The Role of DNA Methylation in Perennial Plants


  • Lia BASDEKI Agricultural University of Athens, School of Food, Biotechnology and Development, Department of Biotechnology, Genetics Laboratory, 75 Iera Odos 11855, Athens (GR)
  • Marianna HAGIDIMITRIOU Agricultural University of Athens, School of Food, Biotechnology and Development, Department of Biotechnology, Genetics Laboratory, 75 Iera Odos 11855, Athens (GR)



anthocyanins, dormancy, fruit trees, 5-methyl-cytosine


DNA methylation is an important epigenetic modification of the genome in all organisms. This review presents the effect of DNA methylation in perennial fruit trees such as chestnut, apple, peach etc. In particular, DNA methylation has been shown to affect bud dormancy, the changes of developmental stages such as: flowering, the synthesis of anthocyanins, among other flavonoid compounds; it also affects the fertilization and perpetuation of many fruit trees. Finally, DNA methylation can be used as a tool for investigating the epigenetic diversity of a species.


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Andreucci AC, Ruffini-Castiglione M, Tagliasacchi AM (1994). RNA synthesis and immunogold localization of 5-methylcitosine rich regions in polytene chromosomes of Phaseolus coccineus L. embryo suspensor, at two stages of embryogenesis. Cytobios 78:99-113.

Arús P, Verde I, Sosinski B, Zhebentyayeva T, Abbott AG (2012). The peach genome. Tree Genetics and Genomes 8:1-17.

Avramidou EV, Ganopoulos IV, Doulis AG, Tsaftaris AS, Aravanopoulos FA (2015). Beyond population genetics: natural epigenetic variation in wild cherry (Prunus avium). Tree Genetics & Genomes 11(95):95.

Barghini E, Natali L, Cossu RM, Giordani T, Pindo M, ... Cavallini A (2014). The peculiar landscape of repetitive sequences in the olive (Olea europaea L.) genome. Genome Biology Evolution 6(4):776-791.

Baurens F, Nicolleau J, Legavre T, Verdeil J, Monteuuis O (2004). Genomic DNA methylation of juvenile and mature Acacia mangium micropropagated in vitro with reference to leaf morphology as a phase change marker. Tree Physiology 24(4):401-407.

Bitonti MB, Cozza R, Chiappetta A, Giannino D, Castiglione MR, ... Innocenti AM (2002). Distinct nuclear organization, DNA methylation pattern and cytokinin distribution mark juvenile, juvenile-like and adult vegetative apical meristems in peach (Prunus persica (L.) Batsch). Journal of Experimental Botany 53(371):1047-1054.

Blazquez MA, Soowal LN, Lee I, Weigel D (1997). LEAFY expression and flower initiation in Arabidopsis. Development 124(19):3835-3844.

Cheng J, Wei G, Zhou H, Gu C, Vimolmangkang S, ... Han Y (2014). Unraveling the mechanism underlying the glycosylation and methylation of anthocyanins in peach. Plant Physiology 166(2):1044-1058.

Chong S, Whitelaw E (2004). Epigentic germline inheritance. Current Opinion in Genetics & Development 14(6):692-696.

Cocciolone SM, Cone KC (1993). Pl-Bh, an anthocyanin regulatory gene of maize that leads to variegated pigmentation. Genetics 135(2):575-588.

Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, ... Jacobsen SE (2008). Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452(7184):215-219.

Doerfler W, Bohm P (2006). DNA methylation: Basic mechanisms. Vol. 301. Springer Science & Business Media.

El-Sharkawy I, Liang D, Xu K (2015). Transcriptome analysis of an apple (Malus × domestica) yellow fruit somatic mutation identifies a gene network module highly associated with anthocyanin and epigenetic regulation. Journal of Experimental Botany 66(22):7359-7376.

Fang J (2015). Classification of fruits based on anthocyanin types and relevance to their health benefits. Nutrition 31(11-12):1301-1306.

Flavell RB (1986). Repetitive DNA and chromosome evolution in plants. Philosophical Transactions of the Royal Society of London. B, Biological Sciences 312(1154):227-242.

Forino LMC, Andreucci AC, Del-Tredici I, Felici C, Giraldi E, Tagliasacchi AM (2003). DNA methylation of tapetum cells during microsporogenesis in Malus domestica Borkh. Israel Journal of Plant Sciences 51(2):91-100.

Hasbún R, Valledor L, Berdasco M, Santamaría E, Cañal MJ, ... Sánchez M (2005). In vitro proliferation and genome DNA methylation in adult chestnuts. Acta Horticulturae 693:333-340.

Hasbún R, Valledor L, Santamaría E, Caña, MJ, Rodríguez R, Berdasco M (2007). Dynamics of DNA methylation in chestnut trees development. Acta Horticulturae 760(2):563-566.

Huh JH, Bauer MJ, Hsieh TF, Fischer RL (2008). Cellular programming of plant gene imprinting. Cell 132(5):735-744.

Jin B, Li Y, Robertson KD (2011). DNA methylation: superior or subordinate in the epigenetic hierarchy. Genes & Cancer 2(6):607-617.

Jones PA (2012). Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nature Reviews Genetics 13(7):484-492.

Kato M, Miura A, Bender J, Jacobsen SE, Kakutani T (2003). Role of CG and non-CG methylation in immobilization of transposons in Arabidopsis. Current Biology 13(5):421-426.

Katsiotis A, Hagidimitriou M, Douka A, Hatzopoulos P (1998). Genomic organization, sequence interrelationship, and physical localization using in situ hybridization of two tandemly repeated DNA sequences in the genus Olea. Genome 41(4):527-534.

Kavarik A, Koukalova B, Bezdek M, Opatrny Z (1997). Hypermethylation of tobacco heterochromatic loci response to osmotic stress. Theoretical & Applied Genetics 95(1-2):301-3069.

Khoo HE, Azlan A, Tang ST, Lin SM (2017). Anthocyanidins and anthocyanins: colored pigments as food, pharmaceutical ingredients, and the potential health benefits. Food & Nutrition Research 61(1):1-21.

Kumar S, Cheng X, Klimasauskas S, Mi S, Posfai J, ... Wilson GG (1994). The DNA (cytosine-5) methyltransferases. Nucleic Acids Research 22(1):1-10.

Kumar G, Rattan UK, Singh AK (2016). Chilling-mediated DNA methylation changes during dormancy and its release reveal the importance of epigenetic regulation during winter dormancy in apple (Malusx domestica Borkh). PloS One 11(2):e0149934.

Lister R, Ecker JR (2009). Finding the fifth base: Genome-wide sequencing of cytosine methylation. Genome Research, Cold Spring Harbor Laboratory Press 19(6):959-966.

Liu I, Li Y, Tollefsbol TO (2008). Gene-environment interactions and epigenetic basis of human diseases. Current Issues in Molecular Biology 10(1-2):25-36.

Michalak M, Barciszewska MZ, Barciszewski J, Plitta BP, Chmielarz P (2013). Global changes in DNA methylation in seeds and seedlings of Pyrus communis after Seed Desiccation and Storage. PLOS ONE 8(8):e70693.

Molfetas S, Leonidas E, Ball E (1994) [Μολφέτας Σ, Λεωνίδας Ε, Ball E (1994)]. Î’iology: A trip to life. Genetics, 2. The Genetic Material and its Expression[ In Greek]. pp 100-102.

Niederhuth CE, Schmitz RJ (2013). Covering your bases: Inheritance of DNA methylation in plant genomes. Molecular Plant 7(3):472-480.

Nikolaou C (2015). Computational Biology [In Greek]. Electronic Library pp 409-411.

Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL (2007). DNA methylation in the Arabidopsis genome. Proceedings of the National Academy of Sciences 104(16):6752-6757.

Pierotti L, Andreucci AC, Giraldi E, Tagliasacchi AM (1998). Polytene chromosomes of the embryo suspensor of Phaseolous coccineus L. during senescence. Cytobios 96:31-43.

Reik W, Dean W, Walter J (2001). Epigenetic reprogramming in mammalian development. Science 293(5532):1089-1093.

Reinders J, Wulff BBH, Mirouze M, Mari-Ordonez A, Dapp M, ... Paszkowski J (2015). Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes. Genes & Development 23(8):939-950.

Rico L, Ogaya R, Barbeta A, Penuelas J (2014). Changes in DNA methylation fingerprint of Quercus ilex trees in response to experimental field drought simulating projected climate change. Plant Biology 16(2):419-427.

Rothkegel K, Sánchez E, Montes C, Greve M, Tapia S, ... Almeida AM (2017). DNA methylation and small interference RNAs participate in the regulation of MADS-box genes involved in dormancy in sweet cherry (Prunus avium L.). Tree Physiology 37(12):1739-1751.

Santamarıa ME, Rodrıguez R, Canal ÎœJ, Toorop PE (2011). Transcriptome analysis of chestnut (Castanea sativa) tree buds suggests a putative role for epigenetic control of bud dormancy. Annals of Botany, Oxford University Press 108(3):485-498.

Singha S, Baugher T (2003). Concise encyclopedia of temperate tree fruit. New York: Food Products Press, pp 3-5.

Slavin JL, Lloyd B (2012). Health benefits of fruits and vegetables. American Society for Nutrition 3(4):506-516.

Smyth DR (1991). Dispersed repeats in plant genomes. Chromosoma 100(6):355-359.

Srinivasan PR, Borek E (1964). DNA modification mechanisms and gene activity during development. Science 187(4173):226-232.

Stergiou G, Katsiotis A, Hagidimitriou M, Loukas M (2002). Genomic and chromosomal organization of Ty1-copia-like sequences in Olea europaea and evolutionary relationships of Olea retroelements. Theoretical and Applied Genetics 104(6-7):926-933.

Tagliasacchi AM, Andreucci AC, Giraldi E, Felici C, Ruberti F, Forino LMC (2007). Structure, DNA content and DNA methylation of synergids during ovule development in Malus domestica Borkh. Caryologia 60(3):290-298.

Tahilliani M, Koh KP, Shen Y, Pastor, WA, Bandukwala H, ... Rao A (2009). Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1. Science 324(5929):930-935.

Telias A, Lin-Wang K, Stevenson DE, Cooney JM, Hellens RP, ... Bradeen JM (2011). Apple skin patterning is associated with differential expression of MYB1. BMC Plant Biology 11(93):1-14.

Tollefsbol T (2011). Handbook of Epigenetics: The New Molecular and Medical Genetics. London, UK, Burlington, USA, San Diego, USA.

Weigel D, Nilsson O (1995). A developmental switch sufficient for flower initiation in diverse plants. Nature 377(6549):495-500.

Winkel-Shirley B (2001). Flavonoid biosynthesis: a colorful model for genetics, biochemistry, cell biology, and biotechnology. Plant Physiology 126(2):485-493.

Xie M, Yu B (2015). siRNA-directed DNA methylation in plants. Current Genomic 16(1):23-31.

Zhang H, Tang K, Wang B, Duan CG, Lang Z, Zhu JK (2014). Protocol: a beginner’s guide to the analysis of RNA-directed DNA methylation in plants. Plant Methods 10(1):18.




How to Cite

BASDEKI, L., & HAGIDIMITRIOU, M. (2019). The Role of DNA Methylation in Perennial Plants. Notulae Scientia Biologicae, 11(1), 1–11.



Review articles
DOI: 10.15835/nsb11110446

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