X Chromosome Reactivation Dynamics Reveal Stages of Reprogramming to Pluripotency
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE58109 | GEO | 2014/12/18
SECONDARY ACCESSION(S): PRJNA248922
REPOSITORIES: GEO
Similar Datasets
Project description:Reprogramming to iPSCs resets the epigenome of somatic cells including the reversal of X chromosome-inactivation. We sought to gain insight into the steps underlying the reprogramming process by examining the means by which reprogramming leads to X chromosome-reactivation (XCR). Analyzing single cells in situ, we found that hallmarks of the inactive X (Xi) change sequentially, providing a direct readout of reprogramming progression. Several epigenetic changes on the Xi occur in the inverse order of developmental X-inactivation, while others are uncoupled from this sequence. Among the latter, DNA methylation has an extraordinary long persistence on the Xi during reprogramming, and, like Xist expression, is erased only after pluripotency genes are activated. Mechanistically, XCR requires both DNA demethylation and Xist silencing, ensuring that only cells undergoing faithful reprogramming initiate XCR. Our study defines the epigenetic state of multiple sequential reprogramming intermediates and establishes a paradigm for studying cell fate transitions during reprogramming. RRBS profiles were generated from female and male ES cells, female iPS cells, SSEA1+ and SSEA1- reprogramming intermediates, and male and female MEFs, for a total of 18 samples.
2014-12-18 | E-GEOD-58109 | biostudies-arrayexpress
Project description:Induction and reversal of chromatin silencing is critical for successful development, tissue homeostasis and the derivation of induced pluripotent stem cells (iPSCs). X-chromosome inactivation (XCI) and reactivation (XCR) in female cells represent chromosome-wide transitions between active and inactive chromatin states. While XCI has long been studied and provided important insights into gene regulation, the dynamics and mechanisms underlying the reversal of stable chromatin silencing of X-linked genes are much less understood. In this work, we use allele-resolution transcriptomic approaches to study XCR during mouse iPSC reprogramming in order to elucidate the timing and mechanisms of chromosome-wide reversal of gene silencing. Our findings reveal a sequential hierarchy of gene reactivation from the inactive X-chromosome (Xi). We show that gene reactivation initiates before the activation of late pluripotency genes and complete silencing of the long non-coding RNA (lncRNA) Xist, and is completed late in reprogramming. We reveal that the gene-specific timing of reactivation correlates with the genomic distance to genes that escape inactivation and with differential targeting by pluripotency transcription factors (TFs). We also show that histone deacetylases restrict XCR in reprogramming intermediates and that the severe hypoacetylation state of the Xi persists until late reprogramming stages. Therefore, randomly inactivated X-linked genes possess different degrees of epigenetic memory, the reversal of which may involve the combined action of chromatin regulators, pluripotency transcription factors and chromatin topology. Taken together, our study provides the chromosome-wide dynamics of gene reactivation from the randomly inactivated X-chromosome and a framework for understanding how transcription factors induce dynamic reversal of stable epigenetic memory by overcoming repressive chromatin barriers.
2019-02-08 | GSE126229 | GEO
Project description:X chromosome reactivation (XCR) represents a paradigm to study epigenetic regulation and the reversal of chromatin silencing, although how it is linked to the pluripotency gene regulatory network, pluripotency transcription factors (TFs) and chromatin remodelling processes remains largely unexplained. Several pluripotency TFs have been linked to XCR through binding to the long non-coding RNA gene Xist, but whether other regulatory elements are involved is unclear. Here, we show that reprogramming to iPSCs induces gradual acquisition of chromatin accessibility at specific sites on the inactive X chromosome (Xi) which is subsequently propagated to other regulatory elements including enhancers and promoters. Regions that are genomically closer to day 0 accessible regions become biallelically accessible earlier, than the more distant ones. For distinct categories of chromatin regions that become biallelically accessible at different times, different sets of transcription factor (TF) motifs are enriched, including the pluripotency TFs KLF4 and cMYC. In addition, regions that become bialleliacally accessible earlier also show increased TF pluripotency binding, supporting the link between pluripotency TFs in XCR. To further explore the relationship between pluripotency TFs and XCR, we construct the active Gene Regulatory Networks (GRNs) during iPSC reprogramming using scRNA-seq and computational analyses. We reveal gene targets of 311 TFs expressed across reprogramming to iPSCs. Using this single-cell regulatory atlas, we show that X-linked genes are preferentially targeted by several pluripotency TFs. Our results suggest a new model where XCR may be coordinated by direct targeting of regulatory elements on the X chromosome by pluripotency TFs, concomitant with step-wise acquisition of chromatin accessibility. Altogether, our results demonstrate how gradual acquisition of a new GRN during reprogramming of cellular identity is linked with dynamic induction of chromatin accessibility and overcomes stable chromatin silencing on the Xi.
