single nucleotide polymorphism–based validation of exonic splicing enhancers单核苷酸polymorphism-based验证其实拼接增强剂.pdfVIP

Open access, freely available online PLoS BIOLOGY Single Nucleotide Polymorphism–Based Validation of Exonic Splicing Enhancers 1,2 2 2* 1,2,3* William G. Fairbrother , Dirk Holste , Christopher B. Burge , Phillip A. Sharp 1 Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America, 2 Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America, 3 McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America Because deleterious alleles arising from mutation are filtered by natural selection, mutations that create such alleles will be underrepresented in the set of common genetic variation existing in a population at any given time. Here, we describe an approach based on this idea called VERIFY (variant elimination reinforces functionality), which can be used to assess the extent of natural selection acting on an oligonucleotide motif or set of motifs predicted to have biological activity. As an application of this approach, we analyzed a set of 238 hexanucleotides previously predicted to have exonic splicing enhancer (ESE) activity in human exons using the relative enhancer and silencer classification by unanimous enrichment (RESCUE)-ESE method. Aligning the single nucleotide polymorphisms (SNPs) from the public human SNP database to the chimpanzee genome allowed inference of the direction of the mutations that created present-day SNPs. Analyzing the set of SNPs that overlap RESCUE-ESE hexamers, we conclude that nearly one-fifth of the mutations that disrupt predicted ESEs have been eliminated by natural selection (odds ratio = 0.82 6 0.05). This s