|
| Status |
Public on Feb 20, 2015 |
| Title |
Escape from X inactivation in mouse tissues (RNA-Seq) |
| Organism |
Mus musculus x Mus spretus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
X chromosome inactivation (XCI) silences most genes on one X chromosome in female mammals, but some genes escape XCI. To identify escape gene in vivo and to explore molecular mechanisms that regulate this process we analyzed the allele-specific expression and chromatin structure of X-linked genes in mouse tissues and cells with skewed XCI and distinguishable alleles based on single nucleotide polymorphisms. Using a new method to estimate allelic expression, we demonstrate a continuum between complete silencing and significant expression from the inactive X (Xi). Few genes (2-3%) escape XCI to a significant level and only a minority differs between mouse tissues, suggesting stringent silencing and escape controls. Allelic profiles of DNase I hypersensitivity and RNA polymerase II occupancy of genes on the Xi correlate with escape from XCI. Allelic binding profiles of the DNA binding protein CCCTC-binding factor (CTCF) in different cell types indicate that CTCF binding at the promoter correlates with escape. Importantly, CTCF binding at the boundary between escape and silenced domains may prevent the spreading of active escape chromatin into silenced domains.
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| |
|
| Overall design |
Examination of allelic expression in mouse hybrid tissues.
|
| |
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| Contributor(s) |
Berletch JB, Ma W, Noble WS, Shendure J, Disteche CM, Deng X |
| Citation(s) |
25785854, 25887447, 26248554 |
| |
| Submission date |
Jul 25, 2014 |
| 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) |
| GPL16617 |
Illumina Genome Analyzer IIx (Mus musculus x Mus spretus) |
|
| Samples (5)
|
|
| This SubSeries is part of SuperSeries: |
| GSE59779 |
Studies of regulation of mouse X inactivation and genes escaping XCI |
|
| Relations |
| BioProject |
PRJNA256188 |
| SRA |
SRP044862 |
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