The frequency and distribution of methylatable DNA sequences in leguminous plant protein coding genes

Methylation of higher plant DNA occurs at up to 25% of all cytosines, primarily in the sequences CpG2 and CpNpG, both of which are over 80% methylated in wheat and tobacco (Gruenbaum et al 1981). CpG and CpNpG frequencies and distributions in the known sequences of cloned genes of leguminous plants were analyzed. In this sample CpG occurred at only 49% of the frequency expected if the bases were distributed at random. This lower frequency may be attributed to the fixation of mutations generated by a high rate of deamination of 5methylcytosine to thymine (Salser 1977). Consistent with this hypothesis, the product of CpG transitions, TpG and CpA, were significantly above their expected frequency. However CpNpG occurred at approximately expected levels and there was no significant increase in its transition products CpNpA and TpNpG. Possible explanations for this phenomenon are discussed. An analysis of the distribution of di- and trinucleotides across functionally classified regions of genes showed CpG to be asymmetrically distributed. CpG was on average significantly enriched in the 3' flanking regions compared to other regions. This may reflect a methylation-mediated regulatory role for this region in some legume genes.