Abstract
This paper considers molecular mechanisms of DNA methylation and histone modifications in plants. The role of these epigenetic processes in plant development is discussed.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Wu, C. and Morris, J.R., Genes, genetics, and epigenetics: a correspondence, Science, 2001, vol. 293, no. 5532, pp. 1103–1105. doi 10.1126/science.293.5532.1103
Jablonka, E. and Lamb, M.J., The changing concept of epigenetics, Ann. N.Y. Acad. Sci., 2002, vol. 981, pp. 82–96. doi 10.1111/j.1749-6632.2002.tb04913.x
Korochkin, L.I., What is epigenetics?, Russ. J. Genet., 2006, vol. 42, no. 9, pp. 958–965. doi 10.1134/S102279540609002X
Chadov, B.F., A new stage in the development of genetics and term epigenetics, Russ. J. Genet., 2006, vol. 42, no. 9, pp. 1053–1065. doi 10.1134/S1022795406090110
Tikhodeev, O.N., Epigenetic and eugenetic processes, Biol. Bull. Rev., 2016, vol. 6, no. 4, pp. 333–343. doi 10.1134/S2079086416040071
Waddington, C.H., The epigenotype, Endeavour, 1942, vol. 1, pp. 18–20.
Holliday, R., DNA methylation and epigenetic inheritance, Philos. Trans. R. Soc., B, 1990, vol. 326, no. 1235, pp. 329–338. doi 10.1098/rstb.1990.0015
Vanyushin, B.F., Epigenetics today and tomorrow, Russ. J. Genet.: Appl. Res., 2014, vol. 4, no. 3, pp. 805–831. doi 10.1134/S2079059714030083
Bird, A. and Macleod, D., Reading the DNA methylation signal, Cold Spring Harbor Symp. Quant. Biol., 2004, vol. 69, pp. 113–118. doi 10.1101/sqb. 2004.69.113
Berger, S.L., Kouzarides, T., Shiekhattar, R., and Shilatifard, A., An operational definition of epigenetics, Genes Dev., 2009, vol. 23, no. 7, pp. 781–783. doi 10.1101/gad.1787609
Marinus, M.G. and Casadesus, J., Roles of DNA adenine methylation in host—pathogen interactions: mismatch repair, transcriptional regulation, and more, FEMS Microbiol. Rev., 2009, vol. 33, no. 3, pp. 488–503. doi 10.1111/j.1574-6976.2008.00159.x
Kumar, R. and Rao, D.N., Role of DNA methyltransferases in epigenetic regulation in bacteria, Subcell. Biochem., 2013, vol. 61, pp. 81–102. doi 10.1007/978-94-007-4525-4_4
Bestor, T.H., The DNA methyltransferases of mammals, Hum. Mol. Genet., 2000, vol. 9, no. 16, pp. 2395–2402. doi 10.1093/hmg/9.16.2395
Jeltsch, A., Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases, Chembiochem, 2002, vol. 3, no. 4, pp. 274–293.
Cokus, S.J., Feng, S., Zhang, X., et al., Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning, Nature, 2008, vol. 452, no. 7184, pp. 215–219. doi 10.1038/nature06745
Smith, Z.D. and Meissner, A., DNA methylation: roles in mammalian development, Nat. Rev. Genet., 2013, vol. 14, no. 3, pp. 204–220. doi 10.1038/nrg3354
Raddatz, G., Guzzardo, P.M., Olova, N., et al., Dnmt2-dependent methylomes lack defined DNA methylation patterns, Proc. Natl. Acad. Sci. U.S.A., 2013, vol. 110, no. 21, pp. 8627–8631. doi 10.1073/pnas.1306723110
Goll, M.G., Kirpekar, F., Maggert, K.A., et al., Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2, Science, 2006, vol. 311, no. 5759, pp. 395–398. doi 10.1126/science.1120976
Ashapkin, V.V., Kutueva, L.I., and Vanyushin, B.F., Dnmt2 is the most evolutionary conserved and enigmatic cytosine DNA methyltransferase in eukaryotes, Russ. J. Genet., 2016, vol. 52, no. 3, pp. 237–248.
