Regulation of the copy number of genes through epigenetics is maintained by methylation of nucleic acid, modifications of histones, and change in the structure of chromosome into a high level of packaging. Chromatin modifications are associated with the changes in chromatin states that result from alterations in the histones and modifications in the specific proteins and small RNAs that associate with a genomic region. Methylation of nucleic acid and modifications of histone are considered as the traits concerned mainly with epigenetics. In recent years, regulation of the copy number of genes through methylation of nucleic acid is emerging as a new area of interest in the field of research in plants, which has significant impact on the developmental process and transcriptional regulation. DNA methylation is involved in various aspects in plants like evolution of plant species, defenses, resistance, shoot regeneration, sex determination, and developmental pathways. In genomes, DNA methylation is partitioned into CG and non-CG methylation pattern, where non-CG methylation is known as CHG and CHH. Methylation pattern has been classified into maintenance and de novo DNA methylation, which occur by DNA methyl transferase (DNMtase). DNMtase reported in plants is classified mainly into two categories, that is, maintenance methyl transferase and de novo methyl transferase. Genome-level study of nucleic acid methylation in plants like Arabidopsis, maize, and rice has shown that H3K9me2-dependent pathway, ribonucleic acid directed nucleic acid methylation pathway, and mobile siRNAs are involved in the regulation of the copy number of genes. Recent technological advances have sped up the research in the area of omics-based genomic approaches and high-throughput analysis for the involvement of nucleic acid methylation in plants.
Yadav1, V. K., Rai, K. M., Kumar, N., & Yadav, V. K. (2019). Regulation of gene expression by global methylation pattern in plants development. In OMICS-Based Approaches in Plant Biotechnology (pp. 287–301). wiley. https://doi.org/10.1002/9781119509967.ch13