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Series GSE119602 Query DataSets for GSE119602
Status Public on Jun 17, 2019
Title Systematic Analysis of Allelic Silencing Defines the Interplay of Key Pathways in Xist-mediated Chromosome Inactivation
Organism Mus musculus
Experiment type Other
Summary Xist RNA, the master regulator of X chromosome inactivation, acts in cis to induce chromosome silencing through the stepwise recruitment of factors that modify underlying chromatin structure. Whilst considerable progress has been made towards defining key silencing factors and the elements to which they bind, their relative contribution to silencing different genes, and their relationship with one another is poorly understood. Here we describe a systematic analysis of Xist-mediated allelic silencing in ES cell-based models. We show that Spen, recruited through the Xist A-repeat, plays a central role, being critical for silencing of all except a subset of low expressed genes. Polycomb, recruited through the Xist B/C-repeat, also plays a key role, favouring silencing of genes with pre-existing H3K27me3 chromatin. LBR and the Rbm15-Mettl3/14 m6A-methyltransferase complex, previously proposed to have a central role, make at most a minor contribution to gene silencing. We integrate our findings in a comprehensive model for Xist-mediated chromosome silencing.
 
Overall design We isolated chromatin-associated RNA (ChrRNA) to analyze the allelic ratio, aiming to understand Xist-mediated Silencing. The ChrRNA was isolated from cells with trangenic Xist model (iXist-Chr3) or endogenous Xist model (iXist-ChrX) derived from mouse embryonic stem cells. Xist is composed of several repetitive elements, which act by interacting with different factors. Cell lines with different factor knockout or Xist domain deletions were generated. The allelic ratios were systematically and comprehensively compared.
 
Contributor(s) Wei G, Nesterova TB, Coker H, Pintacuda G, Pan Q, Zhang T, Bowness JS, Bloechl B, Brockdorff N
Citation(s) 31311937
Submission date Sep 06, 2018
Last update date Aug 31, 2019
Contact name Guifeng Wei
E-mail(s) guifeng.wei@bioch.ox.ac.uk
Organization name University of Oxford
Department Department of Biochemistry
Lab Brockdorff Lab
Street address South Parks Road
City Oxford
ZIP/Postal code OX1 3QU
Country United Kingdom
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (148)
GSM3378572 iXist-Chr3_WT_NoDox_Rep1(Heather)
GSM3378573 iXist-Chr3_WT_Dox1
GSM3378574 iXist-Chr3_WT_Dox2
This SubSeries is part of SuperSeries:
GSE119607 Xist-mediated Chromosome Inactivation
Relations
BioProject PRJNA489699
SRA SRP159940

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE119602_LBR_Ratio_chr3_72h.txt.gz 44.8 Kb (ftp)(http) TXT
GSE119602_Ratio_chr3_WT_Suz12KO_3day.txt.gz 74.1 Kb (ftp)(http) TXT
GSE119602_Ratio_chrX_B2_day6.txt.gz 45.8 Kb (ftp)(http) TXT
GSE119602_Raw_Ratio_C7H8_chrX.txt.gz 20.7 Kb (ftp)(http) TXT
GSE119602_Raw_Ratio_chr3.xlsx 299.5 Kb (ftp)(http) XLSX
GSE119602_Raw_Ratio_chrX.xlsx 196.1 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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