Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells

Siepel, Adam, Zhao, Yixin, Liu, Lingjie (2022) Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells. Research Square. (Submitted)

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Abstract

In metazoans, both transcription initiation and the escape of RNA polymerase (RNAP) from promoter-proximal pausing are key rate-limiting steps in gene expression. These processes play out at physically proximal sites on the DNA template and appear to influence one another through steric interactions, leading to a complex dynamic equilibrium in RNAP occupancy of the ∼100 bp immediately downstream of the transcription start site. In this article, we examine the dynamics of these processes using a combination of statistical modeling, simulation, and analysis of real nascent RNA sequencing data. We develop a simple probabilistic model that jointly describes the kinetics of transcription initiation, pause-escape, and elongation, and the generation of nascent RNA sequencing read counts under steady-state conditions. We then extend this initial model to allow for variability across cells in promoter-proximal pause site locations and steric hindrance of transcription initiation from paused RNAPs. In an extensive series of simulations over a broad range of parameters, we show that this model enables accurate estimation of initiation and pause-escape rates even in the presence of collisions between RNAPs and variable elongation rates. Furthermore, we show by simulation and analysis of data for human cell lines that pause-escape is often more strongly rate-limiting than conventional “pausing indices” would suggest, that occupancy of the pause site is elevated at many genes, and that steric hindrance of initiation can lead to a pronounced reduction in apparent initiation rates. Our modeling framework is generally applicable for all types of nascent RNA sequencing data and can be applied to a variety of inference problems. Our software for estimation and simulation is publicly available.

Item Type: Paper
Subjects: bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transcription
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
CSHL Authors:
Communities: CSHL labs > Siepel lab
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: 2022
Date Deposited: 20 Nov 2023 14:17
Last Modified: 17 Jan 2024 15:14
Related URLs:
URI: https://repository.cshl.edu/id/eprint/41315

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