Journal
GENES & DEVELOPMENT
Volume 31, Issue 5, Pages 451-462Publisher
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1101/gad.293118.116
Keywords
chromatin; MNase; nucleosome; occupancy; UPR; enhancers
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Funding
- National Institute of General Medical Sciences of the National Institutes of Health [R01GM043901, R37GM048405]
- Leukemia and Lymphoma Society
- National Institutes of Health [P30 DK040561]
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Activation of transcription requires alteration of chromatin by complexes that increase the accessibility of nucleosomal DNA. Removing nucleosomes from regulatory sequences has been proposed to play a significant role in activation. Wetested whether changes in nucleosome occupancy occurred on the set of genes that is activated by the unfolded protein response (UPR). We observed no decrease in occupancy on most promoters, gene bodies, and enhancers. Instead, there was an increase in the accessibility of nucleosomes, as measured by micrococcal nuclease (MNase) digestion and ATAC-seq (assay for transposase-accessible chromatin [ATAC] using sequencing), that did not result from removal of the nucleosome. Thus, changes in nucleosome accessibility predominate over changes in nucleosome occupancy during rapid transcriptional induction during the UPR.
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