Distribution of Initiation Times Reveals Mechanisms of Transcriptional Regulation in Single Cells

Overview

Journal Biophys J

Publisher Cell Press

Specialty Biophysics

Date 2018 May 10

PMID 29742401

Citations 7

Authors

Sandeep Choubey

Jane Kondev

Alvaro Sanchez

Affiliations

Soon will be listed here.

Abstract

Transcription is the dominant point of control of gene expression. Biochemical studies have revealed key molecular components of transcription and their interactions, but the dynamics of transcription initiation in cells is still poorly understood. This state of affairs is being remedied with experiments that observe transcriptional dynamics in single cells using fluorescent reporters. Quantitative information about transcription initiation dynamics can also be extracted from experiments that use electron micrographs of RNA polymerases caught in the act of transcribing a gene (Miller spreads). Inspired by these data, we analyze a general stochastic model of transcription initiation and elongation and compute the distribution of transcription initiation times. We show that different mechanisms of initiation leave distinct signatures in the distribution of initiation times that can be compared to experiments. We analyze published data from micrographs of RNA polymerases transcribing ribosomal RNA genes in Escherichia coli and compare the observed distributions of interpolymerase distances with the predictions from previously hypothesized mechanisms for the regulation of these genes. Our analysis demonstrates the potential of measuring the distribution of time intervals between initiation events as a probe for dissecting mechanisms of transcription initiation in live cells.

Citing Articles

RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons.

Tenenbaum D, Inlow K, Friedman L, Cai A, Gelles J, Kondev J Proc Natl Acad Sci U S A. 2023; 120(30):e2301402120.

PMID: 37459525 PMC: 10372574. DOI: 10.1073/pnas.2301402120.

RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons.

Tenenbaum D, Inlow K, Friedman L, Cai A, Gelles J, Kondev J bioRxiv. 2023; .

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Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage.

Liu J, Hansen D, Eck E, Kim Y, Turner M, Alamos S PLoS Comput Biol. 2021; 17(5):e1008999.

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Kinetic sculpting of the seven stripes of the Drosophila gene.

Berrocal A, Lammers N, Garcia H, Eisen M Elife. 2020; 9.

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Short Residence Times of DNA-Bound Transcription Factors Can Reduce Gene Expression Noise and Increase the Transmission of Information in a Gene Regulation System.

Azpeitia E, Wagner A Front Mol Biosci. 2020; 7:67.

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