The transcript interactome of skeletal muscle RNA binding protein motif 3 (RBM3)

Post-transcriptional regulation of gene expression represents a critical regulatory step in the production of a functional proteome. Elevated expression of post-transcriptional regulator RNA binding motif protein 3 (RBM3), an RNA binding protein in the cold-shock family, is positively correlated with skeletal muscle growth in adult mice. However, mechanisms through which RBM3 exerts its effects are largely unknown. The purpose of this study was to perform RNA immunoprecipitation followed by RNA sequencing (RIP-seq) and apply a network science approach to understand biological processes (BPs) most associated with RBM3-bound mRNAs. In addition, through nucleotide-sequence-scanning of enriched transcripts, we predicted the motif for skeletal muscle RBM3 binding. Gene set enrichment analysis followed by enrichment mapping of RBM3-bound transcripts (fold change >3; p.adj <0.01) revealed significant enrichment of BPs associated with “Contractile apparatus,” “Translation initiation,” and “Proteosome complex.” Clusters were driven largely by enrichment of Myh1 (FC: 4.43), Eif4b (FC: 5.03), and Trim63 (FC: 5.84), respectively. Motif scanning of enriched sequences revealed a discrete 14 nucleotide-wide motif found most prominently at the junction between the protein coding region's termination sequence and the start of the 3′ untranslated region (UTR; E-Value: 1.1 e⁻⁰¹⁵). Proof of concept investigation of motif location along enriched transcripts Myh1 and Myl4 revealed 3′ UTR binding, suggesting RBM3 involvement in transcript half-life regulation. Together, these results demonstrate the potential influence of RBM3 in reshaping the skeletal muscle proteome through post-transcriptional regulation of mRNAs crucial to muscle adaptations.