On the role of transcription in positioning nucleosomes
© 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 g...
| Main Authors: | , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2022
|
| Online Access: | https://hdl.handle.net/1721.1/141344 |
| _version_ | 1826211540761575424 |
|---|---|
| author | Jiang, Zhongling Zhang, Bin |
| author2 | Massachusetts Institute of Technology. Department of Chemistry |
| author_facet | Massachusetts Institute of Technology. Department of Chemistry Jiang, Zhongling Zhang, Bin |
| author_sort | Jiang, Zhongling |
| collection | MIT |
| description | © 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. |
| first_indexed | 2024-09-23T15:07:38Z |
| format | Article |
| id | mit-1721.1/141344 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T15:07:38Z |
| publishDate | 2022 |
| publisher | Public Library of Science (PLoS) |
| record_format | dspace |
| spelling | mit-1721.1/1413442023-06-20T17:02:32Z On the role of transcription in positioning nucleosomes Jiang, Zhongling Zhang, Bin Massachusetts Institute of Technology. Department of Chemistry © 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. 2022-03-23T15:58:44Z 2022-03-23T15:58:44Z 2021 2022-03-23T15:48:23Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/141344 Jiang, Zhongling and Zhang, Bin. 2021. "On the role of transcription in positioning nucleosomes." PLoS Computational Biology, 17 (1). en 10.1371/JOURNAL.PCBI.1008556 PLoS Computational Biology Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/ application/pdf Public Library of Science (PLoS) PLoS |
| spellingShingle | Jiang, Zhongling Zhang, Bin On the role of transcription in positioning nucleosomes |
| title | On the role of transcription in positioning nucleosomes |
| title_full | On the role of transcription in positioning nucleosomes |
| title_fullStr | On the role of transcription in positioning nucleosomes |
| title_full_unstemmed | On the role of transcription in positioning nucleosomes |
| title_short | On the role of transcription in positioning nucleosomes |
| title_sort | on the role of transcription in positioning nucleosomes |
| url | https://hdl.handle.net/1721.1/141344 |
| work_keys_str_mv | AT jiangzhongling ontheroleoftranscriptioninpositioningnucleosomes AT zhangbin ontheroleoftranscriptioninpositioningnucleosomes |