The power of fission: yeast as a tool for understanding complex splicing

Abstract

Pre-mRNA splicing is an essential component of eukaryotic gene expression. Many metazoans, including humans, regulate alternative splicing patterns to generate expansions of their proteome from a limited number of genes. Importantly, a considerable fraction of human disease causing mutations manifest themselves through altering the sequences that shape the splicing patterns of genes. Thus, understanding the mechanistic bases of this complex pathway will be an essential component of combating these diseases. Dating almost to the initial discovery of splicing, researchers have taken advantage of the genetic tractability of budding yeast to identify the components and decipher the mechanisms of splicing. However, budding yeast lacks the complex splicing machinery and alternative splicing patterns most relevant to humans. More recently, many researchers have turned their efforts to study the fission yeast, Schizosaccharomyces pombe, which has retained many features of complex splicing, including degenerate splice site sequences, the usage of exonic splicing enhancers, and SR proteins. Here, we review recent work using fission yeast genetics to examine pre-mRNA splicing, highlighting its promise for modeling the complex splicing seen in higher eukaryotes.

Long-read sequencing of nascent RNA reveals coupling among RNA processing events

“…S. pombe introns are very short with a median length of 56 nt, whereas exon lengths are similar to higher eukaryotes with an internal exon median of 137 nt (Kupfer et al 2004;Herzel 2015). This gene architecture is consistent with an intron definition mechanism in S. pombe (Romfo et al 2000;Shao et al 2012;Fair and Pleiss 2017), suggesting that splicing of individual introns in multi-intron transcripts may occur independently of one other. To globally investigate the progression of splicing during transcription, nascent RNA (nRNA) prepared from proliferating S. pombe cells was analyzed by both short-and long-read sequencing (LRS).…”

A genetic screen implicates a CWC16/Yju2/CCDC130 protein and SMU1 in alternative splicing in Arabidopsis thaliana

“…Following early genetic studies to identify components required for constitutive splicing in budding yeast (e.g., Vijayraghavan et al 1989), genetic screens in Arabidopsis and fission yeast are currently proving useful for dissecting more complex splicing pathways (Sasaki et al 2015;Fair and Pleiss 2016;Kanno et al 2016 and this study). Given the evolutionary conservation of many core and auxiliary spliceosomal proteins, knowledge gained from these model organisms could potentially be valuable therapeutically, since CWC16 and SMU1 in alternative splicing in plants www.rnajournal.org 1075 many human disease-causing mutations result in dysregulation of splicing (Douglas and Wood 2011;Scotti and Swanson 2015).…”

Identification of proteins associated with splicing factors Ntr1, Ntr2, Brr2 and Gpl1 in the fission yeast Schizosaccharomyces pombe

“…Nrl1 also suppresses homologous recombination-dependent R-loop formation and targets transcripts with cryptic introns to form heterochromatin domains at developmental genes and retrotransposons in the fission yeast Schizosaccharomyces pombe [3,4]. In this Extra View, we provide an analysis of the spliceosome complex and validate the specificity of interactions between Nrl1 and spliceosome by purifying TAP-tagged splicing factors Ntr1, Ntr2, Brr2 and SPAC20H4.06c, a G-patch domain-containing protein orthologous to human GPATCH1 protein, which we named Gpl1 (GPATCH1 like 1) [5,6]. We also discuss insights into the protein interaction network of splicing factors including a possible functional interaction between G-patch domain-containing protein Gpl1 and putative RNA helicase SPAC20H4.09.…”