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

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 are 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 MNase digestion and by ATAC-seq, 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. Overall design: Time series of nucleosome occupancy, MNase-seq, ATAC-seq, H3K27ac, RNAseq and Pol2 profiles for UPR-induced S2 cells.