Fig. 1: Common and cell type-specific TE subfamilies derepressed by inhibition of CMEs. | Communications Biology

Fig. 1: Common and cell type-specific TE subfamilies derepressed by inhibition of CMEs.

From: Cancer cell type-specific derepression of transposable elements by inhibition of chromatin modifier enzymes

Fig. 1

a Schematic representation of the CME inhibitor treatments and the analysis pipeline. All five cell lines were treated with DNMTi, HDACi, SETDB1i and DNMTi-HDACi. Additionally, GP5d and OE19 cells were treated with DNMTi-SETDB1i and HDACi-SETDB1i. Decitabine (DAC) DNMT inhibitor, SB939 HDAC inhibitor, and Mitramycin A SETDB1 inhibitor. b Differentially expressed TE subfamilies between DMSO-treated GP5d and OE19 cells. Scatter plot shows normalized RNA-seq read counts for TE subfamilies. Differentially expressed TE subfamilies are labeled by TE class. c Comparison of differentially expressed TE subfamilies induced by CMEi in the five cell lines. Differential expression analysis was performed by DESeq2. The heatmap shows log2 fold change (FC) for TE subfamilies with absolute log2FC > 2.5 (treatment vs. vehicle-treated cells from the same cell line) and adjusted p < 0.05 in at least one CME treatment in at least one cell lines. Rows and columns are clustered with hierarchical clustering. d Distinct TE subfamilies derepressed by CMEi in GP5d and OE19 cells. Expression changes for TE subfamilies (log2FC) were compared between different CME treatments in GP5d and OE19 cells. Significance symbols: **** indicates p < 0.0001, ***p < 0.001, **p < 0.01, *p < 0.05, ns = non-significant |log2FC| < 1.5 or p > 0.05. Source data are provided as Supplementary Data 11.

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