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

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.

Author Summary

The eukaryotic genome is packed in a systematic hierarchy to accommodate it within the confines of the cell's nucleus. This packing, however, presents an impediment to the transcription machinery when it must access genomic DNA to regulate gene expression. A fundamental aspect of genome packing is the spooling of DNA around nucleosomes—structures formed from histone proteins—which must be dislodged during transcription. In this study, we identified all the nucleosome displacements associated with a physiological perturbation causing genome-wide transcriptional changes in the eukaryote Saccharomyces cerevisiae. We isolated nucleosomal DNA before and after subjecting cells to heat shock, then identified the ends of these DNA fragments and, thereby, the location of nucleosomes along the genome, using ultra-high–throughput sequencing. We identified localized patterns of nucleosome displacement at gene promoters in response to heat shock, and found that nucleosome eviction was generally associated with activation and their appearance with gene repression. Nucleosome remodeling generally improved the accessibility of DNA to transcriptional regulators mediating the response to stresses like heat shock. However, not all nucleosomal remodeling was associated with transcriptional changes, indicating that the relationship between nucleosome repositioning and transcriptional activity is not merely a reflection of competing access to DNA.

Abstract

Ultra-high-throughput sequencing is used to show that distinct, localized patterns of nucleosome repositioning at promoters underlie the genome-wide transcriptional response to a physiological stimulus.