Single nucleotide polymorphism-based validation of exonic splicing enhancers.

Area of Science:

• Genetics
• Evolutionary Biology
• Bioinformatics

Background:

• Deleterious mutations are removed by natural selection, leading to their underrepresentation in common genetic variation.
• Oligonucleotide motifs with biological activity are subject to evolutionary pressures.
• Exonic splicing enhancers (ESEs) play a crucial role in pre-mRNA splicing.

Purpose of the Study:

• To develop and apply a novel approach, VERIFY (variant elimination reinforces functionality), to quantify natural selection acting on functional motifs.
• To assess the extent to which natural selection has eliminated mutations disrupting predicted exonic splicing enhancers (ESEs).

Main Methods:

• The VERIFY approach infers the direction of mutations creating single nucleotide polymorphisms (SNPs) by aligning human SNPs to the chimpanzee genome.
• Analysis of SNPs overlapping with 238 hexanucleotides predicted to have ESE activity using the RESCUE-ESE method.
• Quantification of natural selection by comparing the observed frequency of mutations disrupting ESEs to expected frequencies.

Main Results:

• Nearly one-fifth of mutations disrupting predicted ESEs have been eliminated by natural selection (odds ratio = 0.82 +/- 0.05).
• Natural selection is strongest on predicted ESEs located near splice sites.
• The VERIFY method provides a quantitative measure of natural selection acting on candidate functional motifs.

Conclusions:

• The study demonstrates a novel method for quantifying natural selection on functional motifs.
• Features such as proximity to splice sites and disruption of predicted ESEs are important indicators for identifying disease-causing variants.
• The findings highlight the significant role of natural selection in shaping genetic variation within functional elements.