Title: A systematic survey of PRMT interactomes reveals the key roles of arginine methylation in the global control of RNA splicing and translation

Abstract

Objectives: Thousands of proteins undergo arginine methylation, a widespread post-translational modification catalyzed by several protein arginine methyltransferases (PRMTs). However, global understanding of their molecular mechanisms and biological functions is limited due to the lack of a complete picture of the catalytic network for each PRMT and the absence of reliable antibodies and mechanically well-defined ‘erasers’ and ‘readers’. Here, we systematically identified interacting proteins for all human PRMTs and hope to contribute to arginine methylation field and help the study of related biological processes. Results: Using a sensitive BioID technology and mass spectrometry, we systematically characterized the interactome and the substrate specificity of all known human PRMTs. The results demonstrated significant overlapping of interactomes of human PRMTs with the known methylarginine-containing proteins. Different PRMTs are functionally redundant with a high degree of overlap in their substrates and high similarities between their putative methylation motifs. After bioinformatics analysis and experimental validation, we revealed that RNA-binding proteins (RBPs) involved in regulating RNA splicing and translation are highly enriched in PRMT interactomes and undergo extensive arginine methylation, indicating their importance in regulating RNA metabolism. Applying RNA-seq and Ribo-seq, we demonstrated that the inhibition of PRMTs leads to global alteration of splicing and translation inhibition.In particular, ribosomal proteins are extensively modified with methylarginine, and mutations in their methylation sites suppress ribosome assembly, translation, and eventually cell growth, indicating arginine methylation of ribosomal proteins is critical to ribosomal assembly. Conclusions: This study provides new insights into biological functions of PRMTs and links individual PRMTs to their arginine methylation events, revealing critical functions of arginine methylation in regulating RNA splicing and translation. We hope that the new findings and the data analysis methods in this study will be of broad interest to investigators in the fields of protein modification and RNA biology. Graphical Abstract: Arginine methylation is highly involved in RNA splicing and translation. The putative PRMT substrates were subjected to protein-protein interaction analysis from the STRING database (v10.5, the minimum required interaction score was set to high confidence at 0.7), the resulting networks were clustered by MCODE in Cytoscape software. The orange nodes indicate functions related to translation and the cyan nodes indicate functional enrichment in RNA processing.