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Escape from X inactivation is directly modulated by Xist non-coding RNA [methylation]

ABSTRACT: X-chromosome inactivation silences one copy of the X-chromosome in female cells, but a number of genes escapes this inactivation. We asked whether increased levels of Xist RNA, the molecular actor driving X-inactivation, impacts expression levels of escapees. To this end, we performed DNA methylation profiling of X-linked genes in clonal neural progenitor cell lines with transgenes that allow for the overexpression of Xist on the inactive X chromosome. We perform Xist overexpression experiments for up to three weeks and also test the reversibility of Xist overexpression using washout experiments.

ORGANISM(S): Mus musculus Mus

PROVIDER: GSE260483 | GEO | 2025/12/09

REPOSITORIES: GEO

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Escape from X inactivation is directly modulated by Xist non-coding RNA [CUT&Run]

Project description:X-chromosome inactivation silences one copy of the X-chromosome in female cells, but a number of genes escapes this inactivation. We asked whether increased levels of Xist RNA, the molecular actor driving X-inactivation, impacts expression levels of escapees. To this end, we performed CUT&RUN profiling for two Xi-enriched histone marks, H2AK119Ub and H3K27me3 in a clonal neural progenitor cell line with transgenes that allow for the overexpression of Xist on the inactive X chromosome. We perform Xist overexpression experiments for up to three weeks and also test the reversibility of Xist overexpression using washout experiments.

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Escape from X inactivation is directly modulated by Xist non-coding RNA [cell line RNA-seq]

Project description:X-chromosome inactivation silences one copy of the X-chromosome in female cells, but a number of genes escapes this inactivation. We asked whether increased levels of Xist RNA, the molecular actor driving X-inactivation, impacts expression levels of escapees. To this end, we performed transcriptomic profiling of X-linked gene expression in clonal neural progenitor cell lines with transgenes that allow for the overexpression of Xist on the inactive X chromosome. We perform Xist overexpression experiments for up to three weeks and also test the reversibility of Xist overexpression using washout experiments. Finally, we demonstrate the role of SPEN in Xist-mediated silencing of escape using an inducible degron.

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Escape from X inactivation is directly modulated by Xist non-coding RNA [Capture Hi-C]

Project description:X-chromosome inactivation silences one copy of the X-chromosome in female cells, but a number of genes escapes this inactivation. Increased levels of Xist RNA, the molecular actor driving X-inactivation, results in silencing of escaping genes. To address how chromosome topology responds to changes in transcriptional activity of escapees, we performed allele-specific Capture Hi-C analysis of clusters of escaping genes on the inactive X chromosome in NPCs. We performed the experiments after 7 and 21 days of Xist induction and upon washout of doxycycline and in presence or absence of Xist’s partner SPEN. We further tested changes in the 3D topology of regions surrounding known constitutive escapees in ESCs upon increased Xist levels.

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Escape from X inactivation is directly modulated by Xist non-coding RNA [E8.5]

Project description:X-chromosome inactivation silences one copy of the X-chromosome in female cells, but a number of genes escapes XCI. We asked whether increased levels of Xist RNA, the molecular actor driving X-inactivation, impacts expression levels of escapees. We tested whether dox-mediated Xist-overexpression affected the expression levels of escapees in extra-embryonic tissues.

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Escape from X inactivation is directly modulated by Xist non-coding RNA [in vivo]

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Escape from X inactivation is directly modulated by Xist non-coding RNA [ESC]

Project description:X-chromosome inactivation silences one copy of the X-chromosome in female cells, but a number of genes escapes this inactivation. We asked whether increased levels of Xist RNA, the molecular actor driving X-inactivation, impacts expression levels of escapees. To this end, we performed transcriptomic profiling of X-linked gene expression in clonal neural progenitor cell lines with transgenes that allow for the overexpression of Xist on the inactive X chromosome. Here, we use the F1 hybrid mouse ESC line from which the NPCs were derived as a control to assess the silencing effect of Xist in ESCs.

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Escape from X inactivation is directly modulated by Xist non-coding RNA [ATAC-seq]

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The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA.

Project description:3D-topology of DNA in the cell nucleus provides a level of transcription regulation beyond the sequence of the linear DNA. To study the relationship between transcriptional activity and spatial environment of a gene, we have used allele-specific 4C-technology to produce high-resolution topology maps of the active and inactive X-chromosomes in female cells. We found that loci on the active X form multiple long-range interactions, with spatial segregation of active and inactive chromatin. On the inactive X, silenced loci lack preferred interactions, suggesting a unique random organization inside the inactive territory. However, escapees, among which is Xist, are engaged in long-range contacts with each other, enabling identification of novel escapees. Deletion of Xist results in partial re-folding of the inactive X into a conformation resembling the active X, without affecting gene silencing or DNA methylation. Our data point to a role for Xist RNA in shaping the conformation of the inactive X-chromosome independently of transcription. Five or six 4C viewpoints were applied on the mouse female wild type active X-chromosome, the wild type inactive X-chromosome, the conditional Xist X-chromosome and the Xist knock out X-chromosome

2011-06-24 | E-GEOD-29509 | biostudies-arrayexpress

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