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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...

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Autores principales: Hatakeyama, Akiko, Shymko, Yuliia, Hartmann, Brigitte, Retureau, Romain, Nogues, Claude, Pasi, Marco, Buckle, Malcolm
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
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.
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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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