Abstract
Modification of DNA bases plays vital roles in the epigenetic control of gene expression in both animals and plants. Though much attention is given to the conventional epigenetic signature 5-methylcytosine (5-mC), the field of epigenetics is attracting increased scientific interest through the discovery of additional modifications of DNA bases and their roles in controlling gene expression. Theoretically, each of the DNA bases can be modified; however, modifications of cytosine and adenine only are known so far. This review focuses on the recent findings of the well-studied cytosine modifications and yet poorly characterized adenine modification which serve as an additional layer of epigenetic regulation in animals and discuss their potential roles in plants. Cytosine modification at symmetric (CG, CHG) and asymmetric (CHH) contexts is a key epigenetic feature. In addition to the ROS1 family mediated demethylation, Ten-Eleven Translocation family proteins-mediated hydroxylation of 5-mC to 5-hydroxymethylcytosine as additional active demethylation pathway are also discussed. The epigenetic marks are known to be associated with the regulation of several cellular and developmental processes, pluripotency of stem cells, neuron cell development, and tumor development in animals. Therefore, the most recently discovered N6-methyladenine, an additional epigenetic mark with regulatory potential, is also described. Interestingly, these newly discovered modifications are also found in the genomes which lack canonical 5-mC, signifying their independent epigenetic functions. These modified DNA bases are considered to be important players in epigenomics. The potential for combinatorial interaction among the known modified DNA bases suggests that epigenetic codon is likely to be substantially more complicated than it is thought today.
Highlights
Modification of DNA base is one of the main epigenetic mechanisms which regulate gene expression in both plants and animals
Epigenetic modifications influence the accessibility of the genomic regions for regulatory proteins, which affect chromatin structure, enhancer/promoter activity, and the transcriptional process
Methylation, are the known epigenetic changes with established maintenance mechanisms and some of the functions which enable their use as an epigenetic mark (Kumar, 2018a)
Summary
Modification of DNA base is one of the main epigenetic mechanisms which regulate gene expression in both plants and animals. Epigenetics is a branch of functional genomics which deals with regulation of gene expression through DNA base and histone modifications (Kumar, 2017). Identification of additional DNA base modifications (5-hmC and 6-mA), known to have epigenetic regulatory functions in animals, resulted in the increased significance of epigenomic studies.
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