Poster abstracts

Poster number 127 submitted by Jarrett Wilson

Mapping Sm Protein Binding Sites on snRNA using RNP-MaP

Jarrett Wilson (University of Michigan), Chase Weidmann (University of Michigan)

Abstract:
RNA-protein interactions influence every step of gene regulation, governing RNA transcription, splicing, localization, stability, and translation and ultimately shape cell identity and fate. However, defining the organization and function of RNA-protein interaction networks remains a major challenge, particularly because many RNAs lack strong primary sequence conservation or well-defined structural annotation. Traditional approaches to study RNA-protein interactions, for example, RNA immunoprecipitation or reconstituted binding assays, often miss the dynamic and cooperative nature of Ribonucleoprotein (RNP) assemblies inside cells and are limited to the interactions of only a few proteins at a time. In contrast, RNP-MaP (Ribonucleoprotein Networks Analyzed by Mutational Profiling) comprehensively maps the locations of protein binding sites on RNA and measures interactions between RNA binding proteins on single RNA molecules inside cells.
Here, we aim to identify RNP networks transcriptome-wide based on their RNP-MaP interaction network signatures. As proof-of-principle, we are investigating interactions between the Sm-protein complex and small nuclear RNAs (snRNAs), which together are central to spliceosomal function. Sms proteins assemble at a conserved Sm binding site, forming well-defined complexes that provide an ideal system for characterizing RNP network formation. Our data reveals consistent RNP-MaP reactivity patterns at the Sm binding site across multiple snRNAs. From these shared reactivity profiles, we constructed a machine learning-based model that accurately identifies Sm binding events from small, targeted RNP-MaP datasets. We aim to use our model to identify novel Sm binding sites from transcriptome-scale RNP-MaP data. This approach will serve as a framework for identifying new RNP-MaP signatures and discovery of novel RNP networks inside the cell.

Keywords: RNP, RNA-Protein, Interaction Networks