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...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2022-01-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9278766/?tool=EBI |
| _version_ | 1818510773639446528 |
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| author | Akiko Hatakeyama Yuliia Shymko Brigitte Hartmann Romain Retureau Claude Nogues Marco Pasi Malcolm Buckle |
| author_facet | Akiko Hatakeyama Yuliia Shymko Brigitte Hartmann Romain Retureau Claude Nogues Marco Pasi Malcolm Buckle |
| author_sort | Akiko Hatakeyama |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-10T23:24:39Z |
| format | Article |
| id | doaj.art-f474f57d423b4e3e9513234ef02ca938 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-10T23:24:39Z |
| publishDate | 2022-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-f474f57d423b4e3e9513234ef02ca9382022-12-22T01:29:37ZengPublic Library of Science (PLoS)PLoS ONE1932-62032022-01-01177Nucleosome assembly and disassembly pathways in vitroAkiko HatakeyamaYuliia ShymkoBrigitte HartmannRomain RetureauClaude NoguesMarco PasiMalcolm BuckleStructural 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.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9278766/?tool=EBI |
| spellingShingle | Akiko Hatakeyama Yuliia Shymko Brigitte Hartmann Romain Retureau Claude Nogues Marco Pasi Malcolm Buckle Nucleosome assembly and disassembly pathways in vitro PLoS ONE |
| 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 |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9278766/?tool=EBI |
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