Fig. 3: SNIP1 binds to chromatin and affects H3K27me3 levels for regulating gene expression.

a Heatmaps representing the binding intensity of 2 biological replicates of SNIP1 CUT&RUN in control and Snip1^Nes-KO NPCs. Binding intensity for 5 kb on either side of all 23,188 SNIP1 CUT&RUN peaks are shown. Blue indicates low intensity and red indicates high intensity. b Bar charts displaying the numbers of upregulated and downregulated genes (Snip1^Nes-KO vs. control, FDR < 0.05) that are bound by SNIP1 at their gene body. c, d Bubble plots of the enriched gene sets in SNIP1-bound genes that became upregulated genes and downregulated genes in Snip1^Nes-KO vs. control NPCs. When adding our H3K27me3/ac CUT&RUN data to the GSEA gene sets, H3K27me3 and H3K27ac levels showed anti-correlation and correlation with gene expression, respectively. Source data are provided in a Source Data file. e Representative GSEA of upregulated genes in Snip1^Nes-KO NPCs vs. control NPCs that are bound by SNIP1 in control NPCs. Intrinsic apoptosis genes were mostly SNIP1-bound and were enriched in the upregulated genes in Snip1^Nes-KO NPCs. Differentially expressed genes were first ranked by their fold-change and p-value before GSEA was performed. f Pie chart showing the proportions of intrinsic apoptosis genes that are upregulated in Snip1^Nes-KO NPCs and/or bound by SNIP1. g Venn diagram displaying the numbers of upregulated intrinsic apoptosis genes in 3 categories. Using our SNIP1, H3K27me3, and H3K27ac CUT&RUN data, the 44 genes were categorized into 1) SNIP1-bound in control NPCs, 2) reduced H3K27me3 levels in Snip1^Nes-KO vs. control NPCs (p < 0.05), and/or 3) increased H3K27ac levels in Snip1^Nes-KO vs. control NPCs (p < 0.05). h H3K27me3 and SNIP1 CUT&RUN tracks visualized by Integrative Genomics Viewer (IGV) at upregulated intrinsic apoptosis genes. Cdkn1a, Chr17: 29,090,888 − 29,095,850. Trp73, Chr4: 154,132,565 − 154,143,373. Msx1, Chr5: 37,818,429 − 37,828,924.