Computational Identification of Post Translational Modification Regulated RNA Binding Protein Motifs

• Published in: PloS one 2015-09, Vol.10 (9), p.e0137696-e0137696
• Main Authors: Brown, Andrew S, Mohanty, Bidyut K, Howe, Philip H
• Format: Article
• Language: English
• Subjects: 3' Untranslated Regions - physiology; Acids; Algorithms; Amino Acid Motifs; Biochemistry; Bioinformatics; Biological evolution; Computation; Computer applications; Databases, Nucleic Acid; Databases, Protein; Exonuclease; Experimentation; Gene expression; Genomes; Localization; mRNA; Mutation; Phosphorylation; Post-translation; Protein Processing, Post-Translational; Proteins; Ribonucleic acid; RNA; RNA modification; RNA-binding protein; RNA-Binding Proteins - chemistry; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; Sequence Analysis, Protein - methods; Signal transduction; Transduction; Translation
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0137696

RNA and its associated RNA binding proteins (RBPs) mitigate a diverse array of cellular functions and phenotypes. The interactions between RNA and RBPs are implicated in many roles of biochemical processing by the cell such as localization, protein translation, and RNA stability. Recent discoveries of novel mechanisms that are of significant evolutionary advantage between RBPs and RNA include the interaction of the RBP with the 3' and 5' untranslated region (UTR) of target mRNA. These mechanisms are shown to function through interaction of a trans-factor (RBP) and a cis-regulatory element (3' or 5' UTR) by the binding of a RBP to a regulatory-consensus nucleic acid motif region that is conserved throughout evolution. Through signal transduction, regulatory RBPs are able to temporarily dissociate from their target sites on mRNAs and induce translation, typically through a post-translational modification (PTM). These small, regulatory motifs located in the UTR of mRNAs are subject to a loss-of-function due to single polymorphisms or other mutations that disrupt the motif and inhibit the ability to associate into the complex with RBPs. The identification of a consensus motif for a given RBP is difficult, time consuming, and requires a significant degree of experimentation to identify each motif-containing gene on a genomic scale. We have developed a computational algorithm to analyze high-throughput genomic arrays that contain differential binding induced by a PTM for a RBP of interest-RBP-PTM Target Scan (RPTS). We demonstrate the ability of this application to accurately predict a PTM-specific binding motif to an RBP that has no antibody capable of distinguishing the PTM of interest, negating the use of in-vitro exonuclease digestion techniques.