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...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2008-03-01
|
| Series: | PLoS Biology |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18351804/pdf/?tool=EBI |
| _version_ | 1818722863195095040 |
|---|---|
| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-17T21:01:23Z |
| format | Article |
| id | doaj.art-5cd3341bbfb84f5c85d446cac481a650 |
| institution | Directory Open Access Journal |
| issn | 1544-9173 1545-7885 |
| language | English |
| last_indexed | 2024-12-17T21:01:23Z |
| publishDate | 2008-03-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Biology |
| spelling | doaj.art-5cd3341bbfb84f5c85d446cac481a6502022-12-21T21:32:42ZengPublic Library of Science (PLoS)PLoS Biology1544-91731545-78852008-03-0163e6510.1371/journal.pbio.0060065Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation.Sushma ShivaswamyAkshay BhingeYongjun ZhaoSteven JonesMartin HirstVishwanath R IyerThe 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.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18351804/pdf/?tool=EBI |
| spellingShingle | 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. PLoS Biology |
| title | 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_short | 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 |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18351804/pdf/?tool=EBI |
| work_keys_str_mv | AT sushmashivaswamy dynamicremodelingofindividualnucleosomesacrossaeukaryoticgenomeinresponsetotranscriptionalperturbation AT akshaybhinge dynamicremodelingofindividualnucleosomesacrossaeukaryoticgenomeinresponsetotranscriptionalperturbation AT yongjunzhao dynamicremodelingofindividualnucleosomesacrossaeukaryoticgenomeinresponsetotranscriptionalperturbation AT stevenjones dynamicremodelingofindividualnucleosomesacrossaeukaryoticgenomeinresponsetotranscriptionalperturbation AT martinhirst dynamicremodelingofindividualnucleosomesacrossaeukaryoticgenomeinresponsetotranscriptionalperturbation AT vishwanathriyer dynamicremodelingofindividualnucleosomesacrossaeukaryoticgenomeinresponsetotranscriptionalperturbation |