Prp40 and early events in splice site definition

Abstract

The alternative splicing (AS) of precursor messenger RNA (pre-mRNA) is a tightly regulated process through which introns are removed to leave the resulting exons in the mRNA appropriately aligned and ligated. The AS of pre-mRNA is a key mechanism for increasing the complexity of proteins encoded in the genome. In humans, more than 90% of genes undergo AS, underscoring the importance of this process in RNA biogenesis. As such, AS misregulation underlies multiple human diseases. The splicing reaction is catalyzed by the spliceosome, a highly dynamic complex that assembles at or near the intron/exon boundaries and undergoes sequential conformational and compositional changes during splicing. The initial recognition of splice sites defines the exons that are going to be removed, which is a critical step in the highly regulated splicing process. Although the available lines of evidence are increasing, the molecular mechanisms governing AS, including the initial interactions occurring at intron/exon boundaries, and the factors that modulate these critical connections by functioning as a scaffold for active-site RNAs or proteins, remain poorly understood. In this review, we summarize the major hallmarks of the initial steps in the splicing process and the role of auxiliary factors that contribute to the assembly of the spliceosomal complex. We also discuss the role of the essential yeast Prp40 protein and its mammalian homologs in the specificity of this pre-mRNA processing event. In addition, we provide the first exhaustive phylogenetic analysis of the molecular evolution of Prp40 family members. WIREs RNA 2016, 7:17-32. doi: 10.1002/wrna.1312 For further resources related to this article, please visit the WIREs website.

Physiologic Expression of Sf3b1 K700E Causes Impaired Erythropoiesis, Aberrant Splicing, and Sensitivity to Therapeutic Spliceosome Modulation

“…Over 90% of human genes undergo alternative splicing of precursor messenger RNA (pre-mRNA), a tightly regulated process that dramatically increases the complexity of the protein repertoire encoded by the genome (Becerra et al, 2015). The 5’ splice site of an intron is typically defined by a GU dinucleotide.…”

Workflow for Genome-Wide Determination of Pre-mRNA Splicing Efficiency from Yeast RNA-seq Data

“…Through interactions with many spliceosome subunits and with the phosphorylated C-terminal domain of the RNA polymerase II, the Prp40 protein is important for cotranscriptional spliceosome assembly (reviewed in [45]). The prp40-1 temperature-sensitive mutant [44] exerts a global splicing defect when shifted to nonpermissive temperature [24], which we confirmed by running the published RNA-seq dataset through our pipeline (Figures 3(c) and 3(d)).…”

Human PRPF40B regulates hundreds of alternative splicing targets and represses a hypoxia expression signature

“…Most information of PRPF40A/B is inferred from their budding yeast homolog PRP40 (Becerra et al 2016), which is part of the U1 small nuclear ribonucleoprotein (snRNP) (Kao and Siliciano 1996) that recognizes the 5 ′ ss early in splicing (Roca et al 2013;Tan et al 2016). PRP40 bridges between U1 on the 5 ′ ss side, and branchpoint-binding protein (BBP) and Mud2p on the BPS and 3 ′ ss (Abovich and Rosbash 1997).…”

“…PRP40 bridges between U1 on the 5 ′ ss side, and branchpoint-binding protein (BBP) and Mud2p on the BPS and 3 ′ ss (Abovich and Rosbash 1997). Prp40 contains two WW and four FF domains in its primary sequence, and it binds BBP directly through the WW domain whereas the binding to Mud2p occurs indirectly (Becerra et al 2016).…”

“…The Prp40 protein structure is shared with a relatively small number of proteins in humans, including PRPF40A, PRPF40B, and hTCERG1, all involved in the coupling of splicing and transcription elongation (Becerra et al 2016). The closest human ortholog PRPF40A (PRP40 pre-mRNA processing factor 40 homolog A) has a similar function as yeast Prp40.…”