PAF1, a molecular regulator of promoter-proximal pausing by RNA Polymerase II

  • Fei Xavier Chen (Contributor)
  • Ashley R. Woodfin (Contributor)
  • Ali Shilatifard (Contributor)



Accession Number: GSE70408

GPL11154: Illumina HiSeq 2000 (Homo sapiens)
GPL18573: Illumina NextSeq 500 (Homo sapiens)
GPL19132: Illumina NextSeq 500 (Drosophila melanogaster)

Organism: Homo sapiens

Published on 2015-08-13

The control of promoter-proximal pausing and the release of RNA polymerase II (RNA Pol II) is a widely used mechanism for regulating gene expression in metazoans, especially for genes that respond to environmental and developmental cues. Here, we identify Pol II associated Factor 1 (PAF1) as a major regulator of promoter-proximal pausing. Knockdown of PAF1 leads to increased release of paused Pol II into gene bodies at thousands of genes. Genes with the highest levels of paused Pol II exhibit the largest redistribution of Pol II from the promoter-proximal region into the gene body in the absence of PAF1. PAF1 depletion results in increased nascent transcription and increased levels of phosphorylation of Pol II’s c-terminal domain on serine 2 (Ser2P). These changes can be explained by the recruitment of the Ser2P kinase Super Elongation Complex (SEC) effecting increased release of paused Pol II into productive elongation, thus establishing a novel function for PAF1 as a major regulator of pausing in metazoans.

Overall Design:
ChIP-seq of Pol II of different forms, SEC subunits, PAFc subunits and H2Bub in human cell lines targeted by PAF1 or scramble shRNA. ChIP-seq of total Pol II in HCT116 cells targeted by BRE1A or scramble shRNA. ChIP-seq of total Pol II in S2 cells targeted by Paf1 or LacZ RNAi. Total RNA-seq, nascent RNA-seq and GRO-seq in HCT116 cells targeted by PAF1 or scramble shRNA.

Name: Ali Shilatifard
Organization: Northwestern University Feinberg School of Medicine
Laboratory: Shilatifard Lab
Deparment: Department of Biochemistry and Molecular Genetics
Address: 320 E Superior St Chicago IL 60611 USA

Organization: GEO
Address: USA
Date made available2015
PublisherGene Expression Omnibus

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