Fig. 3

eCLIP enrichment for rRNA links RBPs with ribosomal RNA processing. a Heatmap indicates relative information at each position along (top) the ribosomal RNA precursor 45S polycistronic transcript and (bottom) within the mature 18S and 28S transcripts. Reads mapping equally to the 45S and mature 18S or 28S are assigned to the mature for quantitation. Purple asterisk indicates RBPs for which knockdown showed rRNA processing defects in Tafforeau et al. [28]. b Lines indicate fold-enrichment in DDX51 eCLIP in K562 cells at the 3′ end of the 28S and 45S transcript. For this and further plots, black line indicates mean and gray region indicates 10th to 90th percentile across all 223 eCLIP datasets. c, d Lines indicate relative information for c UTP18 in K562 and d WDR3 in K562 across the 45S precursor. e Lines indicate fold-enrichment for indicated RBPs within a region flanking putative ribosomal-encoded microRNA rmiR-663. f Red indicates mismatch positions relative to ribosomal rmiR-663 (and 100 nt flanking regions) for genomic-encoded miR-663a, miR-663b, and two additional homologous regions containing putative microRNAs. g Pie chart indicates the fraction of reads in ILF3 HepG2 eCLIP mapping (green) with fewer mismatches to rmiR-663, or (gray) mapping equally well to rmiR-663 and other miR-663 family members as indicated. See Additional file 3: Fig. S3j-k for LIN28B (HepG2) and SSB (HepG2). h, i Points indicate fold-enrichment in each eCLIP dataset for h C/D-box snoRNAs versus 45S precursor RNA, and i H/ACA-box snoRNAs versus C/D-box snoRNAs. Pearson’s correlation and significance were calculated in MATLAB