Extended Data Fig. 10: eCLIP binding patterns in subcellular space.

a, Circos plot with lines indicating co-observed localization patterns (red, within cytoplasm; purple, within nucleus; orange, between cytoplasm and nucleus). b, Fold enrichment for the 45S ribosomal RNA precursor observed for eight RBPs with eCLIP data, nucleolar localization observed in immunofluorescence imaging, and no human RNA processing function identified in literature searches. c, Points indicate nuclear versus cytoplasmic ratio from immunofluorescence imaging (x-axis) versus ratio of spliced versus unspliced exon junction reads (y-axis), normalized to paired input. RBPs profiled by eCLIP and immunofluorescence in HepG2 cells are indicated in blue, and RBPs profiled by eCLIP in K562 cells (in purple) were paired with immunofluorescence experiments performed in Hela cells. eCLIP data shown are from replicate 1. d, As in c, with RBPs separated into nuclear (nuclear:cytoplasmic ratio ≥ 2; n = 48) and cytoplasmic (nuclear:cytoplasmic ratio ≤ 0.5; n = 31) RBPs along with inputs (n = 160). Significance was determined by two-sided Kolmogorov–Smirnov test. Red line indicates mean, and violin plot indicates density of data sets (with kernel smoothing). eCLIP data shown are from replicate 1. e, Points indicate the number of differential splicing events observed upon knockdown of each RBP, separated by the presence or absence of localization in nuclear speckles (left, n = 56) or nuclear but not nuclear speckles (right, n = 41). Significance was determined by two-sided Kolmogorov–Smirnov test. f, Cumulative distribution curves indicate total relative information content for the mitochondrial genome for RBPs with mitochondrial localization by immunofluorescence (red, n = 13) and all other RBPs (grey, n = 78). Significance was determined by two-sided Kolmogorov–Smirnov test. g, Heatmap indicates DHX30 eCLIP enrichment across all exons for all mitochondrial protein-coding and rRNA transcripts.*Significant eCLIP signal (fold enrichment ≥ 4 and P ≤ 0.00001 in IP versus input determined by two-sided Fisher’s exact test (or Yates’s χ² test where appropriate) with no hypothesis testing correction; Methods). eCLIP data are shown for replicate 1; a second replicate showed similar enrichment patterns.