Novel IGF2BP3 RNA targets identified by IR-PAR-CLIP in HCT116 colorectal carcinoma cell line. (A) Overlap of IGF2BP3 targets identified in this study with RNase I and RNase T1 with the aggregated list of IGF2BP3 targets identified in the HEK 293 (Hafner et al. 2010), human pluripotent stem cells (Conway et al. 2016), B-ALL (Palanichamy et al. 2016), hepatocellular carcinoma (HepG2) (ENCODE [Dunham et al. 2012]), and pancreatic ductal adenocarcinoma (PL45 and Panc1) (Ennajdaoui et al. 2016). Concentrations of RNases used for this figure in-lysate and on-beads: RNase I 0.05 U/µL, RNase T1 1 U/µL. (B) Gene Ontology (GO) term analysis of biological process (BP) categories enriched in HCT116 targets identified in this work with both RNase I and RNase T1 (HCT116 all) or when the previously identified targets (A) are excluded (HCT116 only). For visualization, the GO enrichment results were simplified by clustering using the simplify function from the clusterProfiler R package. (C) Examples of IGF2BP3 PAR-CLIP read coverage of 3′UTRs of BCL3, GABARAPL2, and RNF185 transcripts. Transitions color code: (A) green, (C) blue, (G) brown, (T) red.
