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Crosstalk between chromatin structure, cohesin activity and transcription

BACKGROUND: A complex interplay between chromatin and topological machineries is critical for genome architecture and function. However, little is known about these reciprocal interactions, even for cohesin, despite its multiple roles in DNA metabolism. RESULTS: We have used genome-wide analyses to...

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Autores principales: Maya-Miles, Douglas, Andújar, Eloísa, Pérez-Alegre, Mónica, Murillo-Pineda, Marina, Barrientos-Moreno, Marta, Cabello-Lobato, María J., Gómez-Marín, Elena, Morillo-Huesca, Macarena, Prado, Félix
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6647288/
https://www.ncbi.nlm.nih.gov/pubmed/31331360
http://dx.doi.org/10.1186/s13072-019-0293-6
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author Maya-Miles, Douglas
Andújar, Eloísa
Pérez-Alegre, Mónica
Murillo-Pineda, Marina
Barrientos-Moreno, Marta
Cabello-Lobato, María J.
Gómez-Marín, Elena
Morillo-Huesca, Macarena
Prado, Félix
author_facet Maya-Miles, Douglas
Andújar, Eloísa
Pérez-Alegre, Mónica
Murillo-Pineda, Marina
Barrientos-Moreno, Marta
Cabello-Lobato, María J.
Gómez-Marín, Elena
Morillo-Huesca, Macarena
Prado, Félix
author_sort Maya-Miles, Douglas
collection PubMed
description BACKGROUND: A complex interplay between chromatin and topological machineries is critical for genome architecture and function. However, little is known about these reciprocal interactions, even for cohesin, despite its multiple roles in DNA metabolism. RESULTS: We have used genome-wide analyses to address how cohesins and chromatin structure impact each other in yeast. Cohesin inactivation in scc1-73 mutants during the S and G2 phases causes specific changes in chromatin structure that preferentially take place at promoters; these changes include a significant increase in the occupancy of the − 1 and + 1 nucleosomes. In addition, cohesins play a major role in transcription regulation that is associated with specific promoter chromatin architecture. In scc1-73 cells, downregulated genes are enriched in promoters with short or no nucleosome-free region (NFR) and a fragile “nucleosome − 1/RSC complex” particle. These results, together with a preferential increase in the occupancy of nucleosome − 1 of these genes, suggest that cohesins promote transcription activation by helping RSC to form the NFR. In sharp contrast, the scc1-73 upregulated genes are enriched in promoters with an “open” chromatin structure and are mostly at cohesin-enriched regions, suggesting that a local accumulation of cohesins might help to inhibit transcription. On the other hand, a dramatic loss of chromatin integrity by histone depletion during DNA replication has a moderate effect on the accumulation and distribution of cohesin peaks along the genome. CONCLUSIONS: Our analyses of the interplay between chromatin integrity and cohesin activity suggest that cohesins play a major role in transcription regulation, which is associated with specific chromatin architecture and cohesin-mediated nucleosome alterations of the regulated promoters. In contrast, chromatin integrity plays only a minor role in the binding and distribution of cohesins. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13072-019-0293-6) contains supplementary material, which is available to authorized users.
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spelling pubmed-66472882019-07-31 Crosstalk between chromatin structure, cohesin activity and transcription Maya-Miles, Douglas Andújar, Eloísa Pérez-Alegre, Mónica Murillo-Pineda, Marina Barrientos-Moreno, Marta Cabello-Lobato, María J. Gómez-Marín, Elena Morillo-Huesca, Macarena Prado, Félix Epigenetics Chromatin Research BACKGROUND: A complex interplay between chromatin and topological machineries is critical for genome architecture and function. However, little is known about these reciprocal interactions, even for cohesin, despite its multiple roles in DNA metabolism. RESULTS: We have used genome-wide analyses to address how cohesins and chromatin structure impact each other in yeast. Cohesin inactivation in scc1-73 mutants during the S and G2 phases causes specific changes in chromatin structure that preferentially take place at promoters; these changes include a significant increase in the occupancy of the − 1 and + 1 nucleosomes. In addition, cohesins play a major role in transcription regulation that is associated with specific promoter chromatin architecture. In scc1-73 cells, downregulated genes are enriched in promoters with short or no nucleosome-free region (NFR) and a fragile “nucleosome − 1/RSC complex” particle. These results, together with a preferential increase in the occupancy of nucleosome − 1 of these genes, suggest that cohesins promote transcription activation by helping RSC to form the NFR. In sharp contrast, the scc1-73 upregulated genes are enriched in promoters with an “open” chromatin structure and are mostly at cohesin-enriched regions, suggesting that a local accumulation of cohesins might help to inhibit transcription. On the other hand, a dramatic loss of chromatin integrity by histone depletion during DNA replication has a moderate effect on the accumulation and distribution of cohesin peaks along the genome. CONCLUSIONS: Our analyses of the interplay between chromatin integrity and cohesin activity suggest that cohesins play a major role in transcription regulation, which is associated with specific chromatin architecture and cohesin-mediated nucleosome alterations of the regulated promoters. In contrast, chromatin integrity plays only a minor role in the binding and distribution of cohesins. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13072-019-0293-6) contains supplementary material, which is available to authorized users. BioMed Central 2019-07-22 /pmc/articles/PMC6647288/ /pubmed/31331360 http://dx.doi.org/10.1186/s13072-019-0293-6 Text en © The Author(s) 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Maya-Miles, Douglas
Andújar, Eloísa
Pérez-Alegre, Mónica
Murillo-Pineda, Marina
Barrientos-Moreno, Marta
Cabello-Lobato, María J.
Gómez-Marín, Elena
Morillo-Huesca, Macarena
Prado, Félix
Crosstalk between chromatin structure, cohesin activity and transcription
title Crosstalk between chromatin structure, cohesin activity and transcription
title_full Crosstalk between chromatin structure, cohesin activity and transcription
title_fullStr Crosstalk between chromatin structure, cohesin activity and transcription
title_full_unstemmed Crosstalk between chromatin structure, cohesin activity and transcription
title_short Crosstalk between chromatin structure, cohesin activity and transcription
title_sort crosstalk between chromatin structure, cohesin activity and transcription
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6647288/
https://www.ncbi.nlm.nih.gov/pubmed/31331360
http://dx.doi.org/10.1186/s13072-019-0293-6
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