2021-09-30 | GSE184987 | GEO
Project description:X chromosome reactivation (XCR) represents a paradigm to study epigenetic regulation and the reversal of chromatin silencing, although how it is linked to the pluripotency gene regulatory network, pluripotency transcription factors (TFs) and chromatin remodelling processes remains largely unexplained. Several pluripotency TFs have been linked to XCR through binding to the long non-coding RNA gene Xist, but whether other regulatory elements are involved is unclear. Here, we show that reprogramming to iPSCs induces gradual acquisition of chromatin accessibility at specific sites on the inactive X chromosome (Xi) which is subsequently propagated to other regulatory elements including enhancers and promoters. Regions that are genomically closer to day 0 accessible regions become biallelically accessible earlier, than the more distant ones. For distinct categories of chromatin regions that become biallelically accessible at different times, different sets of transcription factor (TF) motifs are enriched, including the pluripotency TFs KLF4 and cMYC. In addition, regions that become bialleliacally accessible earlier also show increased TF pluripotency binding, supporting the link between pluripotency TFs in XCR. To further explore the relationship between pluripotency TFs and XCR, we construct the active Gene Regulatory Networks (GRNs) during iPSC reprogramming using scRNA-seq and computational analyses. We reveal gene targets of 311 TFs expressed across reprogramming to iPSCs. Using this single-cell regulatory atlas, we show that X-linked genes are preferentially targeted by several pluripotency TFs. Our results suggest a new model where XCR may be coordinated by direct targeting of regulatory elements on the X chromosome by pluripotency TFs, concomitant with step-wise acquisition of chromatin accessibility. Altogether, our results demonstrate how gradual acquisition of a new GRN during reprogramming of cellular identity is linked with dynamic induction of chromatin accessibility and overcomes stable chromatin silencing on the Xi.
2021-09-30 | GSE153846 | GEO
Project description:X chromosome reactivation (XCR) represents a paradigm to study epigenetic regulation and the reversal of chromatin silencing, although how it is linked to the pluripotency gene regulatory network, pluripotency transcription factors (TFs) and chromatin remodelling processes remains largely unexplained. Several pluripotency TFs have been linked to XCR through binding to the long non-coding RNA gene Xist, but whether other regulatory elements are involved is unclear. Here, we show that reprogramming to iPSCs induces gradual acquisition of chromatin accessibility at specific sites on the inactive X chromosome (Xi) which is subsequently propagated to other regulatory elements including enhancers and promoters. Regions that are genomically closer to day 0 accessible regions become biallelically accessible earlier, than the more distant ones. For distinct categories of chromatin regions that become biallelically accessible at different times, different sets of transcription factor (TF) motifs are enriched, including the pluripotency TFs KLF4 and cMYC. In addition, regions that become bialleliacally accessible earlier also show increased TF pluripotency binding, supporting the link between pluripotency TFs in XCR. To further explore the relationship between pluripotency TFs and XCR, we construct the active Gene Regulatory Networks (GRNs) during iPSC reprogramming using scRNA-seq and computational analyses. We reveal gene targets of 311 TFs expressed across reprogramming to iPSCs. Using this single-cell regulatory atlas, we show that X-linked genes are preferentially targeted by several pluripotency TFs. Our results suggest a new model where XCR may be coordinated by direct targeting of regulatory elements on the X chromosome by pluripotency TFs, concomitant with step-wise acquisition of chromatin accessibility. Altogether, our results demonstrate how gradual acquisition of a new GRN during reprogramming of cellular identity is linked with dynamic induction of chromatin accessibility and overcomes stable chromatin silencing on the Xi.
