Dynamic Remodeling of Individual Nucleosomes Across a Eukaryotic Genome in Response to Transcriptional Perturbation

Date
2008-03-18
Authors
Shivaswamy, Sushma
Bhinge, Akshay
Zhao, Yongjun
Jones, Steven
Hirst, Martin
Iyer, Vishwanath R
Journal Title
Journal ISSN
Volume Title
Publisher
Public Library of Science
Abstract

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.

Description
Sushma Shivaswamy is with UT Austin, Akshay Bhinge is with UT Austin, Yongjun Zhao is with British Columbia Cancer Agency, Steven Jones is with British Columbia Cancer Agency, Martin Hirst is with British Columbia Cancer Agency, Vishwanath R Iyer is with UT Austin.
Citation
Shivaswamy S, Bhinge A, Zhao Y, Jones S, Hirst M, et al. (2008) Dynamic Remodeling of Individual Nucleosomes Across a Eukaryotic Genome in Response to Transcriptional Perturbation. PLoS Biol 6(3): e65. doi:10.1371/journal.pbio.0060065