Law, J.A. and Jacobsen, S.E., Molecular biology: dynamic DNA methylation, Science, 2009, vol. 323, no. 5921, pp. 1568–1569. doi 10.1126/science.1172782
Teixeira, F.K. and Colot, V., Repeat elements and the Arabidopsis DNA methylation landscape, Heredity (Edinburgh), 2010, vol. 105, no. 1, pp. 14–23. doi 10.1038/hdy.2010.52
Ashapkin, V.V., Kutueva, L.I., and Vanyushin, B.F., Plant DNA methyltransferase genes: multiplicity, expression, methylation patterns, Biochemistry (Moscow), 2016, vol. 81, no. 2, pp. 141–151. doi 10.1134/S0006297916020085
Finnegan, E.J., Peacock, W.J., and Dennis, E.S., Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development, Proc. Natl. Acad. Sci. U.S.A., 1996, vol. 93, no. 16, pp. 8449–8454.
Lindroth, A.M., Cao, X., Jackson, J.P., et al., Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation, Science, 2001, vol. 292, no. 5524, pp. 2077–2080. doi 10.1126/science. 1059745
Cao, X. and Jacobsen, S.E., Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing, Curr. Biol., 2002, vol. 12, no. 13, pp. 1138–1144. doi 10.1126/science.1059745
Vongs, A., Kakutani, T., Martienssen, R.A., and Richards, E.J., Arabidopsis thaliana DNA methylation mutants, Science, 1993, vol. 260, no. 5116, pp. 1926–1928. doi 10.1126/science.8316832
Brzeski, J. and Jerzmanowski, A., Deficient in DNA methylation 1 (DDM1) defines a novel family of chromatin-remodeling factors, J. Biol. Chem., 2003, vol. 278, no. 2, pp. 823–828. doi 10.1074/jbc. M209260200
Lippman, Z., Gendrel, A.V., Black, M., et al., Role of transposable elements in heterochromatin and epigenetic control, Nature, 2004, vol. 430, no. 6998, pp. 471–476. doi 10.1038/nature02651
Kakutani, T., Jeddeloh, J.A., Flowers, S.K., et al., Developmental abnormalities and epimutations associated with DNA hypomethylation mutations, Proc. Natl. Acad. Sci. U.S.A., 1996, vol. 93, no. 22, pp. 12406–12411.
Zilberman, D., Gehring, M., Tran, R.K., et al., Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription, Nat. Genet., 2007, vol. 39, no. 1, pp. 61–69. doi 10.1038/ng1929
Berdasco, M., Alcá zar, R., Garcí a-Ortiz, M.V., et al., Promoter DNA hypermethylation and gene repression in undifferentiated Arabidopsis cells, PLoS One, 2008, vol. 3, no. 10. e3306. doi 10.1371/journal.pone. 0003306
Zhang, X., Yazaki, J., Sundaresan, A., et al., Genomewide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis, Cell, 2006, vol. 126, no. 6, pp. 1189–1201. doi 10.1016/j.cell. 2006.08.003
Borges, F. and Martienssen, R.A., The expanding world of small RNAs in plants, Nat. Rev. Mol. Cell Biol., 2015, vol. 16, no. 12, pp. 727–741. doi 10.1038/nrm4085
Chan, S.W., Henderson, I.R., and Jacobsen, S.E., Gardening the genome: DNA methylation in Arabidopsis thaliana, Nat. Rev. Genet., 2005, vol. 6, no. 5, pp. 351–360. doi 10.1038/nrg1601
Pikaard, C.S., Haag, J.R., Ream, T., and Wierzbicki, A.T., Roles of RNA polymerase IV in gene silencing, Trends Plant Sci., 2008, vol. 13, no. 7, pp. 390–397. doi 10.1016/j.tplants.2008.04.008
Haag, J.R. and Pikaard, C.S., Multisubunit RNA polymerases IVand V: purveyors of non-coding RNA for plant gene silencing, Nat. Rev. Mol. Cell Biol., 2011, vol. 12, no. 8, pp. 483–492. doi 10.1038/nrm3152
