Identification, Classification and Quantitative Expression Analysis of Selected DNA Methyltransferase Genes during Plant Development in Common Bean (Phaseolus vulgaris L.)

DNA methylation is an epigenetic mechanism that is responsible for controlling gene expression during plant growth and development, defense responses and genome stability. Methylation patterns are found to be more prevalent in plants when compared to other organisms due to their occurrence in CpG, CpNpG, and CpNpN (N=A, T or C) contexts. Methylation is catalyzed by an enzyme called DNA methyltransferase (Dnmt). Based on model plant species, there are four classes of Dnmts identified: DNA Methyltransferase (MET), Chromo-methyltransferase (CMT), Domains Rearranged Methyltransferase (DRM), and DNA methyltransferase 2 (Dnmt2) which are differentiated based on their conserved domains. Previous Dnmt studies identified MET, CMT and DRM as functional Dnmts. In this study, we used the BLASTP sequence analysis to identify and clone three homologous Dnmts (MET1, CMT2 and DRM2) using sequences derived from three common bean genotypes: G19833 (sequenced genome), Sierra (resistant), and Olathe (susceptible) to Uromyces appendiculatus (rust race-53). Following cloning and sequencing, these genes were classified based on their evolutionary relationships with homologue Dnmts from other plant species. Analysis of gene expression using quantitative PCR revealed that selected Dnmts are expressed at all developmental stages tested (seedling, flowering and pod). The amino acid sequences obtained from cloning were used to develop unique polypeptide antibodies for further analysis to identify Dnmt-DNA interaction throughout the common bean genome using ChIP-seq methods.