform for these proteins. Without the E-repeat, Xist initially coats the X-chromosome during XCI onset but subsequently disperses across the nucleus with loss of gene silencing. Recruitment of PTBP1, MATR3, TDP-43 or CELF1 to E-Xist rescues these phenotypes, and requires both self-association of MATR3 and TDP-43 and a heterotypic PTBP1-MATR3-interaction. Together, our data reveal that Xist sequesters itself within the Xi-territory and perpetuates gene silencing by seeding a protein-condensate. Our findings uncover an unanticipated mechanism for epigenetic memory and elucidate the interplay between RNA and RNA-binding-proteins in creating compartments for gene regulation.

2020-09-03 | GSE137305 | GEO

4sU-seq analysis for tethering hnRNPK to Xist lacking of XR-PID

Project description:Xist lacking of XR-PID (B-repeat and part of C-repeat) can't recruit the polycomb during X chromsome inactivation. The majoring of Xist-mediated chromosomal silencing wouldn’t be achieved. We found that hnRNPK was the one of main contributors for binding B-repeat of Xist. When we tethered hnRNPK to Xist which lacks of XR-PID region, the silencing and polycomb recruitment are restored.

2017-12-08 | GSE103362 | GEO

A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation

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

Polycomb repressive complexes 1 and 2 are each essential for maintenance of X inactivation in extraembryonic lineages

Project description:In female mammals, one of the two X chromosomes becomes inactivated during development by X-chromosome inactivation (XCI). Although Polycomb repressive complexes (PRC) 1 and PRC2 have both been implicated in gene silencing, their exact roles in XCI during in vivo development have remained elusive. To this end, we have studied mouse embryos lacking either PRC1 or PRC2. Here we demonstrate that the loss of either PRCs has a substantial impact on maintenance of gene silencing on the inactive X (Xi) in extraembryonic tissues, with overlapping yet different genes affected, indicating potentially independent roles of the two complexes. Importantly, a lack of PRC1 does not affect PRC2/H3K27me3 accumulation and a lack of PRC2 does not impact PRC1/H2AK119ub1 accumulation on the Xi. Thus PRC1 and PRC2 contribute independently to the maintenance of XCI in early post-implantation extraembryonic lineages, revealing that both Polycomb complexes can be directly involved and differently deployed in XCI.

2022-10-12 | GSE168140 | GEO

RNAseq on Xist-tetOP FL, ΔA, ΔB+C cell lines, with 2 days of differentiation, without or with DOX induction

Project description:Xist RNA has been established as the master regulator of X-chromosome inactivation in female eutherian mammals but its mechanism of action remain unclear. By creating novel Xist mutants at the endogenous locus in mouse embryonic stem cells, we dissect the role of most of the conserved A-F repeats. We find that transcriptional silencing can be uncoupled from Polycomb repressive complex 1 and 2 (PRC1/2) recruitment, which requires repeats B and C. Xist ΔB+C specifically looses interaction with PCGF3/5 subunits of PRC1, while binding of other Xist partners are largely unaffected. However, a slight relaxation of transcriptional silencing in Xist ΔB+C indicates a role for PRC1/2 proteins in early stabilization of gene repression. Distinct structural modules within the Xist RNA are therefore involved in the convergence of independent chromatin modification and gene repression pathways, with Polycomb recruitment only being of moderate relevance in the initiation of silencing.

2019-08-28 | GSE123742 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data