Herr, A.J., Jensen, M.B., Dalmay, T., and Baulcombe, D.C., RNA polymerase IV directs silencing of endogenous DNA, Science, 2005, vol. 308, no. 5718, pp. 118–120. doi 10.1126/science.1106910
Pikaard, C.S. and Mittelsten-Scheid, O., Epigenetic regulation in plants, Cold Spring Harbor Perspect. Biol., 2014, vol. 6, no. 12. a019315. doi 10.1101/cshperspect. a019315
Zhang, H., He, X., and Zhu, J.K., RNA-directed DNA methylation in plants: where to start?, RNA Biol., 2013, vol. 10, no. 10, pp. 1593–1596. doi 10.4161/rna.26312
Zhong, X., Hale, C.J., Law, J.A., et al., DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons, Nat. Struct. Mol. Biol., 2012, vol. 19, no. 9, pp. 870–875. doi 10.1038/nsmb.2354
Wierzbicki, A.T., Cocklin, R., Mayampurath, A., et al., Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome, Genes Dev., 2012, vol. 26, pp. 1825–1836. doi 10.1101/gad.197772.112
Jullien, P., Mosquna, A., Ingouff, M., et al., Retinoblastoma and its binding partner MSI1 control imprinting in Arabidopsis, PLoS Biol., 2008, vol. 6, no. 8. e194. doi 10.1371/journal.pbio.0060194
Choi, Y., Gehring, M., Johnson, L., et al., DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis, Cell, 2002, vol. 110, no. 1, pp. 33–42. doi 10.1016/S0092-8674(02)00807-3
Gehring, M., Huh, J., Hsieh, T., et al., DEMETER DNA glycosylase establishes MEDEA Polycomb gene self-imprinting by allele-specific demethylation, Cell, 2006, vol. 124, no. 3, pp. 495–506. doi 10.1016/j.cell.2005.12.034
Huh, J., Bauer, M., Hsieh, T., and Fischer, R., Cellular programming of plant gene imprinting, Cell, 2008, vol. 132, no. 5, pp. 735–744. doi 10.1016/j.cell.2008.02.018
Zhu, J., Kapoor, A., Sridhar, V., et al., The DNA glycosylase/lyase ROS1 functions in pruning DNA methylation patterns in Arabidopsis, Curr. Biol., 2007, vol. 17, no. 1, pp. 54–59. doi 10.1016/j.cub.2006. 10.059
Penterman, J., Zilberman, D., Huh, J., et al., DNA demethylation in the Arabidopsis genome, Proc. Natl. Acad. Sci. U.S.A., 2007, vol. 104, no. 16, pp. 6752–6757. doi 10.1073/pnas.0701861104
Ibarra, C., Feng, X., Schoft, V., et al., Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes, Science, 2012, vol. 337, no. 6100, pp. 1360–1364. doi 10.1126/science. 1224839
Huettel, B., Kanno, T., Daxinger, L., et al., Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis, EMBO J., 2006, vol. 25, no. 12, pp. 2828–2836. doi 10.1038/sj.emboj.7601150
Mathieu, O., Reinders, J., C aikovski, M., et al., Transgenerational stability of the Arabidopsis epigenome is coordinated by CGmethylation, Cell, 2007, vol. 130, no. 5, pp. 851–862. doi 10.1016/j.cell.2007.07.007
Zhu, J., Active DNA demethylation mediated by DNA glycosylases, Annu. Rev. Genet., 2009, vol. 43, pp. 143–166. doi 10.1146/annurev-genet-102108-134205
Zheng, X., Pontes, O., Zhu, J., et al., ROS3 is an RNA-binding protein required for DNA demethylation in Arabidopsis, Nature, 2008, vol. 455, no. 7217, pp. 1259–1262. doi 10.1038/nature07305
Zilberman, D., Coleman-Derr, D., Ballinger, T., and Henikoff, S., Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks, Nature, 2008, vol. 456, no. 7218, pp. 125–129. doi 10.1038/ nature07324
