Abstract
Epigenetic regulation mainly refers to histone post-translational modifications and DNA methylation, which are critical to plant gene regulation and contribute to the development of plants and to their response to the environment. Recent molecular and epigenomic studies have shown that epigenetic regulations play critical roles in tomato fruit development and ripening, the current model for climacteric fruit. This led to a new model of ripening control where active DNA demethylation plays a central role being necessary to the induction of several genes that control fruit ripening. Whether this is a general model applying to all type of fruit, including non-climacteric fruit for which grape berry stands as a general model, is an open question that requires investigating the genome-wide variations of epigenetic marks during fruit development and ripening in many different species. Finally, the potential roles of epigenetic regulations in grapevine, a perennial, grafted, and clonally propagated plant, are discussed.
Junhua Kong and Margot Berger contributed equally to this work
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Achour M, Jacq X, Rondé P, Alhosin M, Charlot C, Chataigneau T et al (2008) The interaction of the SRA domain of ICBP90 with a novel domain of DNMT1 is involved in the regulation of VEGF gene expression. Oncogene. https://doi.org/10.1038/sj.onc.1210855
Agius F, Kapoor A, Zhu J-K (2006) Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation. Proc Natl Acad Sci 103(31):11796–11801. https://doi.org/10.1073/pnas.0603563103
Alba R (2005) Transcriptome and selected metabolite analyses reveal multiple points of ethylene control during tomato fruit development. Plant Cell 17(11):2954–2965. https://doi.org/10.1105/tpc.105.036053
Albacete A, Martínez-Andújar C, Martínez-Pérez A, Thompson AJ, Dodd IC, Pérez-Alfocea F (2015) Unravelling rootstock × scion interactions to improve food security. J Exp Bot 66(8):2211–2226. https://doi.org/10.1093/jxb/erv027
Almada R, Cabrera N, Casaretto JA, Peña-Cortés H, Ruiz-Lara S, Villanueva EG (2011) Epigenetic repressor-like genes are differentially regulated during grapevine (Vitis vinifera L.) development. Plant Cell Rep 30(10):1959
Aquea F, Timmermann T, Arce-Johnson P (2010) Analysis of histone acetyltransferase and deacetylase families of Vitis vinifera. Plant Physiol Biochem 48(2–3):194–199
Aquea F, Vega A, Timmermann T, Poupin MJ, Arce-Johnson P (2011) Genome-wide analysis of the SET DOMAIN GROUP family in grapevine. Plant Cell Rep 30(6):1087–1097
An YC, Goettel W, Han Q, Bartels A, Liu Z, Xiao W (2017) Dynamic changes of genome-wide DNA methylation during soybean seed development. Sci Rep 7(12263):1–14
Avramidou E, Kapazoglou A, Aravanopoulos FA, Xanthopoulou A, Ganopoulos I, Tsaballa A et al (2015) Global DNA methylation changes in Cucurbitaceae inter-species grafting. Crop Breed Appl Biotechnol 15(2):112–116
Bai S, Kasai A, Yamada K, Li T, Harada T (2011) A mobile signal transported over a long distance induces systemic transcriptional gene silencing in a grafted partner. J Exp Bot 62(13):4561–4570
Baker K, Dhillon T, Colas I, Cook N, Milne I, Milne L et al (2015) Chromatin state analysis of the barley epigenome reveals a higher-order structure defined by H3K27me1 and H3K27me3 abundance. Plant J 84(1):111–124
Baker M (2011) Making sense of chromatin states. Nature Publishing Group, London
Bannister AJ, Kouzarides T (2011) Regulation of chromatin by histone modifications. Cell Res 21(3):381
Bapat VA, Trivedi PK, Ghosh A, Sane VA, Ganapathi TR, Nath P (2010) Ripening of fleshy fruit: molecular insight and the role of ethylene. Biotechnol Adv 28(1):94–107
Bartee L, Malagnac F, Bender J (2001) Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Genes Dev 15(14):1753–1758. https://doi.org/10.1101/gad.905701
Barth TK, Imhof A (2010) Fast signals and slow marks: the dynamics of histone modifications. Trends Biochem Sci 35(11):618–626
Battilana J, Dunlevy JD, Boss PK (2017) Histone modifications at the grapevine VvOMT3 locus, which encodes an enzyme responsible for methoxypyrazine production in the berry. Funct Plant Biol 44(7):655–664
Baubec T, Pecinka A, Rozhon W, Mittelsten Scheid O (2009) Effective, homogeneous and transient interference with cytosine methylation in plant genomic DNA by zebularine. Plant J 57(3):542–554
Bauer MJ, Fischer RL (2011) Genome demethylation and imprinting in the endosperm. Curr Opin Plant Biol 14(2):162–167
Beck S, Rakyan VK (2008) The methylome: approaches for global DNA methylation profiling. Trends Genet 24(5):231–237
Becker JS, Nicetto D, Zaret KS (2016) H3K9me3-dependent heterochromatin: barrier to cell fate changes. Trends Genet 32(1):29–41
Benvenuto G, Formiggini F, Laflamme P, Malakhov M, Bowler C (2002) The photomorphogenesis regulator DET1 binds the amino-terminal tail of histone H2B in a nucleosome context. Curr Biol 12(17):1529–1534
Berger MMJ, Gallusci P, Teyssier E (2018) Chapter seven—roles of epigenetic mechanisms in grafting and possible applications. Plant Epigenetics Coming Age Breed Appl 88:203–246
Berger SL (2007) The complex language of chromatin regulation during transcription. Nature 447(7143):407
Bernatavichute YV, Zhang X, Cokus S, Pellegrini M, Jacobsen SE (2008) Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana. PLoS ONE 3(9):e3156
Berry S, Dean C (2015) Environmental perception and epigenetic memory: mechanistic insight through FLC. Plant J 83(1):133–148
Bewick AJ, Niederhuth CE, Ji L, Rohr NA, Griffin PT, Leebens-Mack J, Schmitz RJ (2017) The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants. Genome Biol 18(1):65
Bewick AJ, Schmitz RJ (2017) Gene body DNA methylation in plants. Curr Opin Plant Biol 36:103–110
Birnbaum KD, Roudier F (2017) Epigenetic memory and cell fate reprogramming in plants. Regeneration 4(1):15–20
Boureau L, How Kit A, Teyssier E, Drevensek S, Rainieri M, Joubès J et al (2016) A CURLY LEAF homologue controls both vegetative and reproductive development of tomato plants. Plant Mol Biol 90(4–5):485–501
Bu Z, Yu Y, Li Z, Liu Y, Jiang W, Huang Y, Dong A-W (2014) Regulation of Arabidopsis flowering by the histone mark readers MRG1/2 via interaction with CONSTANS to modulate FT expression. PLoS Genet 10(9):e1004617
