Department of Genetics, Yale University School of Medicine, New Haven, CT, United States of America.
Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF), Barcelona, Spain.
PLoS Genet. 2018 Jul 3;14(7):e1007473. doi: 10.1371/journal.pgen.1007473. eCollection 2018 Jul.
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.
前体 mRNA 剪接是真核生物基因表达的一个关键步骤。转录组范围的剪接模式复杂，主要由一组不同的识别元件和相关的 RNA 结合蛋白调控。RES 复合物由三个不同的蛋白质（Bud13p、Pml1p 和 Snu17p）组成，参与酵母中的剪接。然而，RES 复合物对于脊椎动物剪接的重要性、与其活性相关的内含子特征以及其在发育中的作用尚不清楚。在这项研究中，我们在斑马鱼中生成了 RES 复合物三个组成部分的功能丧失突变体，并表明它们在早期发育过程中是必需的。突变体表现出明显的神经表型，大脑中的细胞死亡增加，分化神经元减少。对 bud13、snip1（pml1）和 rbmx2（snu17）突变体的转录组分析显示，内含子剪接存在全局缺陷，其中一部分内含子发生强烈的错误剪接。我们发现这些依赖 RES 的内含子较短，富含 GC，并且侧翼为 GC 耗尽的外显子，所有这些都是内含子定义的特征。我们使用这些特征开发并验证了一个预测模型，该模型可以对依赖 RES 的内含子进行分类。总之，我们的研究揭示了 RES 复合物在脊椎动物发育过程中的重要作用，并为其在剪接过程中的功能提供了新的见解。