Pien, S., Fleury, D., Mylne, J.S., and Crevillen, P., ARABIDOPSIS TRITHORAX1 dynamically regulates FLOWERING LOCUS C activation via histone 3 lysine 4 trimethylation, Plant Cell, 2008, vol. 3, pp. 580–588. doi 10.1105/tpc.108.058172
Tamada, Y., Yun, J.Y., Woo, S.C., and Amasino, R.M., ARABIDOPSIS TRITHORAX-RELATED7 is required for methylation of lysine 4 of histone H3 and for transcriptional activation of FLOWERING LOCUS C, Plant Cell, 2009, vol. 21, no. 10, pp. 3257–3269. doi 10.1105/tpc.109.070060
Tolhuis, B., de Wit, E., Muijrers, I., Teunissen, H., et al., Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster, Nat. Genet., 2006, vol. 38, no. 6, pp. 694–699. doi 10.1038/ng1792
Zhang, X., Clarenz, O., Cokus, S., and Bernatavichute, Y.V., Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis, PLoS Biol., 2007, vol. 5, no. 5. e129. doi 10.1371/journal. pbio.0050129
He, C., Huang, H., and Xu, L., Mechanisms guiding Polycomb activities during gene silencing in Arabidopsis thaliana, Front Plant Sci., 2013, vol. 4, p. 454. doi 10.3389/fpls
Derkacheva, M. and Hennig, L., Variations on a time: Polycomb group protein in plants, J. Exp. Bot., 2014, vol. 65, no. 10, pp. 2769–2784. doi 10.1093/jxb/ert410
Exner, V., Aichinger, E., Shu, H., Wildhaber, T., et al., The chromodomain of LIKE HETEROCHROMATIN PROTEIN 1 is essential for H3K27me3 binding and function during Arabidopsis development, PLoS One, 2009, vol. 4, no. 4. e5335. doi 10.1371/journal.pone.0005335
Xu, L. and Shen, W.H., Polycomb silencing of KNOX genes confines shoot stem cell niches in Arabidopsis, Curr. Biol., 2008, vol. 18, no. 24, pp. 1966–1971. doi 10.1016/j.cub.2008.11.019
Zhang, H., Ma, Z.Y., Zeng, L., et al., DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV, Proc. Natl. Acad. Sci. U.S.A., 2013, vol. 110, no. 20, pp. 8290–8265. doi 10.1073/pnas.1300585110
Law, J.A., Du, J., Hale, C.J., et al., Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1, Nature, 2013, vol. 498, no. 7454, pp. 385–389. doi 10.1038/nature12178
Johnson, L.M., Bostick, M., Zhang, X., et al., The SRA methyl-cytosine-binding domain links DNA and histone methylation, Curr. Biol., 2007, vol. 17, no. 4, pp. 379–384. doi 10.1016/j.cub.2007.01.009
Du, J., Johnson, L.M., Groth, M., et al., Mechanism of DNA methylation-directed histone methylation by KRYPTONITE, Mol. Cell, 2014, vol. 55, no. 3, pp. 495–504. doi 10.1016/j.molcel.2014.06.009
Kakutani, T., Munakata, K., Richards, E.J., and Hirochika, H., Meiotically and mitotically stable inheritance of DNA hypomethylation induced by ddm1 mutation of Arabidopsis thaliana, Genetics, 1999, vol. 151, no. 2, pp. 831–838.
Arteaga-Vazquez, M.A. and Chandler, V.L., Paramutation in maize: RNA-mediated trans-generational gene silencing, Curr. Opin. Genet. Dev., 2010, vol. 20, no. 2, pp. 156–163. doi 10.1016/j.gde.2010.01.008
Hollick, J.B., Paramutation and related phenomena in diverse species, Nat. Rev. Genet., 2016. doi 10.1038/nrg.2016.115
Brink, R.A., Paramutation at the R locus in maize, Cold Spring Harbor Symp. Quant. Biol., 1958, vol. 23, pp. 379–391.
