CDK9-dependent RNA polymerase II pausing controls transcription initiation
- Max Planck Institute for Biophysical Chemistry, Germany
- Helmholtz Center Munich, Germany
- Ludwig-Maximilians-Universität München, Germany
Abstract
Gene transcription can be activated by decreasing the duration of RNA polymerase II pausing in the promoter-proximal region, but how this is achieved remains unclear. Here we use a 'multi-omics' approach to demonstrate that the duration of polymerase pausing generally limits the productive frequency of transcription initiation in human cells ('pause-initiation limit'). We further engineer a human cell line to allow for specific and rapid inhibition of the P-TEFb kinase CDK9, which is implicated in polymerase pause release. CDK9 activity decreases the pause duration but also increases the productive initiation frequency. This shows that CDK9 stimulates release of paused polymerase and activates transcription by increasing the number of transcribing polymerases and thus the amount of mRNA synthesized per time. CDK9 activity is also associated with long-range chromatin interactions, suggesting that enhancers can influence the pause-initiation limit to regulate transcription.
Data availability
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CDK9-dependent RNA polymerase II pausing controls transcription initiationPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE96056).
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Open Chromatin by FAIRE from ENCODE/OpenChrom(UNC Chapel Hill)Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE35239).
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Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genesPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE56869).
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DNA Methylation by Reduced Representation Bisulfite Seq from ENCODE/HudsonAlphaPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE27584).
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Study of Topoisomerase I in humanPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE57628).
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Open Chromatin by DNaseI HS from ENCODE/OpenChrom(Duke University)Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE32970).
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Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivoPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE45803).
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DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of WashingtonPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE29692).
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ENCODE Transcription Factor Binding Sites by ChIP-seq from Stanford/Yale/USC/HarvardPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE31477).
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Tyrosine phosphorylation of RNA Polymerase II CTD is associated with antisense promoter transcription and active enhancers in mammalian cellsPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE52914).
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Brd4 and JMJD6-associated Anti-pause Enhancers in Regulation of Transcriptional Pause ReleasePublicly available at the NCBI Gene Expression Omnibus (accession no: GSE51633).
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PAF1, a molecular regulator of promoter-proximal pausing by RNA Polymerase IIPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE70408).
Article and author information
Author details
Funding
European Research Council (TRANSREGULON)
- Patrick Cramer
Volkswagen Foundation
- Patrick Cramer
Deutsche Forschungsgemeinschaft (SFB 1064 TP A17)
- Heinrich Leonhardt
Deutsche Forschungsgemeinschaft (SFB 1064)
- Dirk Eick
Max Planck Institute for Biophysical Chemistry (Open-access funding)
- Patrick Cramer
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2017, Gressel et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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CDK9-dependent RNA polymerase II pausing controls transcription initiation
eLife 6:e29736.
https://doi.org/10.7554/eLife.29736
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Enhancers and promoters are classically considered to be bound by a small set of transcription factors (TFs) in a sequence-specific manner. This assumption has come under increasing skepticism as the datasets of ChIP-seq assays of TFs have expanded. In particular, high-occupancy target (HOT) loci attract hundreds of TFs with often no detectable correlation between ChIP-seq peaks and DNA-binding motif presence. Here, we used a set of 1003 TF ChIP-seq datasets (HepG2, K562, H1) to analyze the patterns of ChIP-seq peak co-occurrence in combination with functional genomics datasets. We identified 43,891 HOT loci forming at the promoter (53%) and enhancer (47%) regions. HOT promoters regulate housekeeping genes, whereas HOT enhancers are involved in tissue-specific process regulation. HOT loci form the foundation of human super-enhancers and evolve under strong negative selection, with some of these loci being located in ultraconserved regions. Sequence-based classification analysis of HOT loci suggested that their formation is driven by the sequence features, and the density of mapped ChIP-seq peaks across TF-bound loci correlates with sequence features and the expression level of flanking genes. Based on the affinities to bind to promoters and enhancers we detected five distinct clusters of TFs that form the core of the HOT loci. We report an abundance of HOT loci in the human genome and a commitment of 51% of all TF ChIP-seq binding events to HOT locus formation thus challenging the classical model of enhancer activity and propose a model of HOT locus formation based on the existence of large transcriptional condensates.
