Extended Data Fig. 6: Identification of miRNA-mRNA interactions using eCLIP.
a) Dot plot shows expression of mature miRNAs in BT183 cell line assessed by small-RNA sequencing. Detected C19MC members are colored in red (n = 67). Most highly expressed miRNAs of interest are highlighted. b) Histograms show the number of detected reads as a function of paired-end read length for replicate 1 and 2 of the eClip experiment in BT183 cells. Only reads that contain a mature miRNA sequence at the 5′ end (miRNA-only and chimeric reads) are shown. Percentages of reads for each population relative to all reads (chimeric and non-chimeric) are indicated. Over 5 million chimeric reads were detected across replicates. c) Dot plot shows the enrichment of chimeric reads in detected peaks over normalized reads in the input control, combining both replicates. n = 4,009 high-confidence peaks are indicated in black. d) Heatmap shows overlap (Jaccard index) in genes targeted by individual C19MC members. The total number of target genes per C19MC member is indicated in the bar plot on the left, split by genes that are targeted by a single or multiple members. miRNAs of interest are highlighted by arrows. e) Genome plot of region on chromosome 9 encompassing the 3′ UTR of TF transcription factor ZNF367. Top track shows coverage in input control, second track shows coverage of non-chimeric mRNA-only reads. Third track shows coverage of all chimeric reads, combined for all miRNAs. Remaining tracks show coverage of chimeric reads associated with C19MC members miR-512-5p and miR-515-5p and three non-C19MC miRNAs, indicated in red and blue, respectively. f) Genome plot of region on chromosome 5 encompassing EGR1, similar to panel (e). g) Genome plot of region on chromosome 6 encompassing SOX4, similar to (e). h) Genome plot of region on chromosome 2 encompassing SOX11, similar to (e). i) Genome plot of region on chromosome 3 encompassing HES1, similar to (e). j) Genome plot of region on chromosome 1 encompassing HES5, similar to (e). Related to Fig. 4.