2021-09-30 | GSE153845 | GEO
Project description:X chromosome reactivation (XCR) represents a paradigm to study epigenetic regulation and the reversal of chromatin silencing, although how it is linked to the pluripotency gene regulatory network, pluripotency transcription factors (TFs) and chromatin remodelling processes remains largely unexplained. Several pluripotency TFs have been linked to XCR through binding to the long non-coding RNA gene Xist, but whether other regulatory elements are involved is unclear. Here, we show that reprogramming to iPSCs induces gradual acquisition of chromatin accessibility at specific sites on the inactive X chromosome (Xi) which is subsequently propagated to other regulatory elements including enhancers and promoters. Regions that are genomically closer to day 0 accessible regions become biallelically accessible earlier, than the more distant ones. For distinct categories of chromatin regions that become biallelically accessible at different times, different sets of transcription factor (TF) motifs are enriched, including the pluripotency TFs KLF4 and cMYC. In addition, regions that become bialleliacally accessible earlier also show increased TF pluripotency binding, supporting the link between pluripotency TFs in XCR. To further explore the relationship between pluripotency TFs and XCR, we construct the active Gene Regulatory Networks (GRNs) during iPSC reprogramming using scRNA-seq and computational analyses. We reveal gene targets of 311 TFs expressed across reprogramming to iPSCs. Using this single-cell regulatory atlas, we show that X-linked genes are preferentially targeted by several pluripotency TFs. Our results suggest a new model where XCR may be coordinated by direct targeting of regulatory elements on the X chromosome by pluripotency TFs, concomitant with step-wise acquisition of chromatin accessibility. Altogether, our results demonstrate how gradual acquisition of a new GRN during reprogramming of cellular identity is linked with dynamic induction of chromatin accessibility and overcomes stable chromatin silencing on the Xi.
2021-09-30 | GSE153844 | GEO
Project description:To understand the role of DPPA2 in epigenetic memory during X-Chromosome reactivation (XCR) we employed inducible Xist hybrid female embryonic stem cell line (TX1072, hybrid Bl6/Cast). Wild type or Dppa2 knockout TX1072 cells were cultured, in three or two independent biological replicates, respectively, in presence of DOX (1ug/ml) for 6 days to induce Xist overexpression and X-Chomosome inactivation (XCI) on the Bl6 allele. DOX was then washed out to silence Xist and XCR was followed in a time-series at 1, 3 or 7 days after DOX removal. Cell pellets were harvested at the following timepoints: -DOX, +DOX, 1d D-wo, 3d D-wo and 7d D-wo. RNA was extracted and 250 ng used for PolyA mRNA library preparation and Next generation sequencing.
2021-11-23 | E-MTAB-11183 | biostudies-arrayexpress
Project description:At initiation of X chromosome inactivation (XCI), Xist is monoallelically upregulated from the future inactive X (Xi) chromosome, overcoming repression by its antisense transcript Tsix. Xist recruits various chromatin remodelers, amongst them SPEN, which are involved in silencing of X-linked genes in cis and establishment of the Xi. Here, we show that SPEN plays an important role in the initiation of XCI. Spen null female mouse embryonic stem cells (ESCs) are defective in Xist upregulation upon differentiation. We find that Xist-mediated SPEN recruitment to the Xi chromosome happens very early in XCI, and that SPEN-mediated silencing of the Tsix promoter is required for Xist upregulation. Accordingly, failed Xist upregulation in Spen-/- ESCs can be rescued by concomitant removal of Tsix. These findings indicate that SPEN is not only required for the establishment of the Xi, but is also crucial in the initiation of the XCI process.
2021-09-30 | GSE163320 | GEO
Project description:At initiation of X chromosome inactivation (XCI), Xist is monoallelically upregulated from the future inactive X (Xi) chromosome, overcoming repression by its antisense transcript Tsix. Xist recruits various chromatin remodelers, amongst them SPEN, which are involved in silencing of X-linked genes in cis and establishment of the Xi. Here, we show that SPEN plays an important role in the initiation of XCI. Spen null female mouse embryonic stem cells (ESCs) are defective in Xist upregulation upon differentiation. We find that Xist-mediated SPEN recruitment to the Xi chromosome happens very early in XCI, and that SPEN-mediated silencing of the Tsix promoter is required for Xist upregulation. Accordingly, failed Xist upregulation in Spen-/- ESCs can be rescued by concomitant removal of Tsix. These findings indicate that SPEN is not only required for the establishment of the Xi, but is also crucial in the initiation of the XCI process.
2021-09-30 | GSE163319 | GEO
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