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Dual-function RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes

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Title:Dual-function RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes
Creators Name:Schneider-Lunitz, V. and Ruiz-Orera, J. and Hubner, N. and van Heesch, S.
Abstract:RNA-binding proteins (RBPs) are key regulators of RNA metabolism. Many RBPs possess uncharacterized RNA-binding domains and localize to multiple subcellular compartments, suggesting their involvement in multiple biological processes. We searched for such multifunctionality within a set of 143 RBPs by integrating experimentally validated target genes with the transcriptomes and translatomes of 80 human hearts. This revealed that RBP abundance is predictive of the extent of target regulation in vivo, leading us to newly associate 27 RBPs with translational control. Amongst those were several splicing factors, of which the muscle specific RBM20 modulated target translation rates through switches in isoform production. For 21 RBPs, we newly observed dual regulatory effects impacting both mRNA levels and translation rates, albeit for virtually independent sets of target genes. We highlight a subset, including G3BP1, PUM1, UCHL5, and DDX3X, where dual regulation is achieved by differential affinity for targets of distinct length and functionality. Strikingly, in a manner very similar to DDX3X, the known splicing factors EFTUD2 and PRPF8 selectively influence target translation rates depending on 5’ UTR structure. Our results indicate unanticipated complexity of protein-RNA interactions at consecutive stages of gene expression and implicate multiple core splicing factors as key regulators of translational output.
Keywords:RBP, Dual-Function, Translational Efficiency, Ribosome Profiling, Ribo-Seq, Heart, Translational Regulation, CLIP-seq
Publisher:Cold Spring Harbor Laboratory Press
Article Number:2021.04.13.439465
Date:13 April 2021
Official Publication:https://doi.org/10.1101/2021.04.13.439465

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