SMARTIE: A Machine-Learning approach for investigating RBP-RNA interactions identified by Editing

Abstract

RNA-binding proteins (RBPs) play important roles in gene regulation. RNA editing-based approaches, such as TRIBE and STAMP, have gained wider use for identifying RNA targets of RBPs. These methods offer advantages over crosslinking-based approaches in terms of experimental simplicity and in vivo applicability. However, data analysis methods for these approaches remain underdeveloped, limiting sensitivity, and unbiased target prioritization. To address these limitations, we introduce SMARTIE (Systematic Machine-learning Approach for RBP Targets Identified by Editing), a machine-learning-based framework. SMARTIE robustly identifies and ranks RBP target RNAs from editing data by integrating statistical tests with replicate-aware and confidence-weighted features. Reanalysis of multiple published TRIBE datasets demonstrates the effectiveness of SMARTIE. It recovers targets of RBPs like Ataxin-2, TDP-43, Hrp48, Thor, GPATCH8, dFMRP and NonA. Notably, a model trained on TRIBE data generalizes to STAMP datasets, suggesting that SMARTIE learns universal signatures of editing-based RBP targeting there by enabling more accurate inference for RBP-RNA interactions. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/726004v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@8b77e5org.highwire.dtl.DTLVardef@6c9416org.highwire.dtl.DTLVardef@6e33a5org.highwire.dtl.DTLVardef@100b7b5_HPS_FORMAT_FIGEXP M_FIG C_FIG