Fig. 3: BioID-mediated proximity labeling defines RBP neighborhoods and enables functional annotation of RBPs.

A Overview of our pathway annotation workflow for RBPs. The example provided shows the test for the association of ZNF800 and GO:0006361 (transcription initiation from RNA polymerase I promoter). Proximity-labeled proteins were ranked by their z-scores in the ZNF800-BioID dataset, where a higher score implies enrichment relative to control. Experiments were performed in biological triplicates using unlabeled samples as controls (three cases vs. three control designs). Gene-set enrichment analyses were performed on the resulting ranked list across all RBPs. Each enrichment analysis resulted in a p-value and NES score for a given pair of RBP and a pathway. B A heatmap showing the associations between RBPs and pathways as inferred from proximity labeling data. Columns correspond to the RBPs, rows correspond to individual gene ontology terms (Biological Processes; BP), and the color denotes the GSEA normalized enrichment score (NES). The associations showing FDR < 0.05 are marked with a yellow asterisk. The green heatmap in the header shows the RBP binding preferences to particular RNA types, as determined based on eCLIP RNA targets. Some known functions of RBPs are highlighted by boxes and zoomed-in on the right. Source data are provided as a Source Data file.