Rassoulzadegan, M., Grandjean, V., Gounon, P., et al., RNA-mediated non-mendelian inheritance of an epigenetic change in the mouse, Nature, 2006, vol. 441, pp. 469–474. doi 10.1038/nature04674
de Vanssay, A., Bougé, A.L., Boivin, A., et al., Paramutation in Drosophila linked to emergence of a piRNA-producing locus, Nature, 2012, vol. 490, no. 7418, pp. 112–117. doi 10.1038/nature11416
Shirayama, M., Seth, M., Lee, H.C., et al., piRNAs initiate an epigenetic memory of non-self RNA in the C. elegans germline, Cell, 2012, vol. 150, no. 1, pp. 65–77. doi 10.1016/j.cell.2012.06.015
Choi, J., Hyun, Y., Kang, M.-J., et al., Resetting and regulation of flowering locus C expression during Arabidopsis reproductive development, Plant J., 2009, vol. 57, no. 5, pp. 918–931. doi 10.1111/j.1365- 313X.2008.03776.x
Iwasaki, M., Chromatin resetting mechanisms preventing transgenerational inheritance of epigenetic states, Front. Plant Sci., 2015, vol. 6, p. 380. doi 10.3389/fpls.2015.00380
Crevillén, P., Yang, H., Cui, X., et al., Epigenetic reprogramming that prevents transgenerational inheritance of the vernalized state, Nature, 2014, vol. 515, no. 7528, pp. 587–590. doi 10.1038/nature13722
Kwiatkowska, D., Flowering and apical meristem growth dynamics, J. Exp. Bot., 2008, vol. 59, no. 2, pp. 187–201. doi 10.1093/jxb/erm290
Batygina, T.B., Embriologiya tsvetkovykh rastenii: terminologiya i kontseptsii (Embryology of Flowering Plants: Terminology and Concepts), vol. 1: Generativnye organy tsvetka (Generative Organs of Flower), St. Petersburg: Mir i Sem’ya, 1994, vol. 1.
Yang, H., Lu, P., Wang, Y., and Ma, H., The transcriptome landscape of Arabidopsis male meiocytes from high-throughput sequencing: the complexity and evolution of the meiotic process, Plant J., 2011, vol. 65, no. 4, pp. 503–516. doi 10.1111/j.1365-313X.2010. 04439.x
Kawashima, T. and Berger, F., Epigenetic reprogramming in plant sexual reproduction, Nat. Rev. Genet., 2014, vol. 15, no. 9, pp. 613–624. doi 10.1038/nrg3685
Calarco, J., Borges, F., Donoghue, M., et al., Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA, Cell, 2012, vol. 151, no. 1, pp. 194–205. doi 10.1016/j.cell.2012.09.001
Garcia-Aguilar, M., Michaud, C., Leblanc, O., and Grimanelli, D., Inactivation of a DNA methylation pathway in maize reproductive organs results in apomixis- like phenotypes, Plant Cell, 2010, vol. 22, no. 10, pp. 3249–3267. doi 10.1105/tpc.109.072181
Jullien, P., Susaki, D., Yelagandula, R., et al., DNA methylation dynamics during sexual reproduction in Arabidopsis thaliana, Curr. Biol., 2012, vol. 22, no. 19, pp. 1825–1830. doi 10.1016/j.cub.2012.07.061
Mosher, R., Melnyk, C., Kelly, K., et al., Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis, Nature, 2009, vol. 460, no. 7252, pp. 283–286. doi 10.1038/nature08084
Slotkin, R., Vaughn, M., Borges, F., et al., Epigenetic reprogramming and small RNA silencing of transposable elements in pollen, Cell, 2009, vol. 136, no. 3, pp. 461–472. doi 10.1016/j.cell.2008.12.038
Nuthikattu, S., McCue, A., Panda, K., et al., The initiation of epigenetic silencing of active transposable elements is triggered by RDR6 and 21–22 nucleotide small interfering RNAs, Plant Physiol., 2013, vol. 162, no. 1, pp. 116–131. doi 10.1104/pp.113.216481
Grant-Downton, R., Kourmpetli, S., Hafidh, S., et al., Artificial microRNAs reveal cell-specific differences in small RNA activity in pollen, Curr. Biol., 2013, vol. 23, no. 14, pp. 599–601. doi 10.1016/ j.cub.2013.05.055
