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Series GSE107291 Query DataSets for GSE107291
Status Public on Nov 28, 2017
Title An evaluation of the effects of CRISPR/cas9-mediated editing of the Dxz4 locus on regulation of the mouse inactive X chromosome in Patski cells [RNA-seq]
Organism Mus musculus x Mus spretus
Experiment type Expression profiling by high throughput sequencing
Summary The mammalian inactive X chromosome (Xi) condenses into a bipartite structure with two superdomains of frequent long-range contacts separated by a boundary or hinge region. Using in situ DNase Hi-C in mouse cells with deletions or inversions within the hinge, we show that the conserved repeat locus Dxz4 alone is sufficient to maintain the bipartite structure and that Dxz4 orientation controls the distribution of long-range contacts on the Xi. Frequent long-range contacts between Dxz4 and the telomeric superdomain are either lost after its deletion or shifted to the centromeric superdomain after its inversion. This massive reversal in contact distribution is consistent with the reversal of CTCF motif orientation at Dxz4. Decondensation of the Xi after Dxz4 deletion is associated with partial restoration of TADs normally attenuated on the Xi, and with an increase in chromatin accessibility and CTCF binding, but few changes in gene expression, in accordance with multiple epigenetic mechanisms ensuring X silencing. We propose that Dxz4 represents a structural platform for frequent long-range contacts with multiple loci in a direction dictated by the orientation of a bank of CTCF motifs at Dxz4, which may work as a ratchet to form the distinctive bipartite structure of the condensed Xi.
 
Overall design RNA-seq experiment on F1 hybrid wild-type and CRISPR/cas9-modified Patski cells.
 
Contributor(s) Bonora G, Deng X, Fang H, Ramani V, Qui R, Berletch J, Filippova GN, Duan Z, Shendure J, Noble WS, Disteche C
Citation(s) 29654302, 26248554
Submission date Nov 22, 2017
Last update date Oct 09, 2019
Contact name Xinxian Deng
E-mail(s) dengx2@u.washington.edu
Organization name University of Washington
Department Laboratory Medicine and Pathology
Lab HSB C526
Street address 1959 NE Pacific St.
City Seattle
State/province WA
ZIP/Postal code 98195
Country USA
 
Platforms (1)
GPL20213 Illumina NextSeq 500 (Mus musculus x Mus spretus)
Samples (17)
GSM2863766 RNAseq.patski.WT
GSM2863767 RNAseq.patski.WT.0u5aza.rep1
GSM2863768 RNAseq.patski.WT.0u5aza.rep2
This SubSeries is part of SuperSeries:
GSE59779 Studies of regulation of mouse X inactivation and genes escaping XCI
Relations
BioProject PRJNA419576
SRA SRP125520

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
GSE107291_RNAseq.geneCounts.tsv.gz 908.7 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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