“RNA-directed DNA methylation: Evolution of a complex epigenetic pathway in plants”

   Epigenetics refers to heritable changes in gene expression that are not caused due to alterations in DNA sequence. Epigenetic changes in plants involve DNA methylation, histone modification and RNA mediated  DNA methylation. DNA methylation is a broader phenomenon where methyl groups are added to cytosine bases. This occurs through various mechanisms which may or may not involve RNA. RNA-directed DNA methylation (RdDM) is a specific type of DNA methylation guided by RNA molecules. It was discovered in a study involving viroid-infected i.e., [Potato Spindle Tuber Viroid (PSTVd)] tobacco plants by Wassenegger and colleagues in 1994. The RdDM is an epigenetic process in plants that involves both short and long noncoding RNAs. The generation of these RNAs and the induction of RdDM rely on complex transcriptional machineries comprising two plant-specific RNA polymerase II (Pol II)–related RNA polymerases known as Pol IV and Pol V, as well as a host of auxiliary factors that include both novel and refashioned proteins. It involves two pathways i.e., canonical RdDM pathway and canonical RdDM pathway3. In plants RdDM is involved in transposon control and genome stability, development and reproduction, stress responses, short and long range signaling, transgene silencing and stress and RdDM-mediated epigenetic ‘memory’. It is observed that down-regulation of SlAGO4A gene which is a core factor of RdDM in tomato significantly improved tolerance to drought and salt stresses, whereas its overexpression resulted in opposite effects to these two stressors. This gene plays a negative role in salt and drought stress in tomato, probably through the modulation of DNA methylation as well as the classical RNAi pathway2. Upon analysing the wholegenome DNA methylation in rice, it is observed that methylation at CHH sites is high particularly in transposable elements (TEs) in the vegetative shoot apical meristem (SAM) relative to the differentiated SAM, and increases in the reproductive SAM via RdDM-pathway, indicating changes in DNA methylation begin in the SAM long before germ cell differentiation to protect the genome from harmful TEs1. RdDM which plays a great role in plant development and other regulatory processes, still remains unutilized for crop improvement in major crops. It can emerge as a new plant breeding technique by promoting/inhibiting transcriptional silencing of endogenous genes in major field crops. It can also help manipulate the flowering habit of plant which has been achieved in Arabidopsis so far and can be implemented in major crops. It can be used to induce male sterility in crops by silencing the fertility gene through modulating its pathway. It can be an efficient technique for providing biotic and abiotic stress tolerance and climate-resilient crops for the benefit of human kind. With the help of CRISPR/Cas9, DNA methylation at target locus can be achieved to create plants with desirable traits.

References:

1. HIGO, A., SAIHARA, N., MIURA, F., HIGASHI, Y., YAMADA, M., TAMAKI, S., ITO, T., TARUTANI, Y., SAKAMOTO, T., FUJIWARA, M. AND KURATA, T., 2020, DNA methylation is reconfigured at the onset of reproduction in rice shoot apical meristem. Nat. Commun., 11(1):4079.

2. HUANG, W., XIAN, Z., HU, G. AND LI, Z., 2016, SlAGO4A, a core factor of RNA-directed DNA methylation (RdDM) pathway, plays an important role under salt and drought stress in tomato. Mol. Breed., 36:1-13.

3. MATZKE, M. A., KANNO, T. AND MATZKE, A.J., 2015, RNA-directed DNA methylation: the evolution of a complex epigenetic pathway in flowering plants. Annu.Rev. Plant Biol., 66: 243-267.