Schoft, V., Chumak, N., Mosiolek, M., et al., Induction of RNA-directed DNA methylation upon decondensation of constitutive heterochromatin, EMBO Rep., 2009, vol. 10, no. 9, pp. 1015–1021. doi 10.1038/embor.2009.152
Feng, S., Jacobsen, S., and Reik, W., Epigenetic reprogramming in plant and animal development, Science, 2010, vol. 330, no. 6004, pp. 622–627. doi 10.1126/science.1190614
Saze, H., Mittelsten-Scheid, O., and Paszkowski, J., Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis, Nat. Genet., 2003, vol. 34, no. 1, pp. 65–69. doi 10.1038/ng1138
Schoft, V., Chumak, N., Choi, Y., et al., Function of the DEMETER DNA glycosylase in the Arabidopsis thaliana male gametophyte, Proc. Natl. Acad. Sci. U.S.A., 2011, vol. 108, no. 19, pp. 8042–8047. doi 10.1073/pnas.1105117108
Gong, Z., Morales-Ruiz, T., Ariza, R., et al., ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase, Cell, 2002, vol. 111, no. 6, pp. 803–814. doi 10.1016/S0092- 8674(02)01133-9
Becker, C., Hagmann, J., Muller, J., et al., Spontaneous epigenetic variation in the Arabidopsis thaliana methylome, Nature, 2011, vol. 480, no. 7376, pp. 245–249. doi 10.1038/nature10555
Kubo, T., Fujita, M., Takahashi, H., et al., Transcriptome analysis of developing ovules in rice isolated by laser microdissection, Plant Cell Physiol., 2013, vol. 54, no. 5, pp. 750–765. doi 10.1093/pcp/pct029
Singh, M., Goel, S., Meeley, R., et al., Production of viable gametes without meiosis in maize deficient for an ARGONAUTE protein, Plant Cell, 2011, vol. 23, no. 2, pp. 443–458. doi 10.1105/tpc.110.079020
Qi, Y., He, X., Wang, X., et al., Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNAdirected DNA methylation, Nature, 2006, vol. 443, no. 7114, pp. 1008–1012. doi 10.1038/nature05198
Olmedo-Monfil, V., Durán-Figueroa, N., Arteaga-Vázquez, M., et al., Control of female gamete formation by a small RNA pathway in Arabidopsis, Nature, 2010, vol. 464, no. 7288, pp. 628–632. doi 10.1038/ nature08828
Ingouff, M., Rademacher, S., Holec, S., et al., Zygotic resetting of the HISTONE 3 variant repertoire participates in epigenetic reprogramming in Arabidopsis, Curr. Biol., 2010, vol. 20, no. 23, pp. 2137–2143. doi 10.1016/j.cub.2010.11.012
Mayer, K.F., Schoof, H., Haecker, A., Lenhardt, M., et al., Role of WUSCHEL in regulating stem cell fate in the Arabidopsis shoot meristem, Cell, 1998, vol. 95, no. 6, pp. 805–815. doi 10.1104/pp.113.216481
Lohmann, J.U., Hong, R.L., Hobe, M., Busch, M.A., et al., A molecular link between stem cell regulation and floral patterning in Arabidopsis, Cell, 2001, vol. 105, no. 6, pp. 793–803. doi 10.1016/S0092- 8674(01)00384-1
Liu, X., Kim, Y.J., Müller, R., et al., AGAMOUS terminates floral stem cell maintenance in Arabidopsis by directly repressing WUSCHEL through recruitment of Polycomb group proteins, Plant Cell, 2011, vol. 23, no. 10, pp. 3654–3670. doi 10.1105/tpc.111.091538
Gordon, S.P., Heisler, M.G., Reddy, G.V., et al., Pattern formation during de novo assembly of the Arabidopsis shoot meristem, Development, 2007, vol. 134, no. 19, pp. 3539–3548. doi 10.1242/dev.010298
Li, W., Liu, H., Cheng, Z.J., et al., DNA methylation and histone modifications regulate de novo shoot regeneration in Arabidopsis by modulating WUSCHEL expression and auxin signaling, PLoS Genet., 2011, vol. 7. e1002243. doi 10.1371/journal. pgen.1002243
Ezhova, T.A. and Vu, Kh.Ch., Genetic and epigenetic regulation of leaf morphogenesis, Vestn. Tver Gos. Univ., Ser. Biol. Ekol., 2008, no. 9, pp. 66–76.