Bucher E, Kong J, Teyssier E, Gallusci P (2018) Chapter ten—epigenetic regulations of fleshy fruit development and ripening and their potential applications to breeding strategies. In: Mirouze M, Bucher E, Gallusci BR (eds) Plant epigenetics coming of age for breeding applications, vol 88, pp 327–360. https://doi.org/10.1016/bs.abr.2018.09.015
Castellarin SD, Gambetta GA, Wada H, Krasnow MN, Cramer GR, Peterlunger E et al (2015) Characterization of major ripening events during softening in grape: turgor, sugar accumulation, abscisic acid metabolism, colour development, and their relationship with growth. J Exp Bot 67(3):709–722
Chanvivattana Y, Bishopp A, Schubert D, Stock C, Moon Y-H, Sung ZR, Goodrich J (2004) Interaction of Polycomb-group proteins controlling flowering in Arabidopsis. Development 131(21):5263–5276
Chaudhury AM, Ming L, Miller C, Craig S, Dennis ES, Peacock WJ (1997) Fertilization-independent seed development in Arabidopsis thaliana. Proc Natl Acad Sci 94(8):4223–4228. https://doi.org/10.1073/pnas.94.8.4223
Chen W, Kong J, Qin C, Yu S, Tan J, Chen Y et al (2015) Requirement of CHROMOMETHYLASE3 for somatic inheritance of the spontaneous tomato epimutation Colourless non-ripening. Sci Rep 5:9192. https://doi.org/10.1038/srep09192
Chen X, Hu Y, Zhou D-X (2011) Epigenetic gene regulation by plant Jumonji group of histone demethylase. Biochim Biophys Acta: BBA Gene Regul Mech 1809(8):421–426
Cheng J, Niu Q, Zhang B, Chen K, Yang R, Zhu J-K et al (2018a) Downregulation of RdDM during strawberry fruit ripening. Genome Biol 19(1):212
Cheng S, Tan F, Lu Y, Liu X, Li T, Yuan W et al (2018b) WOX11 recruits a histone H3K27me3 demethylase to promote gene expression during shoot development in rice. Nucleic Acids Res 46(5):2356–2369
Cheng X, Zhang S, Tao W, Zhang X, Liu J, Sun J et al (2018c) INDETERMINATE SPIKELET1 recruits histone deacetylase and a transcriptional repression complex to regulate rice salt tolerance. Plant Physiol 1:1. https://doi.org/10.1104/pp.18.00324
Chinnusamy V, Zhu JK (2009) Epigenetic regulation of stress responses in plants. Curr Opin Plant Biol 12(2):133–139. https://doi.org/10.1016/j.pbi.2008.12.006
Chodavarapu RK, Feng S, Ding B, Simon SA, Lopez D, Jia Y et al (2012) Transcriptome and methylome interactions in rice hybrids. Proc Natl Acad Sci 109(30):12040–12045
Choi Y, Gehring M, Johnson L, Hannon M, Harada JJ, Goldberg RB et al (2002) DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis. Cell 110(1):33–42
Cigliano RA, Sanseverino W, Cremona G, Ercolano MR, Conicella C, Consiglio FM (2013) Genome-wide analysis of histone modifiers in tomato: gaining an insight into their developmental roles. BMC Genom 14(1):57
Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD et al (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452(7184):215
Coleman-Derr D, Zilberman D (2012) Deposition of histone variant H2A. Z within gene bodies regulates responsive genes. PLoS Genet 8(10):e1002988
Collepardo-Guevara R, Portella G, Vendruscolo M, Frenkel D, Schlick T, Orozco M (2015) Chromatin unfolding by epigenetic modifications explained by dramatic impairment of internucleosome interactions: a multiscale computational study. J Am Chem Soc 137(32):10205–10215
Conde C, Silva P, Fontes N, Dias AT, Sousa RM, Agasse MJ, Delrot A, Gerós H (2007) Biochemical changes throughout grape berry development and fruit and wine quality. Food 1:1–22
Conde D, Le Gac AL, Perales M, Dervinis C, Kirst M, Maury S et al (2017) Chilling-responsive DEMETER-LIKE DNA demethylase mediates in poplar bud break. Plant, Cell Environ 40(10):2236–2249. https://doi.org/10.1111/pce.13019
Corem S, Doron-Faigenboim A, Jouffroy O, Maumus F, Arazi T, Bouché N (2018) Redistribution of CHH methylation and small interfering RNAs across the genome of tomato ddm1 mutants. Plant Cell 30(7):1628–1644
Crisp PA, Ganguly D, Eichten SR, Borevitz JO, Pogson BJ (2016) Reconsidering plant memory: intersections between stress recovery, RNA turnover, and epigenetics. Sci Adv 2(2):e1501340
Cui X, Lu F, Qiu Q, Zhou B, Gu L, Zhang S et al (2016) REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis. Nat Genet 48(6):694
Cui X, Cao X (2014) Epigenetic regulation and functional exaptation of transposable elements in higher plants. Curr Opin Plant Biol 21:83–88
Daccord N, Celton JM, Linsmith G, Becker C, Choisne N, Schijlen E et al (2017) High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nat Genet 49(7):1099–1106. https://doi.org/10.1038/ng.3886
del Prete S, Mikulski P, Schubert D, Gaudin V (2015) One, two, three: Polycomb proteins hit all dimensions of gene regulation. Genes 6(3):520–542
Deng X, Qiu Q, He K, Cao X (2018) The seekers: how epigenetic modifying enzymes find their hidden genomic targets in Arabidopsis. Curr Opin Plant Biol 45:75–81
Derkacheva M, Hennig L (2013) Variations on a theme: Polycomb group proteins in plants. J Exp Bot 65(10):2769–2784
Du J, Johnson LM, Groth M, Feng S, Hale CJ, Li S et al (2014) Mechanism of DNA methylation-directed histone methylation by KRYPTONITE. Mol Cell 55(3):495–504
Du J, Johnson LM, Jacobsen SE, Patel DJ (2015) DNA methylation pathways and their crosstalk with histone methylation. Nat Rev Mol Cell Biol 16(9):519
Du J, Zhong X, Bernatavichute YV, Stroud H, Feng S, Caro E et al (2012) Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants. Cell 151(1):167–180
Duan C-G, Wang X, Xie S, Pan L, Miki D, Tang K et al (2017) A pair of transposon-derived proteins function in a histone acetyltransferase complex for active DNA demethylation. Cell Res 27(2):226–240. https://doi.org/10.1038/cr.2016.147
Dubin MJ, Zhang P, Meng D, Remigereau M-S, Osborne EJ, Paolo Casale F et al (2015) DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation. ELife 4:e05255–e05255. https://doi.org/10.7554/eLife.05255
Dussert S, Verdeil JL, Jaligot E, Beulé T, Rival A (2000) Somaclonal variation in oil palm (Elaeis guineensis Jacq.): the DNA methylation hypothesis. Plant Cell Rep 19(7):684–690. https://doi.org/10.1007/s002999900177
Eichten SR, Briskine R, Song J, Li Q, Swanson-Wagner R, Hermanson PJ et al (2013) Epigenetic and genetic influences on DNA methylation variation in maize populations. Plant Cell 25(8):2783–2797. https://doi.org/10.1105/tpc.113.114793
