M6A-seq profiling in Xist and Xist_Del_A-repeat cell lines
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE142271 | GEO | 2020/02/01
REPOSITORIES: GEO
Similar Datasets
Project description:XIST is a long non-coding RNA (lncRNA) that mediates transcriptional silencing of X chromosome genes. Here we show that XIST is highly methylated with at least 78 N6-methyladenosine (m6A) residues, a reversible base modification whose function in lncRNAs is unknown. We show that m6A formation in XIST, as well as cellular mRNAs, is mediated by RBM15 and its paralog RBM15B, which bind the m6A-methylation complex and recruit it to specific sites in RNA. This results in methylation of adenosines in adjacent m6A consensus motifs. Furthermore, knockdown of RBM15 and RBM15B, or knockdown of the m6A methyltransferase METTL3 impairs XIST-mediated gene silencing. A systematic comparison of m6A-binding proteins shows that YTHDC1 preferentially recognizes m6A in XIST and is required for XIST function. Additionally, artificial tethering of YTHDC1 to XIST rescues XIST-mediated silencing upon loss of m6A. These data reveal a pathway of m6A formation and recognition required for XIST-mediated transcriptional repression. Three to four biological HEK293T replicates were used to perform iCLIP of endogenous YTH proteins, RBM15, and RBM15B. Crosslinking induced truncations were identified using CIMS-CITS pipeline.
2016-09-07 | E-GEOD-78030 | biostudies-arrayexpress
Project description:By m6A-seq, we examined the m6A pattern on Xist, which immediately after the A-repeat region. The cell line, integrating multiple copy of Xist on chr3, with m6A core machinery knockout (Wtap and Mettl3) were generated. We also profiled m6A-seq in transgenic Xist line, and observed a global reduction of m6A level, validated by m6A-LC-MS/MS. Unexpectedly, we haven’t observed reduced m6A level on Xist m6A region downstream of A-repeat in transgenic Xist line.
2019-06-17 | GSE119487 | GEO
Project description:m6A-seq profiling in Xist and Xist_Del_A-repeat cell lines
| PRJNA596450 | ENA
Project description:We show that a deletion encompassing the entire Xist 5’ m6A region results in a modest reduction in Xist-mediated silencing.
2020-02-01 | GSE142270 | GEO
Project description:XIST is a long non-coding RNA (lncRNA) that mediates transcriptional silencing of X chromosome genes. Here we show that XIST is highly methylated with at least 78 N6-methyladenosine (m6A) residues, a reversible base modification whose function in lncRNAs is unknown. We show that m6A formation in XIST, as well as cellular mRNAs, is mediated by RBM15 and its paralog RBM15B, which bind the m6A-methylation complex and recruit it to specific sites in RNA. This results in methylation of adenosines in adjacent m6A consensus motifs. Furthermore, knockdown of RBM15 and RBM15B, or knockdown of the m6A methyltransferase METTL3 impairs XIST-mediated gene silencing. A systematic comparison of m6A-binding proteins shows that YTHDC1 preferentially recognizes m6A in XIST and is required for XIST function. Additionally, artificial tethering of YTHDC1 to XIST rescues XIST-mediated silencing upon loss of m6A. These data reveal a pathway of m6A formation and recognition required for XIST-mediated transcriptional repression.
2016-09-07 | GSE78030 | GEO
Project description:Allelic silencing analysis for A-repeat and m6A region in mouse Xist
| PRJNA596451 | ENA
Project description:Xist, a pivotal player in X chromosome inactivation (XCI), has long been perceived as a cis-acting long noncoding RNA that binds exclusively to the inactive X chromosome (Xi). However, Xist’s ability to diffuse under select circumstances has long been documented, leading us to suspect that Xist RNA may have targets and functions beyond the Xi. Here, using female mouse embryonic stem cells (ES) and mouse embryonic fibroblasts (MEF) as a model, we demonstrate that Xist RNA indeed can spread beyond the Xi. However, its binding is limited to ~100 genes in differentiating ES and MEF cells. The target genes are diverse in function but are unified by their active chromatin status. Although active, Xist binding is associated with a downregulation of gene expression. Unlike on the Xi, Xist binding does not lead to full silencing and also does not spread beyond the target gene. Deleting Xist’s Repeat B (RepB) domain reduces Xist’s diffusion away from the Xi and inhibits Xist’s localization to autosomal targets. Nonetheless, Xist transcript lacking RepB fails to down-modulate autosomal gene expression. Altogether, our findings reveal Xist targets beyond the Xi and identify Repeat B as a crucial domain for its in-trans function.
