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Series GSE149999 Query DataSets for GSE149999
Status Public on Dec 25, 2020
Title The Paf1 complex positively regulates enhancer activity in mouse embryonic stem cells
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary The RNA polymerase II (RNAPII) associated factor 1 complex (Paf1C) plays critical roles in modulating the release of paused RNAPII into productive elongation. However, regulation of Paf1C-mediated promoter-proximal pausing is complex and context dependent. In fact, in cancer cell lines opposing models of Paf1Cs’ role in RNAPII pause-release control have been proposed. Here we show that the Paf1C positively regulates RNAPII pause-release at both protein-coding genes and at enhancers in mouse embryonic stem cells (mESC). Our analyses reveal extensive Paf1C binding at mESC enhancers, in particular at super enhancers. Importantly, Paf1C occupancy correlates with the strength of enhancer activity. Depletion of Paf1C attenuates the expression of genes regulated by targeted enhancers and affects RNAPII Ser2 phosphorylation at the binding sites, suggesting that mESC self-renewal depends on Paf1C-mediated positive regulation of pluripotency enhancers.
Overall design RNA-Seq transcriptome profiling of murine ES-E14 and NIH-3T3 cells, as well as ChIP-Seq based examination of Ctr9 binding sites and H3K27ac histone modifications in both cell lines.
Contributor(s) Li D, Paszkowski-Rogacz M
Citation(s) 33376128
Submission date May 06, 2020
Last update date Jan 19, 2021
Contact name Maciej Paszkowski-Rogacz
Organization name Technische Universität Dresden
Department UCC / Medical Faculty and University Hospital Carl Gustav Carus
Lab Medical Systems Biology (Prof. Buchholz)
Street address Tatzberg 47/49
City Dresden
ZIP/Postal code 01307
Country Germany
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (12)
GSM4519334 ESC Ctr9-EGFP ChIP-Seq
GSM4519335 ESC H3K27ac ChIP-Seq
GSM4519336 ESC Input ChIP-Seq (A)
BioProject PRJNA630757
SRA SRP260313

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Supplementary file Size Download File type/resource
GSE149999_RAW.tar 11.2 Mb (http)(custom) TAR (of NARROWPEAK, TSV)
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Raw data are available in SRA
Processed data provided as supplementary file

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