Fig. 2
From: CAPRI enables comparison of evolutionarily conserved RNA interacting regions
RNA interactome capture in Drosophila melanogaster. a Protein profiles from interactome capture visualised on a polyacrylamide gel by silver staining. Sample loading: Input (lanes 1–2); Interactomes captured from UV control (noUV), UV crosslinked (UV), formaldehyde control (noFA), formaldehyde-crosslinked (FA), and formaldehyde-crosslinked with RNase treatment (FA-RNase) (lanes 4–8); and finally BSA (20 ng) (lane 9) were utilised to validate the interactome capture protocol. b Validation of the interactome capture by western blot of selected proteins. Antibodies against known Drosophila RBPs (Mle, Glorund, Squid, Rump) were used as positive controls, whereas antibodies against H3 and actin served as negative controls. Source data are provided Supplementary Fig. 19. c Scatter plot of average intensity values of proteins detected in both the UV-RBPome and FA-RBPome. Pearson correlation (r) of 0.83 was observed between the two sets. d Venn diagram of the UV-RBPome (blue), FA-RBPome (orange), previously reported embryo interactomes14,23 (green) and previously reported UV-RBPomes in all species, including the Drosophila embryo RBPomes (light green)2,14,23. e KEGG pathways enriched in the FA-RBPome (Benjamini–Hochberg correction 1% FDR). Numbers of proteins from the full proteome, FA-RBPome and UV-RBPome present in each of the pathways are presented. f Fraction of proteins with known RNA-binding domains (RBDs) in the UV- and FA-RBPomes. g Enriched InterPro domains in the FA-RBPome (Benjamini–Hochberg correction 1% FDR). Number of proteins with enriched InterPro domains along with proteome count (Benjamini–Hochberg correction 1% FDR). Representative RBDs (left panel) and domains related to RNA function (right panel) are shown
