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

Abstract

RNA-binding proteins (RBPs) can regulate more than a single aspect of RNA metabolism. We searched for such previously undiscovered multifunctionality within a set of 143 RBPs, by defining the predictive value of RBP abundance for the transcription and translation levels of known RBP target genes across 80 human hearts. This led us to newly associate 27 RBPs with cardiac translational regulation in vivo. Of these, 21 impacted both RNA expression and translation, albeit for virtually independent sets of target genes. We highlight a subset of these, including G3BP1, PUM1, UCHL5, and DDX3X, where dual regulation is achieved through differential affinity for target length, by which separate biological processes are controlled. Like the RNA helicase DDX3X, the known splicing factors EFTUD2 and PRPF8—all identified as multifunctional RBPs by our analysis—selectively influence target translation rates depending on 5’ UTR structure. Our analyses identify dozens of RBPs as being multifunctional and pinpoint potential novel regulators of translation, postulating unanticipated complexity of protein-RNA interactions at consecutive stages of gene expression.

Phosphorylation of T897 in the dimerization domain of Gemin5 modulates protein interactions and translation regulation

“…Multiple evidences suggest that RBPs, including Gemin5, play a key role as multifunctional gene expression regulators [50] . Additionally, cumulative data adds up in support of the role of Gemin5 outside of the SMN complex, contributing to RNA-dependent processes different than spliceosome assembly.…”

Integrative analysis of macrophage ribo-Seq and RNA-Seq data define glucocorticoid receptor regulated inflammatory response genes into distinct regulatory classes

“…Ribo-seq and RNA-seq were analyzed as previously described [28] . Before genome mapping, Ribo-seq reads were clipped to remove residual adapters using the FASTX toolkit ( https://hannonlab.cshl.edu/fastx_toolkit/ ).…”

The human DEAD-box helicase DDX3X as a regulator of mRNA translation

“…In most studies, inactivation of DDX3X increased translation efficiency of only a few mRNAs, while most targets had decreased translation efficiencies ( Phung et al, 2019 ; Calviello et al, 2021 ; Gong et al, 2021 ; Hoye et al, 2022 ). In contrast, a recent integrated analysis of 80 human heart translatomes found translation efficiency of most DDX3X targets negatively correlated with DDX3X expression levels ( Schneider-Lunitz et al, 2021 ). In addition, higher predicted structural stability of the target mRNA’s 5′UTR was observed in negatively correlating translation efficiency targets ( Schneider-Lunitz et al, 2021 ), contradicting findings from many other studies where DDX3X positively regulated translation of highly structured mRNAs.…”

“…In contrast, a recent integrated analysis of 80 human heart translatomes found translation efficiency of most DDX3X targets negatively correlated with DDX3X expression levels ( Schneider-Lunitz et al, 2021 ). In addition, higher predicted structural stability of the target mRNA’s 5′UTR was observed in negatively correlating translation efficiency targets ( Schneider-Lunitz et al, 2021 ), contradicting findings from many other studies where DDX3X positively regulated translation of highly structured mRNAs. Of note, this is the only study where DDX3X levels were not manipulated experimentally.…”