Signal-noise metrics for RNA binding protein identification reveal broad spectrum protein-RNA interaction frequencies and dynamics

Recent efforts towards the comprehensive identification of RNA-bound proteomes have revealed a large, surprisingly diverse family of candidate RNA-binding proteins (RBPs). Quantitative metrics for characterization and validation of protein-RNA interactions and their dynamic interactions have, however, proven to be analytically challenging and prone to error. Here we report a novel method termed LEAP-RBP for the selective, quantitative recovery of UV-crosslinked RNA-protein complexes. By virtue of its high specificity and yield, LEAP-RBP distinguishes RNA-bound and RNA-free protein levels and reveals common sources of experimental noise in RNA-centric RBP enrichment methods. We introduce new strategies for accurate RBP identification and signal-based metrics for quantifying protein-RNA complex enrichment, relative RNA occupancy, and method specificity. The utility of our approach is validated by comprehensive identification of RBPs whose association with mRNA is modulated in response to global mRNA translation state changes and through in-depth benchmark comparisons with current methodologies. Overall design: The purpose of this experiment was to determine if the UV crosslinking protocol for capturing RNA binding protein - RNA interactions and the associated isolation procedure for enriching RNA binding protein-RNA complexes included RNA binding protein - small RNA interactions. This question is significant because different RNA-centric methods for capturing protein-RNA interactions are biased against protein-small RNA interactions. In this straightforward experiment, biological duplicate cultures of HeLa cells were subjected to UV irradiation and protein-RNA crosslinked complexes were isolated by organic solvent extraction and precipitation via a liquid emulsion assisted RNA binding protein precipitation protocol (LEAP-RBP). The small RNA content of the total HeLa cellular protein-small RNA adducts was then determined by small RNA sequencing, or sRNAseq.