Global analysis of alternative splicing uncovers developmental regulation of nonsense-mediated decay in C. elegans

Abstract

Alternative splicing coupled to nonsense-mediated decay (AS-NMD) is a mechanism for post-transcriptional regulation of gene expression. We analyzed the global effects of mutations in seven genes of the C. elegans NMD pathway on AS isoform ratios. We find that mutations in two NMD factors, smg-6 and smg-7, have weaker global effects relative to mutations in other smg genes. We did an in-depth analysis of 12 pre-mRNA splicing factor genes that are subject to AS-NMD. For four of these, changes in the ratio of alternatively spliced isoforms during development are caused by developmentally regulated inhibition of NMD, and not by changes in alternative splicing. Using sucrose gradient analysis of mRNAs undergoing translation, we find several examples of NMD-dependent enrichment of premature termination codon (PTC) isoforms in the monosome fraction. In contrast, we present evidence of two genes for which the PTC-containing isoforms are found in polysomes and have a translational profile similar to non-PTC-containing transcripts from the same gene. We propose that NMD of certain alternatively spliced isoforms is regulated, and that some stabilized NMD targets may be translated.

Nutritional control of mRNA isoform expression during developmental arrest and recovery in C. elegans

“…The rsp-1 and rsp-6 exons we identify as alternatively expressed (Fig. 7) have been shown to include premature stop codons and trigger nonsense-mediated decay (Morrison et al 1997;Barberan-Soler et al 2009;Ramani et al 2009), demonstrating that inclusion of premature stop codons is under nutritional control. In summary, our results show that factors controlling mRNA metabolism are themselves regulated by alternative isoform expression in response to nutrient availability.…”

“…The C. elegans genome encodes eight serine/arginine (SR)-rich proteins, which function in splice site selection as well as the transcription and export of mRNAs (Long and Cáceres 2009). Many of these genes are regulated by alternative splicing linked to nonsense-mediated decay (Ni et al 2007;Barberan-Soler et al 2009). It has been suggested that this is a form of autoregulation in that high levels of a splicing factor lead to increased inclusion of highly conserved exons with premature stop codons, triggering nonsense-mediated decay (Sureau 2001).…”

Frac-seq reveals isoform-specific recruitment to polyribosomes

“…One possibility is that alternative splicing alters the topology of these cis-acting regulatory elements, resulting in isoform-specific fates Staudacher et al 2011). Another possibility is that multifunctional cis-acting elements, such as the FN1 EDA splicing enhancer, may directly couple splicing decisions to translational control (Lu and Cullen 2003;Nott et al 2004;Barberan-Soler et al 2009). There is also new evidence supporting the idea of functional microRNA targets sites within coding exons (Hausser et al 2013).…”

Quantitative RNA-seq meta analysis of alternative exon usage in C. elegans

“…In humans about 95% of genes have detectable alternative splice forms (Pan et al, 2008). The nematode is a powerful model to explore networks involved in alternative splicing regulation and the physiological impact of their perturbation (Barberan-Soler et al, 2009, 2011, Zahler, 2012. Recent efforts have been made to systematically identify all possible splice variants of the complete C. elegans genome using transcriptome sequencing (RNA-seq) (Ramani et al, 2011, Gerstein et al, 2014, Hillier et al, 2009, Kuroyanagi et al, 2014, Ragle et al, 2015.…”

“…Together, these observations support the widespread existence of biological noise in the splicing process.The sensitivity of modern deep sequencing methods for transcriptome characterisation ensures that even rare aberrantly spliced messengers will be detected alongside functional splice forms. Traces of messengers targeted for decay, that are accumulating in NMD mutants, can be detected in wild type individuals as well (Barberan-Soler et al, 2009, Ramani et al, 2009). Moreover, a recent study unveiled a significant decrease in splicing accuracy correlated with age in C. elegans (Heintz et al, 2016).…”