Extended Data Fig. 9: SETD2 inhibition leads to H3K27me3 spreading on chromatin.

a, Aggregate profile plot of wild-type Karpas-422 H3K36me3 ChIP-Rx signal (y-axis) for SETD2-IN-1 (5 μM) treatment centered around H3K36me3 domains in wild-type cells (x-axis). b, Aggregate profile plot of wild-type Karpas-422 H3K27me3 ChIP-Rx signal (y-axis) for SETD2-IN-1 (5 μM) treatment centered around gene bodies of genes down-regulated upon GSK343 withdrawal in CXCdel^+/− cells (x-axis). c, Volcano plot showing gene expression changes in gene expression in Karpas-422 wild-type cells under SETD2-IN-1 (5 µM) treatment for 10 days versus vehicle. Genes with |log₂(fold-change)| > 0.5 and adjusted P value < 0.05 are defined as differentially expressed. P values were computed with DESeq2 by Benjamini-Hochberg method, adjusted for multiple testing. Data were from three biological replicates. d, Aggregate profile plot of wild-type Karpas-422 H3K27me3 ChIP-Rx signal (y-axis) for SETD2-IN-1 (5 μM) treatment (left) and for vehicle- or GSK343-treated wild-type and CXCdel^+/− cells (right) centered around gene bodies of genes down-regulated upon SETD2-IN-1 (5 µM) treatment (x-axis). e, Boxplot depicting log₂(fold-change) H3K27me3 ChIP-Rx signal across gene bodies (y-axis) with down-regulated, non-differential and up-regulated genes in SETD2-IN-1 (5 μM) treatment annotated (x-axis) (left). Boxplot depicting log₂(fold-change) gene expression (y-axis) by change in H3K27me3 (x-axis) for Karpas-422 wild-type cells treated with SETD2-IN-1 relative to vehicle (right). f, Density heatmap comparing log₂(fold-change) H3K27me3 ChIP-Rx signal of Karpas-422 CXCdel vehicle relative to Karpas-422 CXCdel GSK343 treatment (y-axis) versus log₂(fold-change) H3K27me3 ChIP-Rx signal of Karpas-422 SETD2-IN-1 (5 μM) relative to vehicle treatment (x-axis) across all genes (left) and across down-regulated upon SETD2-IN-1 (5 μM) treatment (right). g, Same as f. but for H3K27me3 ChIP-Rx signal of Karpas-422 SETD2-IN-1 treatment relative to vehicle (y-axis) versus log₂(fold-change) H3K36me3 ChIP-Rx signal of Karpas-422 SETD2-IN-1 (5 μM) relative vehicle treatment (x-axis). h, Top 10 enriched pathways within the down-regulated genes upon SETD2 inhibition in Karpas-422 wild-type cells. Functional enrichment analysis of differentially expressed genes was performed using DAVID and P values were computed with modified Fisher’s Exact test. Results in a, b, d–h represent average of two biological replicates. For e, the interquartile range (IQR) is depicted by the box with the median represented by the center line. Whiskers maximally extend to 1.5 × IQR (with outliers excluded). P values were calculated by a Mann-Whitney-Wilcoxon two-sided test.