Modelling mutational and selection pressures on dinucleotides in eukaryotic phyla--selection against CpG and UpA in cytoplasmically expressed RNA and in RNA viruses.

ABSTRACT:

Background

Loss of CpG dinucleotides in genomic DNA through methylation-induced mutation is characteristic of vertebrates and plants. However, these and other eukaryotic phyla show a range of other dinucleotide frequency biases with currently uncharacterized underlying mutational or selection mechanisms. We developed a parameterized Markov process to identify what neighbour context-dependent mutations best accounted for patterns of dinucleotide frequency biases in genomic and cytoplasmically expressed mRNA sequences of different vertebrates, other eukaryotic groups and RNA viruses that infect them.

Results

Consistently, 11- to 14-fold greater frequencies of the methylation-associated mutation of C to T upstream of G (depicted as C→T,G) than other transitions best modelled di

SUBMITTER: Simmonds P 

PROVIDER: S-EPMC3829696 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature