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Epigenetic Regulation in Plants

Plants utilize a number of gene regulation mechanisms to ensure proper development, function, growth, and survival under different environmental conditions. Plants depend on changes in gene expression to respond to environmental stimuli, in which the full repertoire of histone modifications, DNA methylation, and small ncRNAs play an important role in epigenetic regulation.

Studying the epigenetics of model plants such as Arabidopsis thaliana have allowed researchers to understand pathways that maintain chromatin modifications as well as the mapping of modifications such as DNA methylation on a genome-wide scale. Small RNAs have also been implicated in playing a role in the distribution of chromatin modifications, and RNA may also play a role in the complex epigenetic interactions that occur between homologous sequences (Moazed et al, 2009). In the future, by understanding epigenetic control, researchers can uncover the research necessary to improve plant growth, yields, and transformation efficiency especially in the face of climate change and other environmental factors.


Chromatin consists of nucleosomes formed by a complex of histone proteins and DNA, which allows the packaging of DNA into the nucleus. The less condensed euchromatin represents transcriptionally active regions, while heterochromatin is usually inactive (Vaillant and Paszkowski, 2007). Chromatin state is known to be influenced by both DNA methylation and histone modifications which in turn impact gene expression and the structure of chromosomes. In a recent study, the role of chromatin modifications during plant reproduction elucidated 3-dimensional chromosome reorganization mediated by histones and DNA methylation (Dukowic-Schulze et al. 2017). In addition, gibberellins have been shown in increasing the level of histone acetylation, which affects regions of chromatin involved in maize seed germination (Zheng et al. 2017). Another study reports a novel function of a tomato histone deacetylase gene in the regulation of fruit ripening (Guo et al. 2017).

In addition, multigene families encode transcription factors, with members found throughout the genome or clustered on the same chromosome. Numerous DNA binding proteins that interact with plant promoters have been identified -- some are similar to well-characterized transcription factors in animals or yeast, while others are unique to plants. For example, diverse members of the subfamily X of the plant-specific ethylene response factor (ERF) transcription factors coordinate stress signaling with wound repair activation. Tissue repair is also enhanced through a protein complex of ERF and GRAS TFs (Heyman et. al,.2018). A compilation of known plant transcription factors can be found in the plant transcription factor database at http://plntfdb.bio.uni-potsdam.de/v3.0/.


Recent research shows that a number of classes of small RNAs are key epigenetic regulators. In many cases, small RNAs have been implicated in DNA methylation and chromatin modification (Meyer, 2015). In addition, the role of small RNAs has been implicated in plant stress tolerance (Kumar et al., 2017). López-Galiano et al also provided insight into a coordinated function of a miRNA gene and histone modifications in regulating the expression of a WRKY transcription factor in response to stress.

RNA interference (RNAi) is another epigenetic mechanism that leads to small RNA generation, which mediates gene silencing at the post-transcriptional level. RNAi technology has immense potential for plant disease resistance.

DNA methylation

Plants, unlike animals, have three sites that can be methylated G, CHG (H can be A, C, T), and CHH (Law and Jacobsen, 2010). DNA methylation has attracted particular interest. In Arabidopsis, one-third of methylated genes occur in transcribed regions, and 5% of genes are methylated in promoter regions, suggesting that many of these are epigenetically regulated. (Zhang et al., 2006).

There are thousands of differentially methylated regions (DMRs) that influence phenotype by influencing gene expression. The analysis of epigenetic recombinant inbred line (epiRIL) plants from Arabidopsis points to the evidence of the influence of DMRs. An epiRIL results from crossing two genetically identical plants with differing DNA methylation levels (with one parent as a homozygous mutant for an essential DNA methylation maintenance gene). The offspring of these plants have similar genomes that vary only in methylation levels. Many traits have been studied using epiRILs -- flowering time, plant height, and response to abiotic stress, some of which have now been mapped to DMRs (Zhang et al. 2018)

