Fig. 1: Differential enrichment of H3K23su was positively correlated with differential gene expression in HCT15-FR cells.

a Average profiles (top) and density heatmaps (bottom) indicating H3K23su CUT&Tag signals across a genomic window 2 kb upstream of the TSS and 2 kb downstream of the TES. b Left: heatmap representation of greater (GAIN) and lower (LOSS) H3K23 with CUT&Tag DERs in HCT15-FR cells versus Pa cells. The top panel shows the genomic distribution of 7524 H3K23su GAIN regions; the bottom panel shows the distribution of 6098 H3K23su LOSS regions. The signals are displayed in descending order within the 2-kb window from the center of each DER. Right: average tag density profiles of H3K23su enrichment plotted onto 2-kb regions surrounding the center of DERs. c The distribution of GAIN (red) and LOSS (blue) regions for H3K23su enrichment across chromosomes. d The distance to the closest gene TSS of all regions and the new GAIN and LOSS regions for H3K23su enrichment. e Proportions of GAIN (top) and LOSS (bottom) regions enriched in H3K23su at different genomic loci, such as introns, exons, promoter TSSs, TESs and intergenic regions. f Venn diagram illustrating the overlapping genes between the nearest genes of H3K23su DERs (GAIN and LOSS) revealed by CUT&Tag and the DEGs identified by mRNA-seq. g Box plots showing the relative mRNA expression levels of DEGs associated with H3K23 in the GAIN (left) and LOSS (right) regions. The notches of boxes represent the medians, and the P values were calculated using the Wilcoxon signed-rank test; ****P < 0.0001. h Pearson correlation analysis between H3K23su DERs and their nearest DEGs identified in a. Each blue dot represents a DEG related to differential H3K23su enrichment. The top- and bottom-ranked 20 DEGs with the most substantial difference based on the log₂fold change (FC) are shown in different colors. The Pearson correlation coefficient value (r) and P value are shown in the figure. i, WashU Epigenome Browser tracks showing H3K23su (red), H3K27ac (orange), ATAC-seq (green) and mRNA-seq (blue) signals of representative upregulated IL33 and PARM1 genes in both the HCT15-Pa and HCT15-FR cell lines, each with two replicates. The H3K23su GAIN regions are shaded in red. The dark-blue arrows indicate the TSS and the direction of gene transcription. j Genomic snapshots of H3K23su (red), H3K27ac (orange), ATAC-seq (green) and mRNA-seq (blue) signals of representative downregulated KDM5D and NLRP2 genes. These data are presented for both the HCT15-Pa and HCT15-FR cell lines, with each cell line featuring two replicates. The H3K23su LOSS regions are shaded in blue. The dark-blue arrows indicate the TSS and the direction of gene transcription.