Purifying Selection on Exonic Splice Enhancers in Intronless Genes

Molecular Biology and Evolution
Rosina Savisaar, Laurence D Hurst

Abstract

Exonic splice enhancers (ESEs) are short nucleotide motifs, enriched near exon ends, that enhance the recognition of the splice site and thus promote splicing. Are intronless genes under selection to avoid these motifs so as not to attract the splicing machinery to an mRNA that should not be spliced, thereby preventing the production of an aberrant transcript? Consistent with this possibility, we find that ESEs in putative recent retrocopies are at a higher density and evolving faster than those in other intronless genes, suggesting that they are being lost. Moreover, intronless genes are less dense in putative ESEs than intron-containing ones. However, this latter difference is likely due to the skewed base composition of intronless sequences, a skew that is in line with the general GC richness of few exon genes. Indeed, after controlling for such biases, we find that both intronless and intron-containing genes are denser in ESEs than expected by chance. Importantly, nucleotide-controlled analysis of evolutionary rates at synonymous sites in ESEs indicates that the ESEs in intronless genes are under purifying selection in both human and mouse. We conclude that on the loss of introns, some but not all, ESE motifs are lost, the ...Continue Reading

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Citations

Nov 9, 2017·Genome Biology·Laurence D Hurst, Nizar N Batada
Aug 26, 2018·Genome Research·Rosina Savisaar, Laurence D Hurst
Sep 9, 2018·The Journal of Cell Biology·Ke WangHong Cheng
Dec 17, 2019·Molecular Biology and Evolution·Liam Abrahams, Laurence D Hurst
Apr 14, 2017·Human Genetics·Rosina Savisaar, Laurence D Hurst
May 15, 2021·Genome Biology and Evolution·Christine MordsteinGrzegorz Kudla

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