title: SNP Formation Bias in the Murine Genome Provides Evidence for Parallel Evolution.
abstract: In this study, we show novel DNA motifs that promote single nucleotide polymorphism (SNP) formation and are conserved among exons, introns, and intergenic DNA from mice (Sanger Mouse Genomes Project), human genes (1000 Genomes), and tumor-specific somatic mutations (data from TCGA). We further characterize SNPs likely to be very recent in origin (i.e., formed in otherwise congenic mice) and show enrichment for both synonymous and parallel DNA variants occurring under circumstances not attributable to purifying selection. The findings provide insight regarding SNP contextual bias and eukaryotic codon usage as strategies that favor long-term exonic stability. The study also furnishes new information concerning rates of murine genomic evolution and features of DNA mutagenesis (at the time of SNP formation) that should be viewed as "adaptive."
authors.affiliation: Department of Biology, University of Alabama at Birmingham.
authors.forename: Zackery E
authors.initials: ZE
authors.lastname: Plyler
authors.affiliation: Department of Computer and Information Sciences, University of Alabama at Birmingham.
authors.forename: Aubrey E
authors.initials: AE
authors.lastname: Hill
authors.affiliation: Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham.
authors.forename: Christopher W
authors.initials: CW
authors.lastname: McAtee
authors.affiliation: Department of Biostatistics, University of Alabama at Birmingham.
authors.forename: Xiangqin
authors.initials: X
authors.lastname: Cui
authors.affiliation: Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham.
authors.forename: Leah A
authors.initials: LA
authors.lastname: Moseley
authors.affiliation: Department of Pediatrics, Emory University School of Medicine esorscher@emory.edu.
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Sorscher
mesh_terms: D000818:Animals; D016477:Artifacts; D003062:Codon; D018076:DNA, Complementary / Q000737:chemistry; D019143:Evolution, Molecular; D005091:Exons; D016678:Genome; D006579:Heterozygote; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D051379:Mice / Q000235:genetics*; D009154:Mutation; D009369:Neoplasms / Q000235:genetics; D059372:Nucleotide Motifs; D020641:Polymorphism, Single Nucleotide
chemical_list: D003062:Codon; D018076:DNA, Complementary
keywords: SNP formation bias; mutation; parallel evolution