Fig. 3

Chromatin and transcriptomic profiling of chidamide-resistant and chidamide-sensitive NKTL cells. A Heatmap representation of unsupervised hierarchical clustering based on H3K27ac occupancy at total H3K27ac ChIP-seq peaks (n = 28,727). Samples were clustered based on the Spearman correlation coefficient with average linkage. B Venn diagram showing the overlap of H3K27ac peaks between resistant and sensitive cells. C MA plot of all peaks from comparison of resistant and sensitive samples after normalization by MAnorm3. Each dot represents a peak, the red dots represent the GAIN regions (n = 9267), and the blue dots represent the LOSS regions (n = 3558). D Heatmap representation of GAIN and LOSS regions based on H3K27ac occupancy in resistant and sensitive samples. Ten kb around the center of the GAIN and LOSS regions is displayed for each sample. E Motif analysis of GAIN regions in resistant cells using HOMER, showing significant enrichment of the bZIP family, RHD family, STAT family and IRF family (hypergeometric test). F Scatter plot showing the correlation between ChIP-seq mark intensity and RNA-seq read intensity. Each dot represents an overlapping locus, while the red dots (n = 906) indicate upregulated loci between resistant and sensitive cells, and the blue dots (n = 340) indicate downregulated loci. G Unsupervised hierarchical clustering of differentially expressed genes (DEGs) (p < 0.05, |log2-fold change|> 1) overlapping with H3K27ac GAIN and LOSS regions in sensitive versus resistant cells. H GSEA was performed based on a hypergeometric test that takes the size of the overlap between the hallmark gene set and the list of differentially expressed genes overlapping with H3K27ac GAIN and LOSS regions in resistant versus sensitive cells as the test statistics. I IGV screen shots showing the distribution of H3K27ac mark intensity in resistant versus sensitive cells at two representative genomic loci (TNFRSF8 and TNFRSF9)