RNAmotifs 2.0: a framework for inferring multivalent RNA motifs and their candidate regulators of splicing

Abstract

Alternative splicing expands proteomic diversity and is shaped by RNA‑binding proteins (RBPs) that bind to multivalent RNA motifs. Yet connecting cis-acting motifs to their candidate trans-acting protein remains difficult from sequence information alone. Here we present RNAmotifs 2.0, whose MaRs module couples motif discovery with in vivo binding and splicing responses to infer motif-RBP associations. RNAmotifs 2.0 learns position‑specific binding and regulatory expectations, weights binding quality, and optimizes parameters per RBP. Across ENCODE knockdowns, it prioritizes the perturbed regulator, especially for large splicing effects, and summarizes results in a compact visualization. Validation in HNRNPK‑depleted PC3 cells supports generalization.