Regulation by DNA methylation has been shown to be important in many aspects of plant development and response such as vernalization, hybrid vigor, and self-incompatibility (Itabashi et al. 2017). For example, vernalization treatments have shown reduced DNA methylation and subsequent initiation of flowering (Burn et al., 1993). Stress can also influence DNA methylation in plants as a response to environmental stimuli. (Steward et al., 2002; Song et al., 2012). A high degree of DNA methylation has also suggested the role in the improvement of plant fitness under different environmental conditions (Saéz-Laguna et al., 2014). In addition, methylation can affect normal fruit and hypomethylation predicts homeotic transformation and loss of fruit yield (Ong-Abdullah et al., 2015)

DNA demethylation has also been implied in various aspects of plant development including pollen tube formation, embryogenesis, fruit ripening, stomatal development, and nodule formation ( Li et al. 2017). Demethylation of rice genomic DNA caused an altered pattern of gene expression, inducing dwarf plants (Sano et al., 1990).

Epigenetic modifications contribute to the stability and survival of the plants and their ability to adapt in different environmental conditions.

Diagenode products for your epigenomics research in plants

Chromatin analysis

Understand the role of chromatin in plant function and development

DNA methylation

DNA methylation and demethylation and the effects on plant response and function

Non-coding RNAs

Discover noncoding RNAs in the regulation of gene expression in plants


Burn, J. et al (1993). DNA methylation, vernalization, and the initiation of flowering. Proc. Natl. Acad. Sci. U.S.A. 90, 287–291. doi: 10.1006/scdb.1996.0055

Dukowic-Schulze S, Liu C, Chen C (2017) Not just gene expression: 3D implications of chromatin modifications during sexual plant reproduction. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2222-0

Guo J et al (2017) A histone deacetylase gene, SlHDA3, acts as a negative regulator of fruit ripening and carotenoid accumulation. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2211-3

Heyman J, et.al (2018) Journal of Cell Science Emerging role of the plant ERF transcription factors in coordinating wound defense responses and repair doi: 10.1242/jcs.208215

Itabashi E, Osabe K, Fujimoto R, Kakizaki T (2017) Epigenetic regulation of agronomical traits in Brassicaceae. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2223-z

Kumar V et al (2017) Plant small RNAs: the essential epigenetic regulators of gene expression for salt-stress responses and tolerance. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2210-4

Law, J. A., and Jacobsen, S. E. (2010). Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 11, 204–220. doi: 10.1038/nrg2719

Meyer, P. (2015). Epigenetic variation and environmental change. J. Exp. Bot. 66, 3541–3548. doi: 10.1093/jxb/eru502

Moazed, D. (2009) Small RNAs in transcriptional gene silencing and genome defence. Nature. doi: 10.1038/nature07756

Ong-Abdullah et al. (2015). Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm. Nature 525, 533–537. doi: 10.1038/nature15365

Saéz-Laguna et al. (2014). Epigenetic variability in the genetically uniform forest tree species. PLoS One 9:e103145. doi: 10.1371/journal.pone.0103145

Sano, H. et al. (1990). A single treatment of rice seedlings with 5-azacytidine induces heritable dwarfism and undermethylation of genomic DNA. Mol. Gen. Genet. 220, 441–447. doi: 10.1007/BF00391751

Song, J et al (2012). Vernalization – A cold-induced epigenetic switch. J. Cell Sci. 125, 3723–3731. doi: 10.1242/jcs.084764

Steward, N et al. (2002). Periodic DNA methylation in maize nucleosomes and demethylation by environmental stress. J. Biol. Chem. 277, 37741–37746. doi: 10.1074/jbc.M204050200

Vaillant, I., and Paszkowski, J. (2007). Role of histone and DNA methylation in gene regulation. Curr. Opin. Plant Biol. 10, 528–533. doi: 10.1016/j.pbi.2007.06.008

Zhang, et al. (2006). Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126, 1189–1201. doi: 10.1016/j.cell.2006.08.003

Zhang et al. 2018 Understanding the evolutionary potential of epigenetic variation: a comparison of heritable phenotypic variation in epiRILs, RILs, and natural ecotypes of Arabidopsis thaliana. Heredity 121, 257–265 (2018) doi:10.1038/s41437-018-0095-9

Zheng X et al (2017) Histone acetylation is involved in GA-mediated 45S rDNA decondensation in maize aleurone layers. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2207-z

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