Eichten SR, Schmitz RJ, Springer NM (2014) Epigenetics: beyond chromatin modifications and complex genetic regulation. Plant Physiol 165(3):933–947
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. J Exp Bot 66(22):7359–7376
Engelhorn J, Blanvillain R, Carles CC (2014) Gene activation and cell fate control in plants: a chromatin perspective. Cell Mol Life Sci 71(16):3119–3137
Exner V, Hennig L (2008) Chromatin rearrangements in development. Curr Opin Plant Biol 11(1):64–69
Fan D, Wang X, Tang X, Ye X, Ren S, Wang D, Luo K (2018) Histone H3K9 demethylase JMJ25 epigenetically modulates anthocyanin biosynthesis in poplar. Plant J 96(6):1121–1136
Feng S, Bostick M, Sadler KC, Cokus SJ, Strauss SH, Jain J et al (2010) Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci 107(19):8689–8694. https://doi.org/10.1073/pnas.1002720107
Feng S, Jacobsen SE (2011) Epigenetic modifications in plants: an evolutionary perspective. Curr Opin Plant Biol 14(2):179–186
Ferreira V, Pinto-Carnide O, Arroyo-García R, Castro I (2018) Berry color variation in grapevine as a source of diversity. Plant Physiol Biochem 132:696–707
Finnegan EJ, Ford B, Wallace X, Pettolino F, Griffin PT, Schmitz RJ et al (2018) Zebularine treatment is associated with deletion of FT-B1 leading to an increase in spikelet number in bread wheat. Plant, Cell Environ 41(6):1346–1360
FitzGerald J, Luo M, Chaudhury A, Berger F (2008) DNA methylation causes predominant maternal controls of plant embryo growth. PLoS ONE 3(5):e2298
Fletcher JC (2017) State of the art: trxG factor regulation of post-embryonic plant development. Front Plant Sci 8:1925
Forestan C, Farinati S, Rouster J, Lassagne H, Lauria M, Ferro ND, Varotto S (2018) Control of maize vegetative and reproductive. Genetics 208:1443–1466. https://doi.org/10.1534/genetics.117.300625/-/DC1.1
Fortes AM, Gallusci P (2017) Plant stress responses and phenotypic plasticity in the epigenomics era: perspectives on the grapevine scenario, a model for perennial crop plants. Front Plant Sci 8:82
Fortes A, Teixeira R, Agudelo-Romero P (2015) Complex interplay of hormonal signals during grape berry ripening. Molecules 20(5):9326–9343
Fu C-C, Han Y-C, Guo Y-F, Kuang J-F, Chen J-Y, Shan W, Lu W-J (2018a) Differential expression of histone deacetylases during banana ripening and identification of MaHDA6 in regulating ripening-associated genes. Postharvest Biol Technol 141:24–32
Fu F-F, Dawe RK, Gent JI (2018b) Loss of RNA-directed DNA methylation in maize chromomethylase and DDM1-type nucleosome remodeler mutants. Plant Cell 30(7):1617–1627
Fuchs J, Demidov D, Houben A, Schubert I (2006) Chromosomal histone modification patterns—from conservation to diversity. Trends Plant Sci 11(4):199–208. https://doi.org/10.1016/j.tplants.2006.02.008
Gallusci P, Hodgman C, Teyssier E, Seymour GB (2016) DNA methylation and chromatin regulation during fleshy fruit development and ripening. Front Plant Sci 7:807
Gapper NE, Giovannoni JJ, Watkins CB (2014) Understanding development and ripening of fruit crops in an “omics” era. Horticu Res 1:14034. https://doi.org/10.1038/hortres.2014.34
Gillaspy G, Ben-david H, Gruissem W, Darwin C (1993) Fruits: a developmental perspective. Plant Cell 5(October):1439–1451
Giovannoni J, Nguyen C, Ampofo B, Zhong S, Fei Z (2017) The epigenome and transcriptional dynamics of fruit ripening. Annu Rev Plant Biol 68:61–84
Gong Z, Morales-Ruiz T, Ariza RR, Roldán-Arjona T, David L, Zhu J-K (2002) ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 111(6):803–814
González APR, Chrtek J, Dobrev PI, Dumalasová V, Fehrer J, Mráz P, Latzel V (2016) Stress-induced memory alters growth of clonal offspring of white clover (Trifolium repens). Am J Bot 103(9):1567–1574
González APR, Preite V, Verhoeven KJF, Latzel V (2018) Transgenerational effects and epigenetic memory in the clonal plant Trifolium repens. Front Plant Sci 9:1677. https://doi.org/10.3389/fpls.2018.01677
Goodrich J, Puangsomlee P, Martin M, Long D, Meyerowitz EM, Coupland G (1997) A Polycomb-group gene regulates homeotic gene expression in Arabidopsis. Nature 386(6620):44
Gouil Q, Baulcombe DC (2016) DNA methylation signatures of the plant chromomethyltransferases. PLoS Genet 12(12):e1006526
Gouil Q, Baulcombe DC (2018) Paramutation-like features of multiple natural epialleles in tomato. BMC Genom 19(1):203
Gregory PJ, Atkinson CJ, Bengough AG, Else MA, Fernández-Fernández F, Harrison RJ, Schmidt S (2013) Contributions of roots and rootstocks to sustainable, intensified crop production. J Exp Bot 64(5):1209–1222
Griffin PT, Niederhuth CE, Schmitz RJ (2016) A comparative analysis of 5-azacytidine- and zebularine-induced DNA demethylation. G3 6(9):2773–2780. https://doi.org/10.1534/g3.116.030262
Gu T, Han Y, Huang R, McAvoy RJ, Li Y (2016) Identification and characterization of histone lysine methylation modifiers in Fragaria vesca. Sci Rep 6:23581
Guo J-E, Hu Z, Li F, Zhang L, Yu X, Tang B, Chen G (2017a) Silencing of histone deacetylase SlHDT3 delays fruit ripening and suppresses carotenoid accumulation in tomato. Plant Sci 265:29–38
Guo J-E, Hu Z, Yu X, Li A, Li F, Wang Y et al (2018) A histone deacetylase gene, SlHDA3, acts as a negative regulator of fruit ripening and carotenoid accumulation. Plant Cell Rep 37(1):125–135
Guo J-E, Hu Z, Zhu M, Li F, Zhu Z, Lu Y, Chen G (2017b) The tomato histone deacetylase SlHDA1 contributes to the repression of fruit ripening and carotenoid accumulation. Sci Rep 7(1):7930
Gutzat R, Scheid OM (2012) Epigenetic responses to stress: triple defense? Curr Opin Plant Biol 15(5):568–573
Hadfield KA, Dandekar AM, Romani RJ (1993) Demethylation of ripening specific genes in tomato fruit. Plant Sci 92(1):13–18
Han Y-C, Kuang J-F, Chen J-Y, Liu X-C, Xiao Y-Y, Fu C-C et al (2016) Banana transcription factor MaERF11 recruits histone deacetylase MaHDA1 and represses the expression of MaACO1 and expansins during fruit ripening. Plant Physiol 171(2):1070–1084
He XJ, Chen T, Zhu JK (2011) Regulation and function of DNA methylation in plants and animals. Cell Res 21(3):442–465. https://doi.org/10.1038/cr.2011.23
Hennig L, Bouveret R, Gruissem W (2005) MSI1-like proteins: an escort service for chromatin assembly and remodeling complexes. Trends Cell Biol 15(6):295–302
Heo JB, Sung S (2011) Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331(6013):76–79
