Fig. 4: Genome-wide identification of miRNA targets using chimeric eCLIP.
a, Heatmap showing the relative expression of refined signature genes (n = 100 per signature) in n = 179 cells from the BT183 patient-derived in vitro model. Normalized expression levels of the pri-miRNA of C19MC and cell-type assignments are indicated above the heatmap. b, Schematic illustration of the AGO2 eCLIP experimental workflow. c, Pie charts showing the fractions of mRNA, miRNA and chimeric mRNA-miRNA in both eCLIP replicates (n = 42.7 M and 57.2 M reads). d, Scatter plot showing the number of chimeric reads per miRNA in both technical replicates. C19MC members are highlighted in red. e, Scatter plot showing the number of chimeric reads per peak in both technical replicates. High-confidence peaks are highlighted (n = 4,009). f, Top, Bar plot showing the number of high-confidence peaks for C19MC (red, n = 23 miRNAs), C13MC (green, n = 6 miRNAs) and other (gray, n = 26 miRNAs) miRNAs with at least ten target genes. Middle, Bar plot indicating the percentage of peaks containing the respective seed motifs. Bottom, Bar plot indicating the percentage of peaks in UTRs (5′ and 3′ UTRs), CDS or noncoding transcripts. g, Heatmap showing peak enrichment for high-confidence target genes (n = 1,096) of C19MC members. Target genes for miRNAs with fewer than 20 target genes are summarized in the rightmost column. TFs are highlighted next to the heatmap. Selected TFs are labeled on the left. h, Dot plots showing the correlation of C19MC-targeted TFs (n = 116) to cell-type-specific signature scores in single cells of the patient samples, in the same order as shown in g. Selected TFs are labeled. i, Genome plot of the region on chromosome 15, including the C19MC-targeted TF NR2F2. The track shows coverage in input control; the second track shows coverage of nonchimeric mRNA-only reads; the third track shows coverage of all chimeric reads, combined for all miRNAs; the remaining tracks show the chimeric reads associated with five separate C19MC members (shown in red). j, Genome plot of region on chromosome 1 encompassing the TF ZBTB18. Coverage tracks of chimeric reads associated with C19MC members miR-512-5p and miR-1323, and three non-C19MC miRNAs, are indicated in red and blue, respectively. Schematic in b created with BioRender.com.