2024-08-23 | GSE271097 | GEO
Project description:Xist, a pivotal player in X chromosome inactivation (XCI), has long been perceived as a cis-acting long noncoding RNA that binds exclusively to the inactive X chromosome (Xi). However, Xist’s ability to diffuse under select circumstances has long been documented, leading us to suspect that Xist RNA may have targets and functions beyond the Xi. Here, using female mouse embryonic stem cells (ES) and mouse embryonic fibroblasts (MEF) as a model, we demonstrate that Xist RNA indeed can spread beyond the Xi. However, its binding is limited to ~100 genes in differentiating ES and MEF cells. The target genes are diverse in function but are unified by their active chromatin status. Although active, Xist binding is associated with a downregulation of gene expression. Unlike on the Xi, Xist binding does not lead to full silencing and also does not spread beyond the target gene. Deleting Xist’s Repeat B (RepB) domain reduces Xist’s diffusion away from the Xi and inhibits Xist’s localization to autosomal targets. Nonetheless, Xist transcript lacking RepB fails to down-modulate autosomal gene expression. Altogether, our findings reveal Xist targets beyond the Xi and identify Repeat B as a crucial domain for its in-trans function.
2024-08-23 | GSE271096 | GEO
Project description:Xist represents a paradigm for long non-coding RNA function in epigenetic regulation, although how it mediates X-chromosome inactivation (XCI) remains largely unexplained. Multiple Xist-RNA binding proteins have recently been identified, including SPEN/SHARP, whose knockdown has been associated with deficient XCI at multiple loci. Here we demonstrate that SPEN is a key orchestrator of XCI in vivo and unravel its mechanism of action. We show that SPEN is essential for initiating gene silencing on the X chromosome in preimplantation mouse embryos and embryonic stem cells. On the other hand, SPEN is dispensable for maintenance of XCI in neural progenitor cells, although it significantly dampens expression of genes that escape from XCI. During initiation of XCI, we show by live-cell imaging and CUT&RUN approaches that SPEN is immediately recruited to the X chromosome upon Xist up-regulation, where it is targeted to enhancers and promoters of actively transcribed genes. SPEN rapidly disengages from chromatin once silencing is accomplished, implying a need for active transcription to tether it to chromatin. We define SPEN’s SPOC (SPEN paralog and ortholog C-terminal) domain as a major effector of SPEN’s gene silencing function, and show that artificial tethering of SPOC to Xist RNA is sufficient to mediate X-linked gene silencing. We identify SPOC’s protein partners which include NCOR/SMRT, the m6A RNA methylation machinery, the NuRD complex, RNA polymerase II and factors involved in regulation of transcription initiation and elongation. We propose that SPEN acts as a molecular integrator for initiation of XCI, bridging Xist RNA with the transcription machinery as well as nucleosome remodelers and histone deacetylases, at active enhancers and promoters.
2021-04-19 | PXD015699 | Pride
Project description:The noncoding Xist RNA could mediate chromosome inaccessiblity, especially for the pre-open chromatin regions (enhancer, promoter, CTCF). However, Xist lacking the B-repeats loss the ability of closing the chromatin accessibility. ATAC-seq is consistent with the observation by ATAC-see. XR-PID denotes the Xist RNA polycomb interacting domain, including the entire B-repeats and part of C repeats.
2017-12-08 | GSE102848 | GEO