Hepworth J, Dean C (2015) Flowering Locus C’s lessons: conserved chromatin switches underpinning developmental timing and adaptation. Plant Physiol 168(4):1237–1245
Hirata Y (1980) Graft-induced in tomato changes in skin and flesh color (Lycopersicon esculentum Mill.). Soc Hortic Sci 49(2):211–216
Hirsch CD, Springer NM (2017) Transposable element influences on gene expression in plants. Biochim Biophys Acta (BBA) Gene Regul Mech 1860(1):157–165
Hou X, Zhou J, Liu C, Liu L, Shen L, Yu H (2014) Nuclear factor Y-mediated H3K27me3 demethylation of the SOC1 locus orchestrates flowering responses of Arabidopsis. Nat Commun 5:4601
How Kit A, Boureau L, Stammitti-Bert L, Rolin D, Teyssier E, Gallusci P (2010) Functional analysis of SlEZ1 a tomato Enhancer of zeste (E (z)) gene demonstrates a role in flower development. Plant Mol Biol 74(3):201–213
Hsieh T-F, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, Fischer RL, Zilberman D (2009) Genome-wide demethylation of Arabidopsis endosperm. Science 324(5933):1451–1454
Hu J, McCall CM, Ohta T, Xiong Y (2004) Targeted ubiquitination of CDT1 by the DDB1-CUL4A-ROC1 ligase in response to DNA damage. Nat Cell Biol 6(10):1003
Hu L, Li N, Xu C, Zhong S, Lin X, Yang J et al (2014) Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality. Proc Natl Acad Sci 111(29):10642–10647. https://doi.org/10.1073/pnas.1410761111
Huang H, Liu R, Niu Q, Tang K, Zhang B, Zhang H et al (2019) Global increase in DNA methylation during orange fruit development and ripening. Proc Natl Acad Sci 116(4):1430–1436
Hung FY, Chen FF, Li C, Chen C, Lai YC, Chen JH et al (2018) The Arabidopsis LDL1/2-HDA6 histone modification complex is functionally associated with CCA1/LHY in regulation of circadian clock genes. Nucleic Acids Res 46(20):10669–10681. https://doi.org/10.1093/nar/gky749
Inagaki S, Miura-Kamio A, Nakamura Y, Lu F, Cui X, Cao X et al (2010) Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome. EMBO J 29(20):3496–3506
Jackson JP, Lindroth AM, Cao X, Jacobsen SE (2002) Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416(6880):556
Jacob Y, Feng S, LeBlanc CA, Bernatavichute YV, Stroud H, Cokus S et al (2009) ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing. Nat Struct Mol Biol 16(7):763
Jaillon O, Aury J-M, Noel B, Policriti A, Clepet C, Casagrande A et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449(7161):463–467. https://doi.org/10.1038/nature06148
Janssen BJ, Thodey K, Schaffer RJ, Alba R, Balakrishnan L, Bishop R et al (2008) Global gene expression analysis of apple fruit development from the floral bud to ripe fruit. BMC Plant Biol 8(1):16
Jenuwein T, Allis CD (2001) Translating the histone code. Science 293(5532):1074–1080
Jiang D, Berger F (2017) Histone variants in plant transcriptional regulation. Biochim Biophys Acta (BBA) Gene Regul Mech 1860(1):123–130
Jiang L, Li D, Jin L, Ruan Y, Shen WH, Liu C (2018a) Histone lysine methyltransferases BnaSDG8.A and BnaSDG8.C are involved in the floral transition in Brassica napus. Plant J 95(4):672–685. https://doi.org/10.1111/tpj.13978
Jiang P, Wang S, Jiang H, Cheng B, Wu K, Ding Y (2018b) The COMPASS-like complex promotes flowering and panicle branching in rice. Plant Physiol 176(4):2761–2771
Jiang P, Wang S, Zheng H, Li H, Zhang F, Su Y et al (2018c) SIP 1 participates in regulation of flowering time in rice by recruiting OsTrx1 to Ehd1. New Phytol 219(1):422–435
Joldersma D, Liu Z (2018) The making of virgin fruit: the molecular and genetic basis of parthenocarpy. Oxford University Press, Oxford
Jones MA, Covington MF, DiTacchio L, Vollmers C, Panda S, Harmer SL (2010) Jumonji domain protein JMJD5 functions in both the plant and human circadian systems. Proc Natl Acad Sci 107(50):21623–21628. https://doi.org/10.1073/pnas.1014204108
Kasai A, Bai S, Hojo H, Harada T (2016) Epigenome editing of potato by grafting using transgenic tobacco as siRNA donor. PLoS ONE 11(8):e0161729
Kawakatsu T, Nery JR, Castanon R, Ecker JR (2017) Dynamic DNA methylation reconfiguration during seed development and germination. Genome Biol 18(1):171
Kawakatsu T, Stuart T, Valdes M, Breakfield N, Schmitz RJ, Nery JR et al (2016) Unique cell-type-specific patterns of DNA methylation in the root meristem. Nat Plants 2(5):16058
Kim D-H, Xi Y, Sung S (2017) Modular function of long noncoding RNA, COLDAIR, in the vernalization response. PLoS Genet 13(7):e1006939
Kim DH, Sung S (2017) Vernalization-triggered intragenic chromatin loop formation by long noncoding RNAs. Dev Cell 40(3):302–312.e4. https://doi.org/10.1016/j.devcel.2016.12.021
Kim J, Kim JH, Richards EJ, Chung KM, Woo HR (2014) Arabidopsis VIM proteins regulate epigenetic silencing by modulating DNA methylation and histone modification in cooperation with MET1. Mol Plant 7(9):1470–1485
Kim YJ, Wang R, Gao L, Li D, Xu C, Mang H et al (2016) POWERDRESS and HDA9 interact and promote histone H3 deacetylation at specific genomic sites in Arabidopsis. Proc Natl Acad Sci 113(51):14858–14863
Kinoshita T, Harada J, Goldberg R, Fischer R (2001) Polycomb repression of flowering during early plant development. Proc Natl Acad Sci USA 98(24):14156–14161. https://doi.org/10.1073/pnas.241507798
Kinoshita T, Seki M (2014) Epigenetic memory for stress response and adaptation in plants. Plant Cell Physiol 55(11):1859–1863
Klee HJ, Giovannoni JJ (2011) Genetics and control of tomato fruit ripening and quality attributes. Annu Rev Genet 45:41–59
Kobayashi S, Goto-Yamamoto N, Hirochika H (2004) Retrotransposon-induced mutations in grape skin color. Science 304(5673):982
Kuang J, Chen J, Luo M, Wu K, Sun W, Jiang Y, Lu W (2011) Histone deacetylase HD2 interacts with ERF1 and is involved in longan fruit senescence. J Exp Bot 63(1):441–454
Kumar R, Khurana A, Sharma AK (2014) Role of plant hormones and their interplay in development and ripening of fleshy fruits. J Exp Bot 65(16):4561–4575
Kyriacou MC, Rouphael Y, Colla G, Zrenner R, Schwarz D (2017) Vegetable grafting: the implications of a growing agronomic imperative for vegetable fruit quality and nutritive value. Front Plant Sci 8:741
Lafon-Placette C, Le Gac AL, Chauveau D, Segura V, Delaunay A, Lesage-Descauses MC et al (2018) Changes in the epigenome and transcriptome of the poplar shoot apical meristem in response to water availability affect preferentially hormone pathways. J Exp Bot 69(3):537–551. https://doi.org/10.1093/jxb/erx409
