Extended Data Fig. 7: WSTF inhibits chromatin accessibility of inflammatory genes.

a and b, IMR90 cells were engineered to express control sgRNA or sgRNA against SNF2H, combined with vector or WSTF overexpression. The cells were left untreated or induced to senescence by IR, harvested on day 14, and analysed by immunoblotting (a) or RT-qPCR (b). Mean values with s.d. are shown; n = 3 biologically independent samples; exact P values are shown in the figure; one-way ANOVA coupled with Dunnett’s post hoc test. c, Scheme of experimental design for ATAC-Seq. d, The representative track views of a housekeeper gene Vinculin (VCL). e, GO analysis showing the top downregulated categories of differential accessible regions (DARs) by WSTF in senescent cells. The numbers of genes corresponding to the DARs and the P values are shown. Statistical significance was assessed using a two-sided Fisher exact test with Benjamini–Hochberg correction for multiple comparisons.P values are displayed as -log10 (P). f, The genes from DEGs downregulated by WSTF from RNA-Seq were overlapped with genes from DARs downregulated by WSTF from ATAC-Seq. The overlapping genes were subjected to GO analysis, and the GO terms with the numbers of genes and P values are shown. Statistical significance was assessed using a two-sided Fisher exact test with Benjamini–Hochberg correction for multiple comparisons. P values are displayed as -log10 (P). g and h, Transcription factor prediction from RNA-Seq using DEGs (g) and ATAC-Seq using DARs (h) that are downregulated by WSTF in HRasV12-induced senescence. P values are displayed as -log10 (P). i, IMR90 cells stably expressing HA-WSTF were treated with etoposide to induce senescence, and fractionated into cytoplasm and nucleus, then subjected to p65 immunoprecipitation and immunoblotting with indicated antibodies. Because endogenous WSTF is lost in senescence, HA-WSTF overexpressed senescent cells were used for co-IP. j, In vitro translated Flag-p65, HA-WSTF, and HA-SNF2H were subjected to Flag immunoprecipitation and immunoblotting with indicated antibodies. Note that p65 binds quantitatively more to WSTF than SNF2H. k and l, HeLa and MDA-MB-231 cells were subjected to p65 and WSTF IP at the endogenous level, followed by immunoblotting with indicated antibodies. The western blot experiments shown in i-l were repeated independently at least three times with similar results.