Fig. 3

Super-enhancer (SE)–miRNA interactions and impact of CpG methylation on miRNA expression. a Example of mimQTLs (blue arcs) and ChIA-PET Pol2 loops (red arcs) where mimQTL CpGs (n = 3) or one foot of the ChIA-PET Pol2 loop is located within the hsa-miR-342 SE (purple) and the other loop foot resides within hsa-miR-342-5p/-3p. Also shown are the location of 450k methylation array CpGs and ER-alpha (ERα), FOXA1, and GATA3 binding regions obtained from ChIP-Seq experiments of the MCF7 cell line. The figure was made using the WashU Epigenome Browser v. 46.2 [64]. b mimQTLs and ChIA-PET Pol2 loops where mimQTL CpGs (n = 21) or one foot of the ChIA-PET Pol2 loop is located within the let-7b SE (purple) and the other loop foot resides within hsa-let-7b-5p. c Boxplot showing average DNA methylation in Oslo2 estrogen receptor (ER)-positive (pos) and ER-negative (neg) tumors across all CpGs within the hsa-miR-342 SE and in mimQTL with hsa-miR-342-3p/-5p (n = 3). d Boxplot showing average DNA methylation in Oslo2 ER-positive and ER-negative tumors across all CpGs within the let-7b SE and in mimQTL with hsa-let-7b-5p (n = 21). e Boxplots showing hsa-miR-342-5p/-3p expression in ER-positive and ER-negative tumors of the Oslo2 cohort. f Boxplots showing hsa-let-7b-5p expression in ER-positive and ER-negative tumors of the Oslo2 cohort. P values resulting from Wilcoxon rank-sum tests are indicated in the boxplots