Pre-mRNA splicing is a critical step of gene expression in eukaryotes. Transcriptome-wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA-binding proteins. The retention and splicing (RES) complex is formed by three different proteins (Bud13p, Pml1p and Snu17p) and is involved in splicing in yeast. However, the importance of the RES complex for vertebrate splicing, the intronic features associated with its activity, and its role in development are unknown. In this study, we have generated loss-of-function mutants for the three components of the RES complex in zebrafish and showed that they are required during early development. The mutants showed a marked neural phenotype with increased cell death in the brain and a decrease in differentiated neurons. Transcriptomic analysis of bud13, snip1 (pml1) and rbmx2 (snu17) mutants revealed a global defect in intron splicing, with strong mis-splicing of a subset of introns. We found these RES-dependent introns were short, rich in GC and flanked by GC depleted exons, all of which are features associated with intron definition. Using these features, we developed and validated a predictive model that classifies RES dependent introns. Altogether, our study uncovers the essential role of the RES complex during vertebrate development and provides new insights into its function during splicing.

This research was supported by the National Institutes of Health (https://www.nih.gov/) grants R21 HD073768, R01 HD074078, GM103789, GM102251, GM101108 and 583 GM081602 (AJG). AJG is supported by the Howard Hughes Medical Institute Faculty Scholar program (http://www.hhmi.org/programs/biomedical-research/faculty-scholars), the March of Dimes (https://www.marchofdimes.org/), the Yale Scholars Program (https://globalscholars.yale.edu/) and the Whitman fellowship (http://www.mbl.edu/research/whitman-fellowships/) funds provided by E.E. Just, L.B. Lemann, E. Evelyn and M. Spiegel, the H. Keffer Hartline and E.F. MacNichol Jr at the Marine Biological Laboratory in Woods Hole, MA. MI is supported by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No ERC-StG-LS2-637591) (https://erc.europa.eu/) and the Spanish Ministry of Economy and Competitiveness (BFU2014-55076-P, and the Centro de Excelencia Severo Ochoa 2013-2017’, SEV-2012-0208 to the CRG) (http://www.mineco.gob.es/). MAMM is supported by Programa de Movilidad en Áreas de Investigación priorizadas por la Consejería de Igualdad, Salud y Políticas Sociales de la Junta de Andalucía (http://www.juntadeandalucia.es/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.