Fig. 7: Upregulation of genes and transposable elements in regions of H3K9me3 loss.

a. Log2-fold changes of H3K9me3 signal comparing TKO mMSCs and Cal27 H3K36M-OE cells to their respective parental controls. Following TKO in mMSC, over 90% of genes in cluster B regions (2119/2354) lose H3K9me3 in their gene bodies whereas following H3K36M-OE in Cal27, 81% of genes (342/424) lose H3K9me3 in cluster B regions. b Log2-fold changes of gene expression comparing TKO to parental mMSCs, showing that most of the genes in cluster B regions with significant H3K9me3 loss become upregulated (157 upregulated versus 22 downregulated), whereas a randomized control set of genes have similar numbers of genes up- and downregulated (98 and 81, respectively). A two-sided Wilcoxon rank-sum test was used. c Venn diagram comparing the genes losing H3K9me3 in TKO mMSCs and Cal27 H3K36M-OE cells, respectively, indicates 132 genes common to both conditions; 46 of which are olfactory receptor genes and 7 are gamma-aminobutyric acid (GABA) receptor genes. d Over-representation analysis of KEGG pathways, confirming olfactory transduction as the top enriched pathway for the genes commonly found between TKO mMSCs and Cal27 H3K36M-OE cells that are losing H3K9me3. e Volcano plots showing a large number of transposable elements become upregulated in regions of H3K9me3 loss (cluster B domains) in the TKO mMSCs. **** refers to p-value = 7.7e-22 from a Wilcoxon rank-sum test. In the box plots for a and b, boxes span the lower (first quartile) and upper quartiles (third quartile), 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.