Lafos M, Kroll P, Hohenstatt ML, Thorpe FL, Clarenz O, Schubert D (2011) Dynamic regulation of H3K27 trimethylation during Arabidopsis differentiation. PLoS Genet 7(4):e1002040
Lämke J, Bäurle I (2017) Epigenetic and chromatin-based mechanisms in environmental stress adaptation and stress memory in plants. Genome Biol 18(1):124
Lang Z, Lei M, Wang X, Tang K, Miki D, Zhang H et al (2015) The methyl-CpG-binding protein MBD7 facilitates active DNA demethylation to limit DNA hyper-methylation and transcriptional gene silencing. Mol Cell 57(6):971–983. https://doi.org/10.1016/j.molcel.2015.01.009
Lang Z, Wang Y, Tang K, Tang D, Datsenka T, Cheng J et al (2017) Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit. Proc Natl Acad Sci 114(22):E4511–E4519
Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11(3):204
Lee JM, Joung J, McQuinn R, Chung M, Fei Z, Tieman D et al (2012) Combined transcriptome, genetic diversity and metabolite profiling in tomato fruit reveals that the ethylene response factor SlERF6 plays an important role in ripening and carotenoid accumulation. Plant J 70(2):191–204
Lee S-I, Kim N-S (2014) Transposable elements and genome size variations in plants. Genomics Inform 12(3):87
Lei M, Zhang H, Julian R, Tang K, Xie S, Zhu J-K (2015) Regulatory link between DNA methylation and active demethylation in Arabidopsis. Proc Natl Acad Sci 112(11):3553–3557
Lewsey MG, Hardcastle TJ, Melnyk CW, Molnar A, Valli A, Urich MA et al (2016) Mobile small RNAs regulate genome-wide DNA methylation. Proc Natl Acad Sci 113(6):E801–E810
Li C, Gu L, Gao L, Chen C, Wei CQ, Qiu Q et al (2016) Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis. Nat Genet 48(6):687–693. https://doi.org/10.1038/ng.3555
Li S, Zhou B, Peng X, Kuang Q, Huang X, Yao J et al (2014) OsFIE2 plays an essential role in the regulation of rice vegetative and reproductive development. New Phytol 201(1):66–79
Li X, Wang X, He K, Ma Y, Su N, He H et al (2008) High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression. Plant Cell 20(2):259–276. https://doi.org/10.1105/tpc.107.056879
Li X, Zhu J, Hu F, Ge S, Ye M, Xiang H et al (2012) Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression. BMC Genom 13(1):300. https://doi.org/10.1186/1471-2164-13-300
Li Y, Kumar S, Qian W (2018) Active DNA demethylation: mechanism and role in plant development. Plant Cell Rep 37(1):77–85
Lieberman M, Segev O, Gilboa N, Lalazar A, Levin I (2004) The tomato homolog of the gene encoding UV-damaged DNA binding protein 1 (DDB1) underlined as the gene that causes the high pigment-1 mutant phenotype. Theor Appl Genet 108(8):1574–1581
Lijavetzky D, Ruiz-García L, Cabezas JA, De Andrés MT, Bravo G, Ibáñez A et al (2006) Molecular genetics of berry colour variation in table grape. Mol Genet Genomics 276(5):427–435
Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE (2001) Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292(5524):2077 LP–2080 LP
Lindroth AM, Shultis D, Jasencakova Z, Fuchs J, Johnson L, Schubert D et al (2004) Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J 23(21):4286–4296
Lira-Medeiros CF, Parisod C, Fernandes RA, Mata CS, Cardoso MA, Ferreira PCG (2010) Epigenetic variation in mangrove plants occurring in contrasting natural environment. PLoS ONE 5(4):e10326
Lister R, O’Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133(3):523–536
Liu C, Lu F, Cui X, Cao X (2010) Histone methylation in higher plants. Annu Rev Plant Biol 61:395–420
Liu D-D, Dong Q-L, Fang M-J, Chen K-Q, Hao Y-J (2012) Ectopic expression of an apple apomixis-related gene MhFIE induces co-suppression and results in abnormal vegetative and reproductive development in tomato. J Plant Physiol 169(18):1866–1873
Liu D-D, Zhou L-J, Fang M-J, Dong Q-L, An X-H, You C-X, Hao Y-J (2016) Polycomb-group protein SlMSI1 represses the expression of fruit-ripening genes to prolong shelf life in tomato. Sci Rep 6:31806
Liu J, Zhi P, Wang X, Fan Q, Chang C (2018) Wheat WD40-repeat protein TaHOS15 functions in a histone deacetylase complex to fine-tune defense responses to Blumeria graminis f. sp. tritici. J Exp Bot 70(1):255–268
Liu K, Yu Y, Dong A, Shen W (2017) SET DOMAIN GROUP701 encodes a H3K4-methytransferase and regulates multiple key processes of rice plant development. New Phytol 215(2):609–623
Liu R, How-Kit A, Stammitti L, Teyssier E, Rolin D, Mortain-Bertrand A et al (2015) A DEMETER-like DNA demethylase governs tomato fruit ripening. Proc Natl Acad Sci 112(34):10804–10809. https://doi.org/10.1073/pnas.1503362112
Lü P, Yu S, Zhu N, Chen Y-R, Zhou B, Pan Y et al (2018) Genome encode analyses reveal the basis of convergent evolution of fleshy fruit ripening. Nat Plants 4(10):784–791. https://doi.org/10.1038/s41477-018-0249-z
Lu SX, Knowles SM, Webb CJ, Celaya RB, Cha C, Siu JP, Tobin EM (2011) The Jumonji C domain-containing protein JMJ30 regulates period length in the Arabidopsis circadian clock. Plant Physiol 155(2):906–915. https://doi.org/10.1104/pp.110.167015
Luo C, Sidote DJ, Zhang Y, Kerstetter RA, Michael TP, Lam E (2013) Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production. Plant J 73(1):77–90
Luo X, Gao Z, Wang Y, Chen Z, Zhang W, Huang J et al (2018) The NUCLEAR FACTOR-CONSTANS complex antagonizes Polycomb repression to de-repress FLOWERING LOCUS T expression in response to inductive long days in Arabidopsis. Plant J 95(1):17–29. https://doi.org/10.1111/tpj.13926
Maeji H, Nishimura T (2018) Chapter two-epigenetic mechanisms in plants. https://doi.org/10.1016/bs.abr.2018.09.014
Malagnac F, Bartee L, Bender J (2002) An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation. EMBO J 21(24):6842–6852
Manning K, Tör M, Poole M, Hong Y, Thompson AJ, King GJ et al (2006) A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat Genet 38(8):948
Mathieu O, Reinders J, Čaikovski M, Smathajitt C, Paszkowski J (2007) Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation. Cell 130(5):851–862
Matzke MA, Kanno T, Matzke AJM (2015) RNA-directed DNA methylation: the evolution of a complex epigenetic pathway in flowering plants. Annu Rev Plant Biol 66:243–267
Matzke MA, Mosher RA (2014) RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat Rev Genet 15(6):394
