Assessing the fraction of short-distance tandem splice sites under purifying selection

Abstract

Many alternative splice events result in subtle mRNA changes, and most of them occur at short-distance tandem donor and acceptor sites. The splicing mechanism of such tandem sites likely involves the stochastic selection of either splice site. While tandem splice events are frequent, it is unknown how many are functionally important. Here, we use phylogenetic conservation to address this question, focusing on tandems with a distance of 3-9 nucleotides. We show that previous contradicting results on whether alternative or constitutive tandem motifs are more conserved between species can be explained by a statistical paradox (Simpson's paradox). Applying methods that take biases into account, we found higher conservation of alternative tandems in mouse, dog, and even chicken, zebrafish, and Fugu genomes. We estimated a lower bound for the number of alternative sites that are under purifying (negative) selection. While the absolute number of conserved tandem motifs decreases with the evolutionary distance, the fraction under selection increases. Interestingly, a number of frameshifting tandems are under selection, suggesting a role in regulating mRNA and protein levels via nonsense-mediated decay (NMD). An analysis of the intronic flanks shows that purifying selection also acts on the intronic sequence. We propose that stochastic splice site selection can be an advantageous mechanism that allows constant splice variant ratios in situations where a deviation in this ratio is deleterious.

Alternative Splicing of RNA Triplets Is Often Regulated and Accelerates Proteome Evolution

“…Both isoforms of this NAGNAG event are observed in ESTs from human, mouse, and chicken, and the potential for alternative splicing is conserved at the sequence level to lizard (Figure 1D). Consistent with this example, a previous analysis of EST databases suggested that a subset of alternatively spliced NAGNAGs are under purifying selection in vertebrates [25]. We systematically assessed the global conservation of NAGNAG isoform levels using RNA-Seq data generated from eight mouse tissues (brain, colon, kidney, liver, lung, skeletal muscle, spleen, and testes).…”

Quantifying Student Learning: How to Analyze Assessment Data

“…Simpson's paradox has been shown to affect statistical results in molecular biology (Hiller et al 2008), epidemiology (Asch and Armstrong 2007), and ecology (Piñeiro et al 2006). The paradox states that a statistically significant relationship in one direction, when analyzed with a covariate, can result in a relationship in the opposite direction.…”

Cloning and transcriptional expression of mouse mannosyltransferase IV/V cDNA, which is involved in the synthesis of lipid-linked oligosaccharides

“…Hence, the variant protein might not have any mannosyltransferase activities. Although the alternative donor site selection event might reflect biological significance, 26,27) the function of the variant is unknown at present.…”

“…5(A)). Taking into consideration the GT-AG rule for splicing, the nucleotide sequence of the genomic DNA and the cDNA of mALG11, and the occurrence of the GTAG sequence before the donor site of intron 2 in the variant cDNA, the GTAG insertion may have derived from a splicing variation from the normal donor site GT of intron 2 to the neighboring GT 4 bases downstream of the normal donor site GT of the intron 2 (from … AGAAAAA AGGTATGC … to … AGAAAAAG-TAG ATGC …) by alternative donor site selection 26,27) (Fig. 5(B)).…”