Genetic dissection of the RNA polymerase II transcription cycle
- Cornell University, United States
Abstract
How DNA sequence affects the dynamics and position of RNA Polymerase II (Pol II) during transcription remains poorly understood. Here we used naturally occurring genetic variation in F1 hybrid mice to explore how DNA sequence differences affect the genome-wide distribution of Pol II. We measured the position and orientation of Pol II in eight organs collected from heterozygous F1 hybrid mice using ChRO-seq. Our data revealed a strong genetic basis for the precise coordinates of transcription initiation and promoter proximal pause, allowing us to redefine molecular models of core transcriptional processes. Our results implicate DNA sequence, including both known and novel DNA sequence motifs, as key determinants of the position of Pol II initiation and pause. We report evidence that initiation site selection follows a stochastic process similar to Brownian motion along the DNA template. We found widespread differences in the position of transcription termination, which impact the primary structure and stability of mature mRNA. Finally, we report evidence that allelic changes in transcription often affect mRNA and ncRNA expression across broad genomic domains. Collectively, we reveal how DNA sequences shape core transcriptional processes at single nucleotide resolution in mammals.
Data availability
All data are available at Gene Expression Omnibus under the accession number GSE174171. All scripts are posted publicly with no restrictions on the Danko Lab GitHub organization, at: https://github.com/Danko-Lab/F1_8Organs.
Article and author information
Author details
Funding
National Human Genome Research Institute (R01-HG010346)
- Charles G Danko
National Human Genome Research Institute (R01-HG009309)
- Charles G Danko
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Animal experimentation: All mouse studies were conducted with prior approval by the Cornell Institutional Animal Care and Use Committee, under protocol 2004-0063.
Copyright
© 2022, Chou 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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Genetic dissection of the RNA polymerase II transcription cycle
eLife 11:e78458.
https://doi.org/10.7554/eLife.78458
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