McAtee P, Karim S, Schaffer RJ, David K (2013) A dynamic interplay between phytohormones is required for fruit development, maturation, and ripening. Front Plant Sci 4:79
Melnyk CW, Molnar A, Bassett A, Baulcombe DC (2011) Mobile 24 nt small RNAs direct transcriptional gene silencing in the root meristems of Arabidopsis thaliana. Curr Biol 21(19):1678–1683
Mirouze M, Vitte C (2014) Transposable elements, a treasure trove to decipher epigenetic variation: insights from Arabidopsis and crop epigenomes. J Exp Bot 65(10):2801–2812
Miura A, Nakamura M, Inagaki S, Kobayashi A, Saze H, Kakutani T (2009) An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites. EMBO J 28(8):1078–1086
Mozgova I, Hennig L (2015) The polycomb group protein regulatory network. Annu Rev Plant Biol 66:269–296
Niederhuth CE, Bewick AJ, Ji L, Alabady MS, Do Kim K, Li Q et al (2016) Widespread natural variation of DNA methylation within angiosperms. Genome Biol 17(1):194
Ning YQ, Ma ZY, Huang HW, Mo H, Zhao TT, Li L et al (2015) Two novel NAC transcription factors regulate gene expression and flowering time by associating with the histone demethylase JMJ14. Nucleic Acids Res 43(3):1469–1484. https://doi.org/10.1093/nar/gku1382
Ojolo SP, Cao S, Priyadarshani S, Li W, Yan M, Aslam M et al (2018) Regulation of plant growth and development: a review from a chromatin remodeling perspective. Front Plant Sci 9:1232. https://doi.org/10.3389/fpls.2018.01232
Ollat N, Cookson SJ, Lauvergeat V, Marguerit E, Barrieu F, Gambetta G et al (2017) Grapevine roots: the dark side. Acta Hortic 1188:213–226. https://doi.org/10.17660/ActaHortic.2017.1188.28
Ong-Abdullah M, Ordway JM, Jiang N, Ooi SE, Kok SY, Sarpan N et al (2015) Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm. Nature 525(7570):533–537. https://doi.org/10.1038/nature15365
Ortega-Galisteo AP, Morales-Ruiz T, Ariza RR, Roldán-Arjona T (2008) Arabidopsis DEMETER-LIKE proteins DML2 and DML3 are required for appropriate distribution of DNA methylation marks. Plant Mol Biol 67(6):671–681
Osorio S, Alba R, Damasceno CMB, Lopez-Casado G, Lohse M, Zanor MI et al (2011) Systems biology of tomato fruit development: combined transcript, protein, and metabolite analysis of tomato transcription factor (nor, rin) and ethylene receptor (Nr) mutants reveals novel regulatory interactions. Plant Physiol 157(1):405–425
Osorio S, Scossa F, Fernie A (2013) Molecular regulation of fruit ripening. Front Plant Sci 4:198
Papa CM, Springer NM, Muszynski MG, Meeley R, Kaeppler SM (2001) Maize chromomethylase Zea methyltransferase2 is required for CpNpG methylation. Plant Cell 13(8):1919–1928
Park K, Kim MY, Vickers M, Park J-S, Hyun Y, Okamoto T et al (2016) DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proc Natl Acad Sci 113(52):15138 LP–15143 LP. https://doi.org/10.1073/pnas.1619047114
Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL (2007) DNA demethylation in the Arabidopsis genome. Proc Natl Acad Sci 104(16):6752–6757. https://doi.org/10.1073/pnas.0701861104
Pikaard CS, Scheid OM (2014) Epigenetic regulation in plants. Cold Spring Harb Perspect Biol 6(12):a019315
Qian S, Lv X, Scheid RN, Lu L, Yang Z, Chen W et al (2018) Dual recognition of H3K4me3 and H3K27me3 by a plant histone reader SHL. Nat Commun 9(1):2425
Qian W, Miki D, Zhang H, Liu Y, Zhang X, Tang K et al (2012) Arabidopsis. 336(June): 1445–1448
Quadrana L, Almeida J, Asís R, Duffy T, Dominguez PG, Bermúdez L et al (2014) Natural occurring epialleles determine vitamin E accumulation in tomato fruits. Nat Commun 5:4027
Questa JI, Song J, Geraldo N, An H (2016) The sequence specific transcriptional repressor VAL1 triggers Polycomb silencing at FLC. Science 1(6298):1–5
Raj S, Bräutigam K, Hamanishi ET, Wilkins O, Thomas BR, Schroeder W et al (2011) Clone history shapes Populus drought responses. Proc Natl Acad Sci 108(30):12521–12526
Rival A, Tregear J, Verdeil JL, Richaud F, Beulé T, Duval Y et al (1998) Molecular search for MRNA and genomic markers of the oil palm “mantled” somaclonal variation. Acta Hort 461:165–172. https://doi.org/10.17660/ActaHortic.1998.461.16
Rodriguez-Granados NY, Ramirez-Prado JS, Veluchamy A, Latrasse D, Raynaud C, Crespi M et al (2016) Put your 3D glasses on: plant chromatin is on show. J Exp Bot 67(11):3205–3221
Rossi V, Locatelli S, Varotto S, Donn G, Pirona R, Henderson DA et al (2007) Maize histone deacetylase hda101 Is involved in plant development, gene transcription, and sequence-specific modulation of histone modification of genes and repeats. Plant Cell 19(4):1145–1162. https://doi.org/10.1105/tpc.106.042549
Rothbart SB, Strahl BD (2014) Interpreting the language of histone and DNA modifications. Biochim Biophys Acta (BBA) Gene Regul Mech 1839(8):627–643
Roudier F, Ahmed I, Bérard C, Sarazin A, Mary-Huard T, Cortijo S et al (2011) Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J 30(10):1928–1938. https://doi.org/10.1038/emboj.2011.103
Roy S, Gupta P, Rajabhoj MP, Maruthachalam R, Nandi AK (2018) The polycomb-group repressor MEDEA attenuates pathogen defense. Plant Physiol 177(4):1728–1742
Saleh A, Al-Abdallat A, Ndamukong I, Alvarez-Venegas R, Avramova Z (2007) The Arabidopsis homologs of trithorax (ATX1) and enhancer of zeste (CLF) establish “bivalent chromatin marks” at the silent AGAMOUS locus. Nucleic Acids Res 35(18):6290–6296. https://doi.org/10.1093/nar/gkm464
Satgé C, Moreau S, Sallet E, Lefort G, Auriac M-C, Remblière C et al (2016) Reprogramming of DNA methylation is critical for nodule development in Medicago truncatula. Nat Plants 2:16166
Saze H, Shiraishi A, Miura A, Kakutani T (2008) Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana. Science 319(5862):462–465
Schoft VK, Chumak N, Choi Y, Hannon M, Garcia-Aguilar M, Machlicova A et al (2011) Function of the DEMETER DNA glycosylase in the Arabidopsis thaliana male gametophyte. Proc Natl Acad Sci 108(19):8042–8047
Schubert D, Clarenz O, Goodrich J (2005) Epigenetic control of plant development by Polycomb-group proteins. Curr Opin Plant Biol 8(5):553–561
Sequeira-Mendes J, Araguez I, Peiro R, Mendez-Giraldez R, Zhang X, Jacobsen SE et al (2014) The functional topography of the arabidopsis genome is organized in a reduced number of linear motifs of chromatin states. Plant Cell 26(6):2351–2366. https://doi.org/10.1105/tpc.114.124578
