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Series GSE67516 Query DataSets for GSE67516
Status Public on Jun 19, 2015
Title A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary The inactive X chromosome (Xi) serves as a model to understand gene silencing on a global scale. Here, we perform identification of direct RNA interacting proteins? (iDRiP) to isolate a comprehensive protein interactome for Xist, an RNA required for Xi silencing. We discover multiple classes of interactors, including cohesins, condensins, topoisomerases, RNA helicases, chromatin remodelers and modifiers, which synergistically repress Xi transcription. Inhibiting two or three interactors destabilizes silencing. While Xist attracts some interactors, it repels architectural factors. Xist evicts cohesins from the Xi and directs an Xi-specific chromosome conformation. Upon deleting Xist, the Xi acquires the cohesin-binding and chromosomal architecture of the active X. Our study unveils many layers of Xi repression and demonstrates a central role for RNA in the topological organization of mammalian chromosomes. The RNA-seq data sets generated in this study provide a resource for examining the effects of knockdowns of various Xist-interacting proteins on gene expression. The ChIP-seq data sets provide a comprehensive set of data examining CTCF and cohesion binding the X-chromosome, and the effects of deleting Xist on CTCF and cohesion binding. The Hi-C data is an allele-specific contact map of the X-chromosome higher-order chromatin structure in mouse.
Overall design RNA-seq in 3 control and 10 knockdown cell lines. ChIP-seq for CTCF, Rad21 and Smc1a in wild-type fibroblasts and Xist-deletion fibroblasts. Hi-C in wild-type and Xist-deletion fibroblasts.
Contributor(s) Froberg JE, Wei CY, Kesner B, Lee JT
Citation(s) 26089354
Submission date Apr 01, 2015
Last update date May 15, 2019
Contact name John Edward Froberg
Phone 8479770174
Organization name Harvard University
Department Stem Cell & Regenerative Biology
Lab Macklis Lab
Street address 7 Divinity Avenue
City Cambridge
State/province MA
ZIP/Postal code 02138
Country USA
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (42)
GSM1648474 wild-type ChIP input
GSM1648475 Xist deletion ChIP input
GSM1648476 CTCF ChIP wild-type, replicate 1
BioProject PRJNA280120
SRA SRP056800

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE67516_CTCF_peak_calls.bed.gz 282.1 Kb (ftp)(http) BED
GSE67516_Diff_expression.xlsx 33.1 Mb (ftp)(http) XLSX
GSE67516_RAD21_peak_calls.bed.gz 273.2 Kb (ftp)(http) BED
GSE67516_RAW.tar 36.0 Gb (http)(custom) TAR (of BW, TXT)
GSE67516_RNA_seq_rep1_diffExp_analysis.xls.gz 11.0 Mb (ftp)(http) XLS
GSE67516_SMC1A_peak_calls.bed.gz 500.0 Kb (ftp)(http) BED
GSE67516_WT_HiC_merged.tar.gz 6.4 Gb (ftp)(http) TAR
GSE67516_Xidel_HiC_merged.tar.gz 6.7 Gb (ftp)(http) TAR
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Raw data are available in SRA
Processed data provided as supplementary file

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