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
-
CDK9-dependent RNA polymerase II pausing controls transcription initiationPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE96056).
-
Open Chromatin by FAIRE from ENCODE/OpenChrom(UNC Chapel Hill)Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE35239).
-
Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genesPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE56869).
-
DNA Methylation by Reduced Representation Bisulfite Seq from ENCODE/HudsonAlphaPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE27584).
-
Study of Topoisomerase I in humanPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE57628).
-
Open Chromatin by DNaseI HS from ENCODE/OpenChrom(Duke University)Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE32970).
-
Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivoPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE45803).
-
DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of WashingtonPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE29692).
-
ENCODE Transcription Factor Binding Sites by ChIP-seq from Stanford/Yale/USC/HarvardPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE31477).
-
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).
-
Brd4 and JMJD6-associated Anti-pause Enhancers in Regulation of Transcriptional Pause ReleasePublicly available at the NCBI Gene Expression Omnibus (accession no: GSE51633).
-
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.
Reviewing Editor
- Katherine A Jones, Salk Institute for Biological Studies, United States
Version history
- Received: June 19, 2017
- Accepted: October 6, 2017
- Accepted Manuscript published: October 10, 2017 (version 1)
- Version of Record published: November 3, 2017 (version 2)
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.
Metrics
-
- 9,195
- views
-
- 1,607
- downloads
-
- 174
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
CDK9-dependent RNA polymerase II pausing controls transcription initiation
eLife 6:e29736.
https://doi.org/10.7554/eLife.29736
Further reading
-
- Cell Biology
- Computational and Systems Biology
Bats have unique characteristics compared to other mammals, including increased longevity and higher resistance to cancer and infectious disease. While previous studies have analyzed the metabolic requirements for flight, it is still unclear how bat metabolism supports these unique features, and no study has integrated metabolomics, transcriptomics, and proteomics to characterize bat metabolism. In this work, we performed a multi-omics data analysis using a computational model of metabolic fluxes to identify fundamental differences in central metabolism between primary lung fibroblast cell lines from the black flying fox fruit bat (Pteropus alecto) and human. Bat cells showed higher expression levels of Complex I components of electron transport chain (ETC), but, remarkably, a lower rate of oxygen consumption. Computational modeling interpreted these results as indicating that Complex II activity may be low or reversed, similar to an ischemic state. An ischemic-like state of bats was also supported by decreased levels of central metabolites and increased ratios of succinate to fumarate in bat cells. Ischemic states tend to produce reactive oxygen species (ROS), which would be incompatible with the longevity of bats. However, bat cells had higher antioxidant reservoirs (higher total glutathione and higher ratio of NADPH to NADP) despite higher mitochondrial ROS levels. In addition, bat cells were more resistant to glucose deprivation and had increased resistance to ferroptosis, one of the characteristics of which is oxidative stress. Thus, our studies revealed distinct differences in the ETC regulation and metabolic stress responses between human and bat cells.
-
- Computational and Systems Biology
- Neuroscience
Normal aging leads to myelin alterations in the rhesus monkey dorsolateral prefrontal cortex (dlPFC), which are positively correlated with degree of cognitive impairment. It is hypothesized that remyelination with shorter and thinner myelin sheaths partially compensates for myelin degradation, but computational modeling has not yet explored these two phenomena together systematically. Here, we used a two-pronged modeling approach to determine how age-related myelin changes affect a core cognitive function: spatial working memory. First, we built a multicompartment pyramidal neuron model fit to monkey dlPFC empirical data, with an axon including myelinated segments having paranodes, juxtaparanodes, internodes, and tight junctions. This model was used to quantify conduction velocity (CV) changes and action potential (AP) failures after demyelination and subsequent remyelination. Next, we incorporated the single neuron results into a spiking neural network model of working memory. While complete remyelination nearly recovered axonal transmission and network function to unperturbed levels, our models predict that biologically plausible levels of myelin dystrophy, if uncompensated by other factors, can account for substantial working memory impairment with aging. The present computational study unites empirical data from ultrastructure up to behavior during normal aging, and has broader implications for many demyelinating conditions, such as multiple sclerosis or schizophrenia.
