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| Status |
Public on Feb 15, 2013 |
| Title |
Allele-specific maps of RNA polymerase II phosphorylated at serine 5 in mouse cultured hybrid cells and mouse hybrid brain |
| Organism |
Mus musculus x Mus spretus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
We report the application of single-molecule-based sequencing technology for high-throughput profiling of RNA polymerase II phosphorylated at serine 5 (PolII-S5p; the transcription initiation form) in female mouse cultured hybrid cells and female hybrid brain derived from mouse systems with skewed X inactivation based on crosses between C57BL/6J (BL6) and M. spretus. In these systems, alleles can be differentiated by frequent SNPs between mouse species, and the active X (Xa) compared to the haploid set of autosomes from the same species. To examine PolII-S5p occupancy in vivo, ChIP-seq was done in brain from an adult female F1 mouse in which the BL6 X is always active and the spretus X inactive. Uniquely mapped reads containing informative SNPs were assigned to each haploid chromosome set (BL6 or spretus) and were counted to establish allele-specific PolII-S5p occupancy profiles. We found that PolII-S5p allele-specific occupancy with or without normalization by input genomic DNA sequencing data showed that expressed genes on the Xa (>1RPKM) had 30% higher PolII-S5p peak levels at their promoters compared to autosomal genes from the same species (BL6). This result was confirmed by performing an independent allele-specific ChIP-seq analysis on fibroblasts derived from embryonic kidney (Patski cell line) that have the opposite X inactivation pattern from the brain sample, i.e. an Xa from M. spretus and an Xi from BL6. These findings suggest that transcription initiation of X-linked genes is enhanced to contribute to X upregulation in cell lines and in vivo.
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| Overall design |
Examination of allele-specific PolII-S5p occupancy in mouse hybrid cells and brain.
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| Contributor(s) |
Deng X, Berletch JB, Ma W, Noble WS, Shendure J, Disteche CM |
| Citation(s) |
23523075, 26248554 |
| |
| Submission date |
Feb 11, 2013 |
| 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
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| Lab |
HSB C526
|
| Street address |
1959 NE Pacific St.
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
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| Platforms (2) |
| GPL16616 |
Illumina HiSeq 2000 (Mus musculus x Mus spretus) |
| GPL16617 |
Illumina Genome Analyzer IIx (Mus musculus x Mus spretus) |
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| Samples (3) |
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| This SubSeries is part of SuperSeries: |
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| Relations |
| BioProject |
PRJNA189398 |
| SRA |
SRP018597 |
