Fig. 5: Cell type-specific TEs derepressed by SETDB1 inhibition in cancer cell lines.

a Comparison of SETDB1 KO/inhibition-induced changes in the expression of TE subfamilies between six different cell lines. Differential expression analysis of RNA-seq data was performed with DESeq2. All TE subfamilies with absolute log2FC > 1.5 (treatment vs DMSO or A375 KO vs A375) and adjusted p < 0.05 in at least one CMEi treatment in one cell line were selected and their expression changes in log2FC was plotted. Rows and columns are clustered with hierarchical clustering. b Number of differentially expressed TE loci by SETDB1 KO/inhibition in A375, WT and p53-KO GP5d, OE19, and WT and p53-KO LNCaP-1F5 cells. c The proportion of TEs derepressed by SETDB1 KO/inhibition belonging to the major TE classes among the derepressed TEs by in A375, WT and p53-KO GP5d, OE19, and WT and p53-KO LNCaP-1F5 cells. d Number of Alu SINEs derepressed by SETDB1 KO/inhibition in A375, WT and p53-KO GP5d, OE19, and WT and p53-KO LNCaP-1F5 cells. Number above the bar represents the percentage of Alu SINEs in total derepressed TEs. e Motif enrichment analysis for TEs derepressed by SETDB1 KO/inhibition in A375, WT and p53-KO GP5d, OE19, and WT and p53-KO LNCaP-1F5 cells. The analysis was performed as described in Fig. 4a. Source data are provided as Supplementary Data 11.