On the role of transcription in positioning nucleosomes
Name
journal.pcbi.1008556 (1).pdf
Description
Published version
Size
2 MB
Format
Adobe PDF
Checksum (MD5)
6ace2e6dcfe2235680843b944826da88
Author(s)
Jiang, Zhongling
Zhang, Bin
Date Issued
2021
Journal
PLoS Computational Biology
Publisher
Public Library of Science (PLoS)
Citation
Jiang, Zhongling and Zhang, Bin. 2021. "On the role of transcription in positioning nucleosomes." PLoS Computational Biology, 17 (1).
Version
Final published version
Abstract
© 2021 Jiang, Zhang. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Nucleosome positioning is crucial for the genome's function. Though the role of DNA sequence in positioning nucleosomes is well understood, a detailed mechanistic understanding on the impact of transcription remains lacking. Using numerical simulations, we investigated the dependence of nucleosome density profiles on transcription level across multiple species. We found that the low nucleosome affinity of yeast, but not mouse, promoters contributes to the formation of phased nucleosomes arrays for inactive genes. For the active genes, a heterogeneous distribution of +1 nucleosomes, caused by a tug-ofwar between two types of remodeling enzymes, is essential for reproducing their density profiles. In particular, while positioning enzymes are known to remodel the +1 nucleosome and align it toward the transcription start site (TSS), spacer enzymes that use a pair of nucleosomes as their substrate can shift the nucleosome array away from the TSS. Competition between these enzymes results in two types of nucleosome density profiles with well- and ill-positioned +1 nucleosome. Finally, we showed that Pol II assisted histone exchange, if occurring at a fast speed, can abolish the impact of remodeling enzymes. By elucidating the role of individual factors, our study reconciles the seemingly conflicting results on the overall impact of transcription in positioning nucleosomes across species.
MIT Department
Massachusetts Institute of Technology. Department of Chemistry
Terms of Use
Creative Commons Attribution 4.0 International license
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1371/JOURNAL.PCBI.1008556