Serrano A, Espinoza C, Armijo G, Inostroza-Blancheteau C, Poblete E, Meyer-Regueiro C et al (2017) Omics approaches for understanding grapevine berry development: regulatory networks associated with endogenous processes and environmental responses. Front Plant Sci 8:1486
Seymour DK, Koenig D, Hagmann J, Becker C, Weigel D (2014) Evolution of DNA methylation patterns in the Brassicaceae is driven by differences in genome organization. PLoS Genet 10(11):e1004785
Seymour GB, Østergaard L, Chapman NH, Knapp S, Martin C (2013) Fruit development and ripening. Annu Rev Plant Biol 64:219–241
Sharif J, Muto M, Takebayashi S, Suetake I, Iwamatsu A, Endo TA et al (2007) The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Nature 450(7171):908
Shen Y, Issakidis-Bourguet E, Zhou D-X (2016) Perspectives on the interactions between metabolism, redox, and epigenetics in plants. J Exp Bot 67(18):5291–5300
Spillane C, MacDougall C, Stock C, Köhler C, Vielle-Calzada JP, Nunes SM et al (2000) Interaction of the Arabidopsis polycomb group proteins FIE and MEA mediates their common phenotypes. Curr Biol 10(23):1535–1538
Stroud H, Do T, Du J, Zhong X, Feng S, Johnson L et al (2014) Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nat Struct Mol Biol 21(1):64
Stroud H, Greenberg MVC, Feng S, Bernatavichute YV, Jacobsen SE (2013) Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell 152(1–2):352–364
Sun B, Looi L-S, Guo S, He Z, Gan E-S, Huang J et al (2014) Timing mechanism dependent on cell division is invoked by Polycomb eviction in plant stem cells. Science 343(6170):1248559
Takuno S, Gaut BS (2011) Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly. Mol Biol Evol 29(1):219–227
Talbert PB, Henikoff S (2017) Histone variants on the move: substrates for chromatin dynamics. Nat Rev Mol Cell Biol 18(2):115
Taller J, Hirata Y, Yagishita N, Kita M, Ogata S (1998) Graft-induced genetic changes and th inheritance of several characteristics in pepper. Theor Appl Genet 97:705–713
Tang N, Ma S, Zong W, Yang N, Lv Y, Yan C et al (2016a) MODD mediates deactivation and degradation of OsbZIP46 to negatively regulate ABA signaling and drought resistance in rice. Plant Cell 28(9):2161–2177
Tang X, Miao M, Niu X, Zhang D, Cao X, Jin X et al (2016b) Ubiquitin-conjugated degradation of golden 2-like transcription factor is mediated by CUL4-DDB1-based E3 ligase complex in tomato. New Phytol 209(3):1028–1039. https://doi.org/10.1111/nph.13635
Tang Y, Liu X, Liu X, Li Y, Wu K, Hou X (2017) Arabidopsis NF-YCs mediate the light-controlled hypocotyl elongation via modulating histone acetylation. Mol Plant 10(2):260–273
Telias A, Lin-Wang K, Stevenson DE, Cooney JM, Hellens RP, Allan AC et al (2011) Apple skin patterning is associated with differential expression of MYB10. BMC Plant Biol 11(1):93
Teyssier E, Bernacchia G, Maury S, How Kit A, Stammitti-Bert L, Rolin D, Gallusci P (2008) Tissue dependent variations of DNA methylation and endoreduplication levels during tomato fruit development and ripening. Planta 228(3):391
This P, Lacombe T, Cadle-Davidson M, Owens CL (2007) Wine grape (Vitis vinifera L.) color associates with allelic variation in the domestication gene VvmybA1. Theor Appl Genet 114(4):723–730
Thompson AJ, Tor M, Barry CS, Vrebalov J, Orfila C, Jarvis MC et al (1999) Molecular and genetic characterization of a novel pleiotropic tomato-ripening mutant. Plant Physiol 120(2):383–390
Torres IO, Fujimori DG (2015) Functional coupling between writers, erasers and readers of histone and DNA methylation. Curr Opin Struct Biol 35:68–75
Trindade I, Schubert D, Gaudin V (2017) Epigenetic regulation of phase transitions in Arabidopsis thaliana. In: Rajewsky N, Jurga S, Barciszewski J (ed) Plant epigenetics. Springer, Berlin, pp 359–383. https://link.springer.com/book/10.1007/978-3-319-55520-1
Uthup TK, Karumamkandathil R, Ravindran M, Saha T (2018) Heterografting induced DNA methylation polymorphisms in Hevea brasiliensis. Planta 248(3):579–589
Vachon G, Engelhorn J, Carles CC (2018) Interactions between transcription factors and chromatin regulators in the control of flower development. Oxford University Press, Oxford
van Leeuwen C, Darriet P (2016) The impact of climate change on viticulture and wine quality. J Wine Econ 11(1):150–167
Veluchamy A, Jégu T, Ariel F, Latrasse D, Mariappan KG, Kim S-K et al (2016) LHP1 regulates H3K27me3 spreading and shapes the three-dimensional conformation of the Arabidopsis genome. PLoS ONE 11(7):e0158936
Vergara Z, Gutierrez C (2017) Emerging roles of chromatin in the maintenance of genome organization and function in plants. Genome Biol 18(1):96
Verhoeven KJF, Preite V (2014) Epigenetic variation in asexually reproducing organisms. Evolution 68(3):644–655
Verriès C, Bès C, This P, Tesnière C (2000) Cloning and characterization of Vine-1, a LTR-retrotransposon-like element in Vitis vinifera L., and other Vitis species. In: Genome, vol 43. https://doi.org/10.1139/g99-139
Vongs A, Kakutani T, Martienssen RA, Richards EJ (1993) Arabidopsis thaliana DNA methylation mutants. Science 260(5116):1926 LP–1928 LP. https://doi.org/10.1126/science.8316832
Waddington CH (1942) The epigenotype. Endeavour 1:18–20
Wang C, Liu C, Roqueiro D, Grimm D, Schwab R, Becker C et al (2015) Genome-wide analysis of local chromatin packing in Arabidopsis thaliana. Genome Res 25(2):246–256
Wang G, Köhler C (2017) Epigenetic processes in flowering plant reproduction. J Exp Bot 68(4):797–807
Wang H, Zhai L, Xu J, Joo H-Y, Jackson S, Erdjument-Bromage H et al (2006) Histone H3 and H4 ubiquitylation by the CUL4-DDB-ROC1 ubiquitin ligase facilitates cellular response to DNA damage. Mol Cell 22(3):383–394
Wang Z, Meng D, Wang A, Li T, Jiang S, Cong P, Li T (2013) The methylation of the PcMYB10 promoter is associated with green-skinned sport in Max Red Bartlett pear. Plant Physiol 162(2):885–896
Warschefsky EJ, Klein LL, Frank MH, Chitwood DH, Londo JP, von Wettberg EJB, Miller AJ (2016) Rootstocks: diversity, domestication, and impacts on shoot phenotypes. Trends Plant Sci 21(5):418–437
Weinert BT, Narita T, Satpathy S, Srinivasan B, Hansen BK, Schölz C et al (2018) Time-resolved analysis reveals rapid dynamics and broad scope of the CBP/p300 acetylome. Cell 174(1):231–244
