Regulation of splicing factors by alternative splicing and NMD is conserved between kingdoms yet evolutionarily flexible.

Liana F Lareau,Steven E Brenner

doi:10.1093/molbev/msv002

Abstract

Ultraconserved elements, unusually long regions of perfect sequence identity, are found in genes encoding numerous RNA-binding proteins including arginine-serine rich (SR) splicing factors. Expression of these genes is regulated via alternative splicing of the ultraconserved regions to yield mRNAs that are degraded by nonsense-mediated mRNA decay (NMD), a process termed unproductive splicing (Lareau et al. 2007; Ni et al. 2007). As all human SR genes are affected by alternative splicing and NMD, one might expect this regulation to have originated in an early SR gene and persisted as duplications expanded the SR family. But in fact, unproductive splicing of most human SR genes arose independently (Lareau et al. 2007). This paradox led us to investigate the origin and proliferation of unproductive splicing in SR genes. We demonstrate that unproductive splicing of the splicing factor SRSF5 (SRp40) is conserved among all animals and even observed in fungi; this is a rare example of alternative splicing conserved between kingdoms, yet its effect is to trigger mRNA degradation. As the gene duplicated, the ancient unproductive splicing was lost in paralogs, and distinct unproductive splicing evolved rapidly and repeatedly to take its place. SR genes have consistently employed unproductive splicing, and while it is exceptionally conserved in some of these genes, turnover in specific events among paralogs shows flexible means to the same regulatory end.

Highlights

Evolution has provided diverse and sometimes startling ways to regulate gene expression, taking advantage of essentially every step from the birth to the death of an mRNA (Moore 2005)
Some serine rich (SR) proteins can bind their own pre-mRNAs and promote unproductive splicing events (Jumaa and Nielsen 1997; Lejeune et al 2001; Sureau et al 2001); SRSF4, a gene we investigate in this study, was shown to bind its own pre-mRNA and autoregulate its protein levels (A€ nko€ et al 2010, 2012)
Cassette exons in all three human genes have been shown to trigger nonsense-mediated mRNA decay (NMD) when included; when NMD was inhibited in HeLa cells, the exon-included mRNAs were dramatically stabilized, representing between 40% and 70% of the spliced mRNA from each gene (Lareau et al 2007)

Summary

Introduction

Evolution has provided diverse and sometimes startling ways to regulate gene expression, taking advantage of essentially every step from the birth to the death of an mRNA (Moore 2005). Regulation can impose strong constraints on sequence evolution; the most pronounced sequence constraints have resulted in ultraconserved DNA elements, long regions of at least 200 nt of perfect identity between human and rodent genomes (Bejerano et al 2004). All 11 human SR genes are alternatively spliced to produce mRNAs with early stop codons, which are degraded by nonsense-mediated mRNA decay (NMD) rather than producing protein (Lareau et al 2007; Ni et al 2007) This process, known as unproductive splicing, downregulates expression by shunting a fraction of a gene’s pre-mRNA into a decay pathway. Ultraconserved elements overlap poison cassette exons in four SR genes, and the poison cassette exons of other SR genes have exceptional sequence identity between human and mouse

Methods

Results

Conclusion