title: CpG + CpNpG analysis of protein-coding sequences from tomato.
abstract: We develop codon-based models for simultaneously inferring the mutational effects of CpG and CpNpG methylation in coding regions. In a data set of 369 tomato genes, we show that there is very little effect of CpNpG methylation but a strong effect of CpG methylation affecting almost all genes. We further show that the CpNpG and CpG effects are largely uncorrelated. Our results suggest different roles of CpG and CpNpG methylation, with CpNpG methylation possibly playing a specialized role in defense against transposons and RNA viruses.
authors.affiliation: Bioinformatics Research Center, North Carolina State University, USA. asger@daimi.au.dk
authors.forename: Asger
authors.initials: A
authors.lastname: Hobolth
authors.forename: Rasmus
authors.initials: R
authors.lastname: Nielsen
authors.forename: Ying
authors.initials: Y
authors.lastname: Wang
authors.forename: Feinan
authors.initials: F
authors.lastname: Wu
authors.forename: Steven D
authors.initials: SD
authors.lastname: Tanksley
mesh_terms: D001482:Base Composition; D018899:CpG Islands / Q000235:genetics*; D019175:DNA Methylation; D017343:Genes, Plant; D018551:Solanum lycopersicum / Q000235:genetics*; D008957:Models, Genetic; D009154:Mutation