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| Status |
Public on Aug 11, 2015 |
| Title |
Nucleophosmin binding on the mouse X chromosomes |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
|
| Summary |
In mammals, one of the female X chromosomes and all imprinted genes are expressed exclusively from a single allele in somatic cells. To evaluate structural changes associated with allelic silencing, we have applied a recently developed Hi-C assay that uses DNase I for chromatin fragmentation to mouse F1 hybrid systems. Results We find radically different conformations for the two female mouse X chromosomes. The inactive X has two superdomains of frequent intrachromosomal contacts separated by a boundary/hinge region. Comparison with the recently reported bipartite 3D structure of the human inactive X shows that the genomic content of the superdomains differs between species, but part of the hinge is conserved and located near the Dxz4/DXZ4 locus. In mouse, the hinge region also contains a minisatellite Ds-TR, and both Dxz4 and Ds-TR appear to be anchored to the nucleolus. Genes that escape X inactivation do not cluster but are located near the periphery of the 3D structure, as are regions enriched in CTCF or RNA polymerase. Fewer short-range intrachromosomal contacts are detected for the inactive alleles of genes subject to X inactivation, compared to the active alleles and to genes that escape X inactivation. This pattern is also evident for imprinted genes, in which more chromatin contacts are detected for the expressed allele. Conclusions By applying a novel Hi-C method to map allelic chromatin contacts, we discover a specific bipartite organization of the mouse inactive X chromosome that probably plays an important role in maintenance of gene silencing.
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| |
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| Overall design |
Examination of Nucleophosmin-binding profiles in male and female mouse livers
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| |
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| Contributor(s) |
Yang F, Deng X, Disteche CM |
| Citation(s) |
25887447, 26248554 |
| Submission date |
Aug 10, 2015 |
| 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) |
| GPL10129 |
NimbleGen Mouse 2.1 M array 10 of 10 |
|
| Samples (2) |
| GSM1847271 |
female liver_Nucleophosmin_genome tiling |
| GSM1847272 |
male liver_Nucleophosmin_genome tiling |
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| This SubSeries is part of SuperSeries: |
| GSE59779 |
Studies of regulation of mouse X inactivation and genes escaping XCI |
|
| Relations |
| BioProject |
PRJNA292428 |
