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Nucleosome assembly and disassembly pathways in vitro
Structural fluctuations of nucleosomes modulate the access to internal DNA in eukaryotic cells; clearly characterisation of this fundamental process is crucial to understanding gene regulation. Here we apply PhAST (Photochemical Analysis of Structural Transitions) to monitor at a base pair level, st...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9278766/ https://www.ncbi.nlm.nih.gov/pubmed/35830437 http://dx.doi.org/10.1371/journal.pone.0267382 |
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author | Hatakeyama, Akiko Shymko, Yuliia Hartmann, Brigitte Retureau, Romain Nogues, Claude Pasi, Marco Buckle, Malcolm |
author_facet | Hatakeyama, Akiko Shymko, Yuliia Hartmann, Brigitte Retureau, Romain Nogues, Claude Pasi, Marco Buckle, Malcolm |
author_sort | Hatakeyama, Akiko |
collection | PubMed |
description | Structural fluctuations of nucleosomes modulate the access to internal DNA in eukaryotic cells; clearly characterisation of this fundamental process is crucial to understanding gene regulation. Here we apply PhAST (Photochemical Analysis of Structural Transitions) to monitor at a base pair level, structural alterations induced all along the DNA upon histone binding or release. By offering the first reliable, detailed comparison of nucleosome assembly and disassembly in vitro, we reveal similarities and differences between the two processes. We identify multiple, sequential intermediate states characterised by specific PhAST signals whose localisation and amplitude reflect asymmetries of DNA/histone interactions with respect to the nucleosome pseudo dyad. These asymmetries involve not only the DNA extremities but also regions close to the pseudo dyad. Localisations of asymmetries develop in a consistent manner during both assembly and disassembly processes; they primarily reflect the DNA sequence effect on the efficiency of DNA-histone binding. More unexpectedly, the amplitude component of PhAST signals not only evolves as a function of intermediate states but does so differently between assembly and disassembly pathways. Our observation of differences between assembly and disassembly opens up new avenues to define the role of the DNA sequence in processes underlying the regulation of gene expression. Overall, we provide new insights into how the intrinsic properties of DNA are integrated into a holistic mechanism that controls chromatin structure. |
format | Online Article Text |
id | pubmed-9278766 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-92787662022-07-14 Nucleosome assembly and disassembly pathways in vitro Hatakeyama, Akiko Shymko, Yuliia Hartmann, Brigitte Retureau, Romain Nogues, Claude Pasi, Marco Buckle, Malcolm PLoS One Research Article Structural fluctuations of nucleosomes modulate the access to internal DNA in eukaryotic cells; clearly characterisation of this fundamental process is crucial to understanding gene regulation. Here we apply PhAST (Photochemical Analysis of Structural Transitions) to monitor at a base pair level, structural alterations induced all along the DNA upon histone binding or release. By offering the first reliable, detailed comparison of nucleosome assembly and disassembly in vitro, we reveal similarities and differences between the two processes. We identify multiple, sequential intermediate states characterised by specific PhAST signals whose localisation and amplitude reflect asymmetries of DNA/histone interactions with respect to the nucleosome pseudo dyad. These asymmetries involve not only the DNA extremities but also regions close to the pseudo dyad. Localisations of asymmetries develop in a consistent manner during both assembly and disassembly processes; they primarily reflect the DNA sequence effect on the efficiency of DNA-histone binding. More unexpectedly, the amplitude component of PhAST signals not only evolves as a function of intermediate states but does so differently between assembly and disassembly pathways. Our observation of differences between assembly and disassembly opens up new avenues to define the role of the DNA sequence in processes underlying the regulation of gene expression. Overall, we provide new insights into how the intrinsic properties of DNA are integrated into a holistic mechanism that controls chromatin structure. Public Library of Science 2022-07-13 /pmc/articles/PMC9278766/ /pubmed/35830437 http://dx.doi.org/10.1371/journal.pone.0267382 Text en © 2022 Hatakeyama et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Hatakeyama, Akiko Shymko, Yuliia Hartmann, Brigitte Retureau, Romain Nogues, Claude Pasi, Marco Buckle, Malcolm Nucleosome assembly and disassembly pathways in vitro |
title | Nucleosome assembly and disassembly pathways in vitro |
title_full | Nucleosome assembly and disassembly pathways in vitro |
title_fullStr | Nucleosome assembly and disassembly pathways in vitro |
title_full_unstemmed | Nucleosome assembly and disassembly pathways in vitro |
title_short | Nucleosome assembly and disassembly pathways in vitro |
title_sort | nucleosome assembly and disassembly pathways in vitro |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9278766/ https://www.ncbi.nlm.nih.gov/pubmed/35830437 http://dx.doi.org/10.1371/journal.pone.0267382 |
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