Fig. 2: Loss of ASH1L-mediated H3K36me2 results in the downregulation of genes marked by H3K36me2, decreased H3K27ac and increased H3K27me3 at cis-regulatory elements.

a Genome-browser tracks showing one of 84 genes that is marked by residual H3K36me2 in QKO cells, which is lost following ASH1L-KO in QuiKO cells. b Log2 fold changes of gene expression for the 84 genes marked by residual H3K36me2 in QKO, showing that more genes become downregulated (62) than upregulated (22) following loss of ASH1L-mediated H3K36me2. Within this gene set, 51 genes are downregulated while 33 are upregulated when comparing ASH1L-KO to the parental cells. This trend of downregulation is not observed when comparing QKO to TKO for this gene set, where 60 genes are upregulated and only 24 are downregulated. c Violin plots showing that the 84 genes in b only significantly decrease in expression when comparing QKO to QuiKO. ** p-value = 0.0017 from a two-sided Wilcoxon rank-sum test. d Scatterplot illustrating a significant negative correlation between the size of the H3K36me2 peak and gene expression log2 fold changes following ASH1L-dependent H3K36me2 loss in the QKO cell line. Reported values are Pearson’s correlation coefficient (R) and the associated p-value. Each point represents a gene. e, f Aggregate plots showing H3K36me2 and H3K27ac decreases whereas H3K27me3 increases at accessible enhancers (n = 72) and promoters (n = 55) marked with residual H3K36me2. Genome-wide, chromatin accessibility increases in QuiKO cells compared to QKO, although the CREs marked with residual H3K36me2 gain considerably less. Greater decreases are found at enhancers than promoters marked with residual H3K36me2. For f, since an intersection of ATAC-seq peaks between QKO and QuiKO was used to identify accessible promoters, only 55 out of the 60 H3K36me2-flanked promoters had an ATAC-seq peak detected at their promoter. Normalized signals were either depth-normalized (ATAC-seq) or MS-normalized (all other tracks), as previously described. In the box plots for b and c, boxes span the first quartile and third quartile, the median is indicated with a center line, and whiskers extend to a maximum of 1.5 times the interquartile range. Source data are provided as a Source Data file.