Fig. 5

Chimeric eCLIP for spliceosomal RNA-associated RBPs enrich for snoRNA-snRNA interactions. A Fold-enrichment of non-chimeric C/D snoRNA reads from FBL versus LARP7 chimeric eCLIP in HepG2 cells. Datapoints for C/D snoRNAs with U6 interactions annotated in snoDB are colored. Datapoints with < 5 IP reads were discarded. B C/D box snoRNA chimeric read abundance (RPM) from FBL versus LARP7 chimeric eCLIP. Datapoints for C/D snoRNAs with U6 interactions annotated in snoDB are colored. C Heatmap of snoRNA chimeric read abundance (RPM) from FBL, LARP7, and NOLC1 chimeric eCLIP replicates for all snoRNAs with annotated U6 interactions. D Browser tracks show read density (per million chimeric reads) for U6-interacting snoRNA chimeras along the U6 snRNA for a single representative replicate. E SnoRNA:U6 chimeric read abundance (RPM) from FBL or LARP7 chimeric eCLIP. Colors indicate snoRNAs classified as (green) LARP7-associated U6 snoRNAs, (light green) non-LARP7-associated U6 snoRNAs, and (gray) all other snoRNAs. * indicates P < 0.05, unpaired two sample t-test. F SnoRNA:rRNA chimeric read abundance (RPM) for snoRNAs with known rRNA target sites from FBL or LAPR7 chimeric eCLIP. * indicates P < 0.05, unpaired two-sample t-test. G Target distribution of snoRNA:snRNA chimeric reads (RPM) recovered in chimeric eCLIP for the indicated RBPs. H Fold-enrichment of non-chimeric snoRNA reads in FBL versus NOLC1 chimeric eCLIP in HepG2 cells. Datapoints with < 5 IP reads were discarded. Circle outline color represents the type of SCARNA with (blue) C/D box motif, including Tandem-C/D SCARNAs, (pink) H/ACA box motif, including Tandem-H/ACA SCARNAs, and (orange) hybrid SCARNAs that possess both C/D and H/ACA box motifs. I SnoRNA chimeric read abundance (RPM) in FBL versus NOLC1 chimeric eCLIP. J Browser tracks show read density (per million chimeric reads) for snoRNA:U2 chimeric reads along the U2 snRNA for known and candidate U2-interacting snoRNAs for a single representative replicate (see Fig. S6L for second replicate). RPM: reads per million sequenced reads. Unless otherwise indicated, data shown is average of two replicates (FBL, NOLC1) or a single replicate (LARP7)