An Evo-Devo approach to the role of RNA-RBP binding on Alternative Splicing – EvoRNAs

Alternative splicing (AS) is one of the major sources of transcriptome and proteome diversity in higher organisms and strongly influences phenotypic diversity. Cis-regulatory elements located in exons or introns influence AS through interaction with trans-acting proteins, notably serine/arginine-rich proteins, such as the NUCLEAR SPECKLE RNA-BINDING PROTEIN A (NSRa), and heterogeneous nuclear ribonucleoproteins, like the GLYCINE-RICH RNA-BINDING PROTEIN 7 (GRP7). In addition to pre-mRNAs, long non-coding RNAs (lncRNAs) specifically bind to NSRa and GRP7 proteins and affect their function in AS regulation of NSRa and GRP7 target genes. The EvoRNAs project aims to leverage the evolution of RNA-RNA Binding Protein (RBP) interactions and machine learning to predict RNA recognition rules of two highly conserved key RBPs and their interacting lncRNAs and mRNAs, to assess the impact on the generation of splicing diversity across evolutionary distant species. To avoid the common bottleneck inherent to sequence homology driven-search for conserved patterns in RNAs, we propose here a new approach which is centered on highly conserved RBP partners (NSRa and GRP7) interacting with lncRNAs and mRNAs. Using a multidisciplinary approach including RNA biochemistry, evolutionary biology and modelling, we will (1) define the RNA binding preference of NSR and GRP7 across divergent species; (2) determine the functional conservation of these proteins during evolution; (3) use machine learning to define the hallmarks of RBP binding to lncRNA; (4) test the robustness of the model to predict new lncRNAs affecting alternative splicing patterns through the plant lineage, including crops. The project is based on a high complementarity of disciplines and expertises (RNA biochemistry and genomics, Evo-devo analysis and modelling) within the consortia. We expect the results of the EVORNA project to shed light on the molecular mechanisms driving the co-evolution of lncRNA with their protein partners across species. More generally, results and methods from EvoRNAs may allow predicting the regulatory consequences of genetic variation in both lncRNA and/or RBP (natural polymorphisms or disease associated variants) on their interaction and regulatory consequences on their activity in splicing regulation. This may establish a new molecular mechanism for the regulation of AS in evolutionary distant species. These may have broad impacts to understand the basis of regulatory variation on lncRNAs and RBP partners spanning from plant breeding to predicting variant functions on disease mechanisms.