Byrne, M.E., Barley, R., Curtis, M., et al., Asymmetric leaves1 mediates leaf patterning and stem cell function in Arabidopsis, Nature, 2000, vol. 408, no. 6815, pp. 967–971. doi 10.1038/35050091
Semiarti, E., Ueno, Y., Tsukaya, H., et al., The ASYMMETRIC LEAVES2 gene of Arabidopsis thaliana regulates formation of a symmetric lamina, establishment of venation and repression of meristem-related homeobox genes in leaves, Development, 2001, vol. 128, no. 10, pp. 1771–1783.
Lodha, M., Marco, C.F., and Timmermans, M.C., The ASYMMETRIC LEAVES complex maintains repression of KNOX homeobox genes via direct recruitment of Polycomb-repressive complex2, Genes Dev., 2013, vol. 27, no. 6, pp. 596–601. doi 10.1101 /gad.211425.112
Baubec, T., Finke, A., Mittelsten-Scheid, O., and Pecinka, A., Meristem-specific expression of epigenetic regulators safeguards transposon silencing in Arabidopsis, EMBO Rep., 2014, vol. 15, no. 4, pp. 446–452. doi 10.1002/embr.201337915
Jiang, D., Gu, X., and He, Y., Establishment of the winter-annual growth habit via FRIGIDA-mediated histone methylation at FLOWERING LOCUS C in Arabidopsis, Plant Cell, 2009, vol. 21, no. 6, pp. 1733–1746. doi 10.1105/tpc.109.067967
Deal, R.B., Topp, C.N., McKinney, E.C., and Meagher, R.B., Repression of flowering in Arabidopsis requires activation of FLOWERING LOCUS C expression by the histone variant H2A.Z, Plant Cell, 2007, vol. 19, no. 1, pp. 74–83. doi 10.1105/ tpc.106.048447
He, Y., Doyle, M.R., and Amasino, R., MPAF1-complex-mediated histone methylation of FLOWERING LOCUS C chromatin is required for the vernalizationresponsive, winter-annual habit in Arabidopsis, Genes Dev., 2004, vol. 18, no. 22, pp. 2774–2784. doi 10.1101/gad.1244504
Gu, X., Jiang, D., Wang, Y., et al., Repression of the floral transition via histone H2B monoubiquitination, Plant J., 2009, vol. 57, no. 3, pp. 522–533. doi 10.1111/j.1365-313X.2008.03709.x
Swiezewski, S., Liu, F., Magusin, A., and Dean, C., Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target, Nature, 2009, vol. 462, no. 7274, pp. 799–802. doi 10.1038/ nature08618
Heo, J.B. and Sung, S., Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA, Science, 2011, vol. 331, no. 6013, pp. 76–79. doi 10.1126/science.1197349
De Lucia, F., Crevillen, P., Jones, A.M., et al., A PHD-polycomb repressive complex 2 triggers the epigenetic silencing of FLC during vernalization, Proc. Natl. Acad. Sci. U.S.A., 2008, vol. 105, no. 44, pp. 16831–16836. doi 10.1073/pnas.0808687105
Li, W., Wang, Z., Li, J., et al., Overexpression of AtBMI1C, a polycomb group protein gene, accelerates flowering in Arabidopsis, PLoS One, 2011, vol. 6, no. 6. e21364. doi 10.1371/journal.pone.0021364
Vining, K., Pomraning, K., Wilhelm, L., et al., Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa, BMC Plant Biol., 2013, vol. 13, p. 92. doi 10.1186/1471-2229-13- 92
Leljak-Levanic, D., Bauer, N., Mihaljevic, S., and Jelaska, S., Changes in DNA methylation during somatic embryogenesis in Cucurbita pepo L., Plant Cell Rep., 2004, vol. 23, no. 3, pp. 120–127. doi 10.1007/s00299-004-0819-6
