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. Author manuscript; available in PMC: 2021 Nov 20.
Published in final edited form as: Nat Immunol. 2021 May 20;22(6):711–722. doi: 10.1038/s41590-021-00928-y

Fig. 6. Global Chromatin Accessibility Increase Upon NSP and H3ΔNThr22 Depletion.

Fig. 6

(a) Differential gene expression in response to NSP depletion. Heatmap representation of differentially expressed genes between ΔNSPs and control cells under a FDR 5% cutoff. Z-score transformed gene expression levels (color) of differential genes (y-axis) in the indicated cell lines (x-axis). Dendrogram, unsupervised clustering.

(b) Reintroducing H3ΔN into ΔNSPs cells attenuates the expression of genes upregulated in ΔNSPs cells. Gene expression analysis of ΔNSPs cells with (white) or without (gray) H3ΔN reintroduction as in Extended Data Fig. 2m. Data represent mean ± S.E.M. (three technical replicates and two biological replicates (independent ΔNSPs clones) (N=6)). Statistical significance is determined by two-tailed Student’s t-test. **, P≤0.01; ***, P≤0.001.

(c) Increased chromatin accessibility in ΔNSPs cells. ATAC-seq analysis of three controls and three ΔNSPs cell lines. The numbers of differentially accessible peaks are shown. Top, differentially accessible peaks in ΔNSPs clones over the average of controls; bottom, differentially accessible peaks in controls over the average of ΔNSPs clones.

(d-f) Increased chromatin accessibility at H3ΔNThr22-enriched peaks upon NSP and H3ΔNThr22 depletion. Venn diagram depicts the number of H3ΔNThr22 peaks identified in wild-type U937 cells associated with differentially accessible peaks between ΔNSPs and control cells (d). Representative genomic tracks of the H3ΔNThr22 ChIP-seq dataset from wild-type U937 cells (top) and ATAC-seq datasets from control (middle) or ΔNSPs (bottom) cells (e). Pie chart depicts the percentage of overlapped peaks in (d) (N=9,654) that are existing accessible chromatin peaks in control cells (f).