Fig. 3: Drosha genomic occupancy is sensitive to DNA methylation.

a Plot of expression of transcripts encoding miRNA biogenesis proteins (n = 40) and other RNA-binding proteins (n = 166) in WT vs. TKO cells. R- and p-values of Pearson’s product-moment correlation are given. b Drosha mRNA levels in WT and TKO mouse ESCs quantified by qRT-PCR. Bars represent means of three independent experiments. Values were normalized to tubulin. c Relative Drosha occupancy over miRNA genomic regions in WT and TKO mouse ESCs determined by ChIP with an antibody against Drosha. Immunoprecipitated DNA was quantified by qRT-PCR with primers spanning the indicated pre-miRNA sequences. Data were normalized to input DNA. d Efficiency of miRNA biogenesis measured as the ratio of mature miRNA to pri-miRNA expression levels for the indicated miRNAs in WT mouse ESCs upon treatment with 2.5 µM 5-Aza relative to vehicle control. Data were normalized to RPLP0 for pri-miRNAs and RNU6 for mature miRNAs. e Drosha protein levels in untreated control WT mouse ESCs and cells treated with 2.5 µM 5-Aza. GAPDH was used as the loading control. f Relative Drosha occupancy over miRNA genomic regions in untreated WT mouse ESCs and cells treated with 2.5 µM 5-Aza determined by ChIP with an antibody against Drosha. Immunoprecipitated DNA was quantified by qRT-PCR with primers spanning the indicated pre-miRNA sequences of the methylated and unmethylated groups. Data were normalized to input DNA. All Error bars represent ± SEM (n = 3). * represents p < 0.05; ** represents p < 0.01; *** represents p < 0.001; NS = not significant; t-test. Source data are provided as a Source Data file.