Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation.

The eukaryotic genome is packaged as chromatin with nucleosomes comprising its basic structural unit, but the detailed structure of chromatin and its dynamic remodeling in terms of individual nucleosome positions has not been completely defined experimentally for any genome. We used ultra-high-throu...

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Autores principales:	Sushma Shivaswamy, Akshay Bhinge, Yongjun Zhao, Steven Jones, Martin Hirst, Vishwanath R Iyer
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2008
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/5cd3341bbfb84f5c85d446cac481a650
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spelling	oai:doaj.org-article:5cd3341bbfb84f5c85d446cac481a6502021-11-25T05:33:26ZDynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation.1544-91731545-788510.1371/journal.pbio.0060065https://doaj.org/article/5cd3341bbfb84f5c85d446cac481a6502008-03-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18351804/pdf/?tool=EBIhttps://doaj.org/toc/1544-9173https://doaj.org/toc/1545-7885The eukaryotic genome is packaged as chromatin with nucleosomes comprising its basic structural unit, but the detailed structure of chromatin and its dynamic remodeling in terms of individual nucleosome positions has not been completely defined experimentally for any genome. We used ultra-high-throughput sequencing to map the remodeling of individual nucleosomes throughout the yeast genome before and after a physiological perturbation that causes genome-wide transcriptional changes. Nearly 80% of the genome is covered by positioned nucleosomes occurring in a limited number of stereotypical patterns in relation to transcribed regions and transcription factor binding sites. Chromatin remodeling in response to physiological perturbation was typically associated with the eviction, appearance, or repositioning of one or two nucleosomes in the promoter, rather than broader region-wide changes. Dynamic nucleosome remodeling tends to increase the accessibility of binding sites for transcription factors that mediate transcriptional changes. However, specific nucleosomal rearrangements were also evident at promoters even when there was no apparent transcriptional change, indicating that there is no simple, globally applicable relationship between chromatin remodeling and transcriptional activity. Our study provides a detailed, high-resolution, dynamic map of single-nucleosome remodeling across the yeast genome and its relation to global transcriptional changes.Sushma ShivaswamyAkshay BhingeYongjun ZhaoSteven JonesMartin HirstVishwanath R IyerPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Biology, Vol 6, Iss 3, p e65 (2008)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Sushma Shivaswamy Akshay Bhinge Yongjun Zhao Steven Jones Martin Hirst Vishwanath R Iyer Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation.
description	The eukaryotic genome is packaged as chromatin with nucleosomes comprising its basic structural unit, but the detailed structure of chromatin and its dynamic remodeling in terms of individual nucleosome positions has not been completely defined experimentally for any genome. We used ultra-high-throughput sequencing to map the remodeling of individual nucleosomes throughout the yeast genome before and after a physiological perturbation that causes genome-wide transcriptional changes. Nearly 80% of the genome is covered by positioned nucleosomes occurring in a limited number of stereotypical patterns in relation to transcribed regions and transcription factor binding sites. Chromatin remodeling in response to physiological perturbation was typically associated with the eviction, appearance, or repositioning of one or two nucleosomes in the promoter, rather than broader region-wide changes. Dynamic nucleosome remodeling tends to increase the accessibility of binding sites for transcription factors that mediate transcriptional changes. However, specific nucleosomal rearrangements were also evident at promoters even when there was no apparent transcriptional change, indicating that there is no simple, globally applicable relationship between chromatin remodeling and transcriptional activity. Our study provides a detailed, high-resolution, dynamic map of single-nucleosome remodeling across the yeast genome and its relation to global transcriptional changes.
format	article
author	Sushma Shivaswamy Akshay Bhinge Yongjun Zhao Steven Jones Martin Hirst Vishwanath R Iyer
author_facet	Sushma Shivaswamy Akshay Bhinge Yongjun Zhao Steven Jones Martin Hirst Vishwanath R Iyer
author_sort	Sushma Shivaswamy
title	Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation.
title_short	Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation.
title_full	Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation.
title_fullStr	Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation.
title_full_unstemmed	Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation.
title_sort	dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation.
publisher	Public Library of Science (PLoS)
publishDate	2008
url	https://doaj.org/article/5cd3341bbfb84f5c85d446cac481a650
work_keys_str_mv	AT sushmashivaswamy dynamicremodelingofindividualnucleosomesacrossaeukaryoticgenomeinresponsetotranscriptionalperturbation AT akshaybhinge dynamicremodelingofindividualnucleosomesacrossaeukaryoticgenomeinresponsetotranscriptionalperturbation AT yongjunzhao dynamicremodelingofindividualnucleosomesacrossaeukaryoticgenomeinresponsetotranscriptionalperturbation AT stevenjones dynamicremodelingofindividualnucleosomesacrossaeukaryoticgenomeinresponsetotranscriptionalperturbation AT martinhirst dynamicremodelingofindividualnucleosomesacrossaeukaryoticgenomeinresponsetotranscriptionalperturbation AT vishwanathriyer dynamicremodelingofindividualnucleosomesacrossaeukaryoticgenomeinresponsetotranscriptionalperturbation
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Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation.

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