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Series GSE48649 Query DataSets for GSE48649
Status Public on Nov 04, 2013
Title High-resolution chromosomal maps of Xist RNA reveal a two-step spreading mechanism during X-inactivation
Organism Mus musculus
Experiment type Other
Summary 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.
Overall design 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).
Contributor(s) Simon MD, Pinter SF, Fang R, Sarma K, Rutenberg-Schoenberg M, Bowman SK, Kesner BA, Maier VK, Kingston RE, Lee JT
Citation(s) 24162848
Submission date Jul 09, 2013
Last update date May 15, 2019
Contact name Stefan F Pinter
Organization name University of Connecticut, UConn Health
Department Genetics and Genome Sciences
Lab Pinter lab
Street address 263 Farmington Avenue
City Farmington
State/province CT
ZIP/Postal code 06030-6403
Country USA
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (27)
GSM1182874 dRF18: MEF Xist CHART sense oligo
GSM1182875 dRF4: MEF Xist CHART
GSM1182876 dRF13: MEF Xist CHART 40 C-oligo
BioProject PRJNA210928
SRA SRP026660

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
GSE48649_MEF.EZH2.cas.bedGraph.gz 44.5 Mb (ftp)(http) BEDGRAPH
GSE48649_MEF.EZH2.comp.bedGraph.gz 45.0 Mb (ftp)(http) BEDGRAPH
GSE48649_MEF.EZH2.mus.bedGraph.gz 44.5 Mb (ftp)(http) BEDGRAPH
GSE48649_MEF.K27me3.cas.bedGraph.gz 44.3 Mb (ftp)(http) BEDGRAPH
GSE48649_MEF.K27me3.comp.bedGraph.gz 44.6 Mb (ftp)(http) BEDGRAPH
GSE48649_MEF.K27me3.mus.bedGraph.gz 44.2 Mb (ftp)(http) BEDGRAPH
GSE48649_RAW.tar 1.9 Gb (http)(custom) TAR (of BEDGRAPH)
GSE48649_d0.EZH2.cas.bedGraph.gz 35.2 Mb (ftp)(http) BEDGRAPH
GSE48649_d0.EZH2.comp.bedGraph.gz 45.0 Mb (ftp)(http) BEDGRAPH
GSE48649_d0.EZH2.mus.bedGraph.gz 44.5 Mb (ftp)(http) BEDGRAPH
GSE48649_d0.K27me3.cas.bedGraph.gz 35.3 Mb (ftp)(http) BEDGRAPH
GSE48649_d0.K27me3.comp.bedGraph.gz 45.0 Mb (ftp)(http) BEDGRAPH
GSE48649_d0.K27me3.mus.bedGraph.gz 44.4 Mb (ftp)(http) BEDGRAPH
GSE48649_d7.EZH2.cas.bedGraph.gz 35.2 Mb (ftp)(http) BEDGRAPH
GSE48649_d7.EZH2.comp.bedGraph.gz 44.9 Mb (ftp)(http) BEDGRAPH
GSE48649_d7.EZH2.mus.bedGraph.gz 44.5 Mb (ftp)(http) BEDGRAPH
GSE48649_d7.K27me3.cas.bedGraph.gz 35.2 Mb (ftp)(http) BEDGRAPH
GSE48649_d7.K27me3.comp.bedGraph.gz 44.9 Mb (ftp)(http) BEDGRAPH
GSE48649_d7.K27me3.mus.bedGraph.gz 44.3 Mb (ftp)(http) BEDGRAPH
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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