Genomics

Dataset Information

0

Allele-specific maps of RNA polymerase II phosphorylated at serine 5 in mouse cultured hybrid cells and mouse hybrid brain


ABSTRACT: 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.

ORGANISM(S): Mus musculus x Mus spretus

PROVIDER: GSE44255 | GEO | 2013/02/15

SECONDARY ACCESSION(S): PRJNA189398

REPOSITORIES: GEO

Dataset's files

Source:
Action DRS
Other
Items per page:
1 - 1 of 1

Similar Datasets

2013-02-15 | E-GEOD-44255 | biostudies-arrayexpress
2015-08-18 | PXD002337 | Pride
2012-01-06 | E-GEOD-33823 | biostudies-arrayexpress
2013-03-05 | GSE44835 | GEO
2011-07-18 | E-GEOD-30689 | biostudies-arrayexpress
2011-07-19 | GSE30689 | GEO
2013-03-05 | E-GEOD-44835 | biostudies-arrayexpress
2012-01-06 | GSE33823 | GEO
| PRJNA104257 | ENA
2022-01-01 | GSE157481 | GEO