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

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.

Single cell phototransfection of mRNAs encoding SARS-CoV2 spike and nucleocapsid into human astrocytes results in RNA dependent translation interference

“…The co-mRNA transfection data in Figure 3C show that in situ competition in the translation of Spike and Nuc mRNAs, are consistent with previous studies showing that endogenous cellular RNAs compete with each other for resources used in translation including association with RNA binding proteins that are integral to the process of translation (Asselbergs et al, 1978;Godefroy-Colburn and Thach, 1981;Jain et al, 2022;Ray et al, 1983;Schneider-Lunitz et al, 2021). Studies have further shown that SARS-CoV-2 infection results in reduced translation of host-cell mRNAs that have a preponderance of the same codons that are enriched in SARS-CoV-2 (Alonso and Diambra, 2020) also known as epistasis (Mogro et al, 2022;Fumagalli et al, 2023).…”

Protein Binding to Cis-Motifs in mRNAs Coding Sequence Is Common and Regulates Transcript Stability and the Rate of Translation

“…The described examples of stability regulation achieved via CDS binding are so far sparse and seem to be well-connected to the regulation of translation, which is in line with the above reasoning. In fact, dual regulatory effects of the same RBPs, impacting both mRNA stability and translation rates, have been postulated for some RBPs [ 19 ]. The two functionalities seem to be intertwined also in the case of CDS-binding RBPs.…”

Inhibiting a mRNA motif binding protein that mediates TGF-β1 upregulation of translation attenuates pulmonary fibrosis in mice

“…The copyright holder for this preprint this version posted October 23, 2022. ; https://doi.org/10.1101/2022.10.23.513405 doi: bioRxiv preprint 2017; Mo et al, 2021;Schneider-Lunitz et al, 2021). DDX3 overexpression has been implicated in many diseases including viral infections, inflammatory autoimmune diseases, and many forms of cancer (Bol et al, 2015;Kukhanova et al, 2020;Tantravedi et al, 2019).…”

“…RNA binding proteins (RBPs) are capable of regulating translation for the rapid modulation of protein synthesis from the existing mRNA (Hentze et al, 2018). RBPs can either sequester mRNA to slow translation, such as the P-body proteins AGO2 and UPF1; promote translation, such as DDX3, or actively suppress and degrade mRNA, such as CELF2 (Hubstenberger et al, 2017; Mo et al, 2021; Schneider-Lunitz et al, 2021). DDX3 overexpression has been implicated in many diseases including viral infections, inflammatory autoimmune diseases, and many forms of cancer (Bol et al, 2015; Kukhanova et al, 2020; Tantravedi et al, 2019).…”