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. 2018 May 1;32(9-10):695–710. doi: 10.1101/gad.312850.118

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© 2018 Rawal et al.; Published by Cold Spring Harbor Laboratory Press

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genesdev.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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Figure 1. — Promoter nucleosomes are disassembled and repositioned on SM-induced transcriptional activation. (A) Plots of H3 and H2B occupancies at each base pair, normalized to the average occupancy on the respective chromosome for each gene, calculated from ChIP-seq data of sonicated chromatin, averaged over the 70 SM-induced genes, and aligned to the TSS. (Blue and yellow) WT_U; (red and purple) WT_I. (B,C) Notched box plots of H3 and H2B occupancies per nucleotide in the [−1,NDR,+1] region calculated from ChIP-seq data of sonicated chromatin from at least three replicates of WT_U and WT_I cultures for 70 SM-induced genes (B) and 134 SM-induced genes (C). If the notches of two plots do not overlap, there is 95% confidence that the true medians of the two distributions differ. Each box depicts the interquartile range containing 50% of the data, intersected by the median; the notch indicates a 95% confidence interval (CI) around the median. (D) Heat map depictions of changes in H3 or Rpb3 occupancies upon SM induction of wild-type cells (WT_I vs. WT_U) calculated from MNase (H3) or (Rpb3) ChIP-seq data for the 204 SM-induced genes, divided between 70 (top) and 134 (bottom) SM-induced genes, and sorted by induced Rpb3 levels for each group. (Panel i) H3 occupancy differences relative to the +1_Nuc dyad. (Panel ii) Rpb3 occupancies averaged over the CDSs in WT_U and WT_I cells. (Panel iii) Differences in Rpb3. (Panel iv) Rpb3 induction ratios between WT_I and WT_U cells for the same gene order, color-coded as shown at the right of each panel. (E) Average dyad density from MNase-ChIP-seq data aligned to the +1_Nuc for 70 SM-induced genes. Midpoints (dyads) of nucleosomal size sequences between 120 and 160 bp were determined with respect to the +1_Nuc and summed for 70 genes. Average profiles were smoothed using a moving average filter with a span of 31 bp. The data were normalized internally to the average value for each data set. (F) Box plots depicting shift in +1_Nuc and −1_Nuc positions and change in NDR width for 70 SM-induced genes, calculated from H3 MNase-ChIP-seq data by calculating change in dyad peak position in WT_I versus WT_U cells for the +1_Nuc and −1_Nuc, respectively. (G). Box plots depicting nucleosome spacing for 70 SM-induced genes in SM-induced or uninduced wild-type cells for the array of +1_Nuc to +5_Nuc, calculated from H3 MNase-ChIP-seq data.