Genomics

Dataset Information

155

The functional impact of RNA Polymerase II pausing across multiple mamamlian cell types


ABSTRACT: We analyzed the breadth and functional relationships of RNA Polymerase II pausing across many human and mouse cell types to understand what roles RNA Polymerase II pausing plays in gene regulation. We identified a novel association of H2A.Z at the TSS of increasingly paused genes. We knocked down H2A.Z to test whether H2A.Z positively or negatively affects RNA Polymerase II pausing to find that pausing globally increased upon knockdown. Overall design: We tested the effect of H2A.Z knockdown on RNA Polymerase II pausing by setting up a case vs. control experiment in which MCF7 breast cancer cells were treated with a siRNA against H2A.Z. We tested for changes in RNA Polymerase II pausing as a result.

INSTRUMENT(S): Illumina HiSeq 2500 (Homo sapiens)

SUBMITTER: Peter J Park  

PROVIDER: GSE60872 | GEO | 2016-04-28

SECONDARY ACCESSION(S): PRJNA259708

REPOSITORIES: GEO

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Publications

Comprehensive analysis of promoter-proximal RNA polymerase II pausing across mammalian cell types.

Day Daniel S DS   Zhang Bing B   Stevens Sean M SM   Ferrari Francesco F   Larschan Erica N EN   Park Peter J PJ   Pu William T WT  

Genome biology 20160603 1


BACKGROUND:For many genes, RNA polymerase II stably pauses before transitioning to productive elongation. Although polymerase II pausing has been shown to be a mechanism for regulating transcriptional activation, the extent to which it is involved in control of mammalian gene expression and its relationship to chromatin structure remain poorly understood. RESULTS:Here, we analyze 85 RNA polymerase II chromatin immunoprecipitation (ChIP)-sequencing experiments from 35 different murine and human s  ...[more]

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