Wendte JM, Pikaard CS (2017) The RNAs of RNA-directed DNA methylation. Biochim Biophys Acta (BBA) Gene Regul Mech 1860(1):140–148
Whittaker C, Dean C (2017) The FLC locus: a platform for discoveries in epigenetics and adaptation. Annu Rev Cell Dev Biol 33:555–575
Williams BP, Pignatta D, Henikoff S, Gehring M (2015) Methylation-sensitive expression of a DNA demethylase gene serves as an epigenetic rheostat. PLoS Genet 11(3):e1005142
Woo HR, Dittmer TA, Richards EJ (2008) Three SRA-domain methylcytosine-binding proteins cooperate to maintain global CpG methylation and epigenetic silencing in Arabidopsis. PLoS Genet 4(8):e1000156
Woong C, Roh H, Vi T, Do Y, Fischer RL, Seob J et al (2011) An E3 ligase complex regulates SET-domain polycomb group protein activity in Arabidopsis thaliana. PNAS 108(19):8036–8041. https://doi.org/10.1073/pnas.1104232108
Wu C, Morris JR (2001) Genes, genetics, and epigenetics: a correspondence. Science 293(5532):1103 LP–1105 LP. https://doi.org/10.1126/science.293.5532.1103
Wu HW, Deng S, Xu H, Mao HZ, Liu J, Niu QW et al (2018) A noncoding RNA transcribed from the AGAMOUS (AG) second intron binds to CURLY LEAF and represses AG expression in leaves. New Phytol 219(4):1480–1491. https://doi.org/10.1111/nph.15231
Wu R, Wang X, Lin Y, Ma Y, Liu G, Yu X et al (2013) Inter-species grafting caused extensive and heritable alterations of DNA methylation in Solanaceae plants. PLoS ONE 8(4):e61995
Xanthopoulou A, Tsaballa A, Ganopoulos I, Kapazoglou A, Avramidou E, Aravanopoulos FA et al (2019) Ιntra-species grafting induces epigenetic and metabolic changes accompanied by alterations in fruit size and shape of Cucurbita pepo L. Plant Growth Regul 87(1):93–108
Xiao J, Jin R, Yu X, Shen M, Wagner JD, Pai A et al (2017) Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis. Nat Genet 49(10):1546–1552. https://doi.org/10.1038/ng.3937
Xiao J, Lee U-S, Wagner D (2016) Tug of war: adding and removing histone lysine methylation in Arabidopsis. Curr Opin Plant Biol 34:41–53
Xie H, Konate M, Sai N, Tesfamicael KG, Cavagnaro T, Gilliham M et al (2017) Global DNA methylation patterns can play a role in defining terroir in grapevine (Vitis vinifera cv. Shiraz). Front Plant Sci 8:1860
Xing L, Liu Y, Xu S, Xiao J, Wang B, Deng H et al (2018) Arabidopsis O-GlcNAc transferase SEC activates histone methyltransferase ATX1 to regulate flowering. EMBO J 37(19):e98115
Xu J, Xu H, Liu Y, Wang X, Xu Q, Deng X (2015) Genome-wide identification of sweet orange (Citrus sinensis) histone modification gene families and their expression analysis during the fruit development and fruit-blue mold infection process. Front Plant Sci 6:607
Yadegari R, Kinoshita T, Lotan O, Cohen G, Katz A, Choi Y et al (2000) Mutations in the FIE and MEA genes that encode interacting Polycomb proteins cause parent-of-origin effects on seed development by distinct mechanisms. Plant Cell 12(12):2367–2382. https://doi.org/10.1105/tpc.12.12.2367
Yagishita N (1961) Studies on graft hybrids of Capsicun annuum L. II. Variation in fruit shape caused by grafting for three generations and the effects in the progeny. Bot Mag Tokyo 74:480–489
Yamamuro C, Zhu J-K, Yang Z (2016) Epigenetic modifications and plant hormone action. Mol Plant 9(1):57–70
Yong W-S, Hsu F-M, Chen P-Y (2016) Profiling genome-wide DNA methylation. Epigenetics Chromatin 9(1):26
Yu C-W, Tai R, Wang S-C, Yang P, Luo M, Yang S et al (2017) HISTONE DEACETYLASE6 acts in concert with histone methyltransferases SUVH4, SUVH5, and SUVH6 to regulate transposon silencing. Plant Cell 29(8):1970–1983
Yuan W, Luo X, Li Z, Yang W, Wang Y, Liu R et al (2016) A cis cold memory element and a trans epigenome reader mediate Polycomb silencing of FLC by vernalization in Arabidopsis. Nat Genet 48(12):1527
Zemach A, Kim MY, Hsieh P-H, Coleman-Derr D, Eshed-Williams L, Thao K et al (2013) The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell 153(1):193–205
Zemach A, McDaniel IE, Silva P, Zilberman D (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328(5980):916–919
Zhang S, Zhou B, Kang Y, Cui X, Liu A, Deleris A et al (2015) C-terminal domains of histone demethylase JMJ14 interact with a pair of NAC transcription factors to mediate specific chromatin association. Cell Discov 1:15003
Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW-L, Chen H et al (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126(6):1189–1201
Zhao H, Zhao K, Wang J, Chen X, Chen Z, Cai R, Xiang Y (2015) Comprehensive analysis of Dicer-like, Argonaute, and RNA-dependent RNA polymerase gene families in grapevine (Vitis vinifera). J Plant Growth Regul 34(1):108–121
Zheng M, Wang Y, Wang Y, Wang C, Ren Y, Lv J et al (2015) DEFORMED FLORAL ORGAN1 (DFO1) regulates floral organ identity by epigenetically repressing the expression of OsMADS58 in rice (Oryza sativa). New Phytol 206(4):1476–1490
Zheng X, Pontes O, Zhu J, Miki D, Zhang F, Li W-X et al (2008) ROS3 is an RNA-binding protein required for DNA demethylation in Arabidopsis. Nature 455(7217):1259
Zheng Y, Liu X (2019) Chromatin organization in plant and animal stem cell maintenance. Plant Sci 281:173–179. https://doi.org/10.1016/j.plantsci.2018.12.026
Zheng Y, Thomas PM, Kelleher NL (2013) Measurement of acetylation turnover at distinct lysines in human histones identifies long-lived acetylation sites. Nat Commun 4:2203
Zhong S, Fei Z, Chen Y-R, Zheng Y, Huang M, Vrebalov J et al (2013) Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat Biotechnol 31(2):154
Zhou Y, Wang Y, Krause K, Yang T, Dongus JA, Zhang Y, Turck F (2018) Telobox motifs recruit CLF/SWN–PRC2 for H3K27me3 deposition via TRB factors in Arabidopsis. Nat Genet 50(5):638
Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S (2007) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39(1):61
Zuo J, Wang Y, Zhu B, Luo Y, Wang Q, Gao L (2018) Comparative analysis of DNA methylation reveals specific regulations on ethylene pathway in tomato fruit. Genes 9(5):266
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Kong, J., Berger, M., Colling, A., Stammitti, L., Teyssier, E., Gallusci, P. (2019). Epigenetic Regulation in Fleshy Fruit: Perspective for Grape Berry Development and Ripening. In: Cantu, D., Walker, M. (eds) The Grape Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-18601-2_9
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