Grafi, G., Ben-Meir, H., Avivi, Y., et al., Histone methylation controls telomerase-independent telomere lengthening in cells undergoing dedifferentiation, Dev. Biol., 2007, vol. 306, no. 2, pp. 838–846. doi 10.1016/j.ydbio.2007.03.023
Nic-Can, G., López-Torres, A., Barredo-Pool, F., et al., New insights into somatic embryogenesis: LEAFY COTYLEDON1, BABY BOOM1 and WUSCHEL-RELATED HOMEOBOX4 are epigenetically regulated in Coffea canephora, PLoS One, 2013, vol. 8, no. 8. e72160. doi 10.1371/journal.pone.0072160
Us-Camas, R., Rivera-Solís, G., Duarte-Aké, F., and De-la-Peña, C., In vitro culture: an epigenetic challenge for plants, Plant Cell Tiss. Organ Cult., 2014, vol. 118, no. 2, pp. 187–201. doi 10.1007/s11240-014- 0482-8
He, C., Chen, X., Huang, H., and Xu, L., Reprogramming of H3K27me3 is critical for acquisition of pluripotency from cultured Arabidopsis tissues, PLoS Genet., 2012, vol. 8, no. 8. e1002911. doi 10.1371/journal. pgen.1002911
Pischke, M., Huttlin, E., Hegeman, A., and Sussman, M., A transcriptome-based characterization of habituation in plant tissue culture, Plant Physiol., 2006, vol. 140, no. 4, pp. 1255–1278. doi 10.1104/pp.105.076059
Ong-Abdullah, M., Ordway, J., Jiang, N., et al., Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm, Nature, 2015, vol. 525, no. 7570, pp. 533–537. doi 10.1038/ nature15365
Hodar, J.A., Leaf fluctuating asymmetry of Holm oak in response to drought under contrasting climatic conditions, J. Arid Environ., 2002, vol. 52, no. 2, pp. 233–243. doi 10.1006/jare.2002.0989
Trubyanov, A.B. and Glotov, N.V., Fluctuating asymmetry: trait variation and the left–right correlation, Dokl. Biol. Sci., 2010, vol. 431, nos. 1–6, pp. 103–105.
Tikhodeev, O.N., Fluctuational variation of the flower structure in Trientalis europaea L. (Primulaceae), Bot. Zh., 2012, vol. 97, no. 7, pp. 901–917.
De Craene, L.R., Meristic changes in flowering plants: how flowers play with numbers, Flora, 2016, vol. 221, pp. 22–37. doi 10.1016/ j.flora.2015.08.005
Lutova, L.A., Bondarenko, L.V., Buzovkina, I.S., et al., The influence of plant genotype on regeneration process, Russ. J. Genet., 1994, vol. 30, no. 8, pp. 1065–1074.
Lutova, L.A., Buzovkina, I.S., Smirnova, O.A., et al., Genetic control of in vitro regeneration processes in radish, In Vitro Cell Dev. Biol. Plant., 1997, vol. 33, pp. 269–274.
Author information
Authors and Affiliations
Corresponding author
Additional information
Original Russian Text © M.A. Lebedeva, V.E. Tvorogova, O.N. Tikhodeyev, 2017, published in Genetika, 2017, Vol. 53, No. 10, pp. 1115–1131.
Rights and permissions
About this article
Cite this article
Lebedeva, M.A., Tvorogova, V.E. & Tikhodeyev, O.N. Epigenetic mechanisms and their role in plant development. Russ J Genet 53, 1057–1071 (2017). https://doi.org/10.1134/S1022795417090083
Received:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S1022795417090083