Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction

Britta Mueller; Jakub Mieczkowski; Sharmistha Kundu; Peggy Wang; Ruslan Sadreyev; Michael Y. Tolstorukov; Robert E. Kingston

doi:10.1101/gad.293118.116

Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction

¹Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA;
²Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA

Corresponding authors: kingston{at}molbio.mgh.harvard.edu, tolstorukov{at}molbio.mgh.harvard.edu

↵5 These authors contributed equally to this work.

↵Present addresses: ³Neurobiology Center, Nencki Institute of Experimental Biology, Warsaw 02-093, Poland; ⁴Global Obesity Prevention Center (GOPC), Johns Hopkins University, Baltimore, MD 21205, USA.

Abstract

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. We tested 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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Footnotes

Supplemental material is available for this article.
Article published online ahead of print. Article and publication date are online at http://www.genesdev.org/cgi/doi/10.1101/gad.293118.116.
Freely available online through the Genes & Development Open Access option.

Received November 1, 2016.
Accepted February 27, 2017.

This article, published in Genes & Development, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.