Abstract

DNA methylation is considered to be the most important epigenetic mark in eukaryotes. Plant epigenetic mechanisms are remarkably complex when compared to mammals. The RdDM mechanism serves multiple functions including genome defense, imprinting, paramutation and gene expression control in response to growth, developmental or stress signals. The RdDM involves the production of 24-nt-long siRNAs that can be produced from heterochromatin repetitive sequences, inverted repeats or overlapping transcription. The hallmark of the RdDM is that cytosine methylation occurs in all sequence contexts. The sources and targets of RdDM reside in high-density heterochromatic regions of transposons and repetitive sequence and with less density in euchromatic regions. The core genes of RdDM epigenetic pathway are conserved between monocots and dicots and the mutation in any of these genes exhibits similar phenotypes. However, recent data show that methylation patterns and levels may vary in different genomes. Thus, RdDM plays much wider and more pronounced roles in complex genomes. The current review is aimed at reviewing the RdM mediated mechanisms and its role in plant biology. Further the evolutionary and biotechnology applications are described. As the technology for whole-genome microarrays and high throughput sequencing and profiling of DNA methylation are being used to analyze several plant genomes, comparative epigenomic approaches are identifying newer RdM players and targets. These developments will enable basic gene expression studies and enable biotechnological applications to improve plants for several traits.