Journal of Genetics

, Volume 92, Issue 3, pp 629–666 | Cite as

Roles, and establishment, maintenance and erasing of the epigenetic cytosine methylation marks in plants

  • SUSHIL KUMAREmail author
Review Article


Heritable information in plants consists of genomic information in DNA sequence and epigenetic information superimposed on DNA sequence. The latter is in the form of cytosine methylation at CG, CHG and CHH elements (where H = A, T or C) and a variety of histone modifications in nucleosomes. The epialleles arising from cytosine methylation marks on the nuclear genomic loci have better heritability than the epiallelic variation due to chromatin marks. Phenotypic variation is increased manifold by epiallele comprised methylomes. Plants (angiosperms) have highly conserved genetic mechanisms to establish, maintain or erase cytosine methylation from epialleles. The methylation marks in plants fluctuate according to the cell/tissue/organ in the vegetative and reproductive phases of plant life cycle. They also change according to environment. Epialleles arise by gain or loss of cytosine methylation marks on genes. The changes occur due to the imperfection of the processes that establish and maintain the marks and on account of spontaneous and stress imposed removal of marks. Cytosine methylation pattern acquired in response to abiotic or biotic stress is often inherited over one to several subsequent generations. Cytosine methylation marks affect physiological functions of plants via their effect(s) on gene expression levels. They also repress transposable elements that are abundantly present in plant genomes. The density of their distribution along chromosome lengths affects meiotic recombination rate, while their removal increases mutation rate. Transposon activation due to loss of methylation causes rearrangements such that new gene regulatory networks arise and genes for microRNAs may originate. Cytosine methylation dynamics contribute to evolutionary changes. This review presents and discusses the available evidence on origin, removal and roles of cytosine methylation and on related processes, such as RNA directed DNA methylation, imprinting, paramutation and transgenerational memory in plants.


cytosine methylation DNA methylation mechanisms DNA demethylation mechanisms Darwinian-cum-Lamarckian evolution epialleles epigenetic modifications genetic recombination heritable induced defence mutational hotspots transgenerational inheritance 



Authors thank the Indian National Science Academy and the Council of Scientific and Industrial Research, Government of India, for the scientistship schemes to SK, and Department of Biotechnology and SKA Institution for Research, Education and Development for Postgraduate fellowships respectively to RK and VS.


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Copyright information

© Indian Academy of Sciences 2013

Authors and Affiliations

    • 1
    • 2
    Email author
    • 1
    • 3
    • 1
    • 2
    • 3
  1. 1.National Institute of Plant Genome Research (NIPGR)New DelhiIndia
  2. 2.SKA Institution for Research, Education and Development (SKAIRED)New DelhiIndia
  3. 3.Banasthali UniversityBanasthaliIndia

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