Fig. 4: Distinct epigenetic mechanisms govern the derepression of LTR12C by co-inhibition of DNMT and HDAC.

a TF motif enrichment at TE sequences derepressed by DNMTi-HDACi in GP5d and OE19 cells. After performing motif enrichment analysis for individual motifs, similar motifs were combined into motif clusters from ref. ⁷⁸. The representative TF clusters are labeled on the right. The minimum E-value found for an individual TF for each motif cluster was plotted in the final figure. b Boxplots comparing the expression of derepressed LTR12C in DMSO and DNMTi-HDACi GP5d, OE19 and GP5d-p53-KO cells (two-sided Wilcoxon paired test). The lower and upper hinges of the boxes represent the 25th to 75th percentiles, the midline is the median, and the whiskers extend from the hinges to the minimum and maximum values by 1.5 * interquartile range (IQR). c, Venn diagram showing the overlap between LTR12Cs derepressed by DNMTi-HDACi in GP5d and OE19 (shown in Fig. 4b). d Metaplots of ATAC-seq and CUT&TAG for H3K27me3, H3K4me1, RNAPII and Ser5p-RNAPII at derepressed LTR12Cs in DNMTi-HDACi OE19 cells (shown in Fig. 4b). Derepressed LTR12C elements show a poised chromatin state in OE19 cells, whereas LTR12C in GP5d cells were enriched with repressive H3K27me3 marks (see Supplementary Fig. 7b). e Heatmap showing the KAS-seq signal at derepressed LTR12C elements in DNMTi-HDACi OE19 cells (shown in Fig. 4b). f Volcano plot of nanopore sequencing data comparing CpG methylation levels at derepressed LTR12C elements (n = 499) in control and DNMTi-HDACi GP5d cells (shown in Fig. 4b). Significance was determined with a one-sided Fisher’s exact test. P-values were corrected with Benjamini-Hochberg method. g Heatmaps showing the ChIP-seq signals for H3K27ac and H3K4me3 in control and DNMTi-HDACi GP5d cells (shown in Fig. 4b). h Heatmaps showing the ChIP-seq signals for H3K27ac and H3K4me3 in control and DNMTi-HDACi OE19 cells (shown in Fig. 4b). i Derepressed LTR12C elements in DNMTi-HDACi GP5d and OE19 cells. Volcano plots show the changes in gene expression for derepressed LTR12C-associated genes for OE19 cells. Analysis of differentially expressed genes in OE19 cells with DNMTi-HDACi revealed significant upregulation of genes in the vicinity of derepressed LTR12C elements (±50 kb). In total, 102 out of 132 and 70 out of 89 differentially expressed genes were upregulated in GP5d and OE19 cells, respectively. j Genome browser snapshot of a derepressed LTR12C in control and DNMTi-HDACi GP5d cells. Panels show the ChIP-seq signals for H3K27ac, H3K4me3, and an RNA-seq signal track. k Genome browser snapshot of a derepressed LTR12C in control and DNMTi-HDACi OE19 cells. Each panel shows the ChIP-seq signals for H3K27ac, H3K4me3 and an RNA-seq signal track. Source data are provided as Supplementary Data 11.