ArticleNucleic acids research2017
Crowding-induced transcriptional bursts dictate polymerase and nucleosome density profiles along genes.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed, 14 citations in OpenAlex.
- Collective polymerase dynamics emerge from DNA supercoiling during transcription.Biophysical journal · 2022Article
- Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts.PLoS computational biology · 2022Article
- Altering transcription factor binding reveals comprehensive transcriptional kinetics of a basic gene.Nucleic acids research · 2021Article
- EGGTART: A tool to visualize the dynamics of biophysical transport under the inhomogeneous l-TASEP.Biophysical journal · 2021Article
- Probing Mechanisms of Transcription Elongation Through Cell-to-Cell Variability of RNA Polymerase.Biophysical journal · 2020Article
- Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation.PLoS genetics · 2020Article
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2 authors at 1 institution in 1 country.
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Abstract
During eukaryotic transcription, RNA polymerase (RNAP) translocates along DNA molecules covered with nucleosomes and other DNA binding proteins. Though the interactions between a single nucleosome and RNAP are by now fairly well understood, this understanding has not been synthesized into a description of transcription on crowded genes, where multiple RNAP transcribe through nucleosomes while preserving the nucleosome coverage. We here take a deductive modeling approach to establish the consequences of RNAP-nucleosome interactions for transcription in crowded environments. We show that under physiologically crowded conditions, the interactions of RNAP with nucleosomes induce a strong kinetic attraction between RNAP molecules, causing them to self-organize into stable and moving pelotons. The peloton formation quantitatively explains the observed nucleosome and RNAP depletion close to the initiation site on heavily transcribed genes. Pelotons further translate into short-timescale transcriptional bursts at termination, resulting in burst characteristics consistent with instances of bursty transcription observed in vivo. To facilitate experimental testing of our proposed mechanism, we present several analytic relations that make testable quantitative predictions.
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