Skip to main content
SpringerLink
Log in

Landscaping Plant Epigenetics

  • Protocol
  • First Online:
Plant Epigenetics and Epigenomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1112))

Abstract

The understanding of epigenetic mechanisms is necessary for assessing the potential impacts of epigenetics on plant growth, development and reproduction, and ultimately for the response of these factors to evolutionary pressures and crop breeding programs. This volume highlights the latest in laboratory and bioinformatic techniques used for the investigation of epigenetic phenomena in plants. Such techniques now allow genome-wide analyses of epigenetic regulation and help to advance our understanding of how epigenetic regulatory mechanisms affect cellular and genome function. To set the scene, we begin with a short background of how the field of epigenetics has evolved, with a particular focus on plant epigenetics. We consider what has historically been understood by the term “epigenetics” before turning to the advances in biochemistry, molecular biology, and genetics which have led to current-day definitions of the term. Following this, we pay attention to key discoveries in the field of epigenetics that have emerged from the study of unusual and enigmatic phenomena in plants. Many of these phenomena have involved cases of non-Mendelian inheritance and have often been dismissed as mere curiosities prior to the elucidation of their molecular mechanisms. In the penultimate section, consideration is given to how advances in molecular techniques are opening the doors to a more comprehensive understanding of epigenetic phenomena in plants. We conclude by assessing some opportunities, challenges, and techniques for epigenetic research in both model and non-model plants, in particular for advancing understanding of the regulation of genome function by epigenetic mechanisms.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Haig D (2004) The (dual) origin of epigenetics. Cold Spring Harb Symp Quant Biol 69:67–70

    CAS  PubMed  Google Scholar 

  2. Huang S (2012) The molecular and mathematical basis of Waddington’s epigenetic landscape: a framework for post-Darwinian biology? Bioessays 34:149–157

    CAS  PubMed  Google Scholar 

  3. Waddington CH (1939) An introduction to modern genetics. Allen and Unwin, London

    Google Scholar 

  4. Waddington CH (1957) The strategy of the genes. Allen and Unwin, London

    Google Scholar 

  5. Waddington CH (1942) Canalization of development and the inheritance of acquired characters. Nature 150:563–565

    Google Scholar 

  6. Nanney DL (1958) Epigenetic control systems. Proc Natl Acad Sci U S A 44:712–717

    CAS  PubMed Central  PubMed  Google Scholar 

  7. Slack JM (2002) Conrad Hal Waddington: the last renaissance biologist? Nat Rev Genet 3:889–895

    CAS  PubMed  Google Scholar 

  8. Richards EJ (2011) Natural epigenetic variation in plant species: a view from the field. Curr Opin Plant Biol 14:204–209

    CAS  PubMed  Google Scholar 

  9. Woltereck R (1909) Weitere experimentelle undersuchungen über Artveranderung, speziell über das Wesen quantitativer Artunterscheide bei Daphnien. Verhandlungen der Deutschen Zoologischen Gesellschaft 19:110–173

    Google Scholar 

  10. Pigliucci M (2007) Do we need an extended evolutionary synthesis? Evolution 61:2743–2749

    PubMed  Google Scholar 

  11. Bird A (2007) Perceptions of epigenetics. Nature 447:396–398

    CAS  PubMed  Google Scholar 

  12. Russo VEA, Martienssen RA, Riggs AD (eds) (1996) Epigenetic mechanisms of gene regulation. Cold Spring Harbor Laboratory Press, Woodbury

    Google Scholar 

  13. Grant-Downton RT, Dickinson HG (2006) Epigenetics and its implications for plant biology 2. The ‘epigenetic epiphany’: epigenetics, evolution and beyond. Ann Bot 97:11–27

    CAS  PubMed  Google Scholar 

  14. Berger SL, Kouzarides T, Shiekhattar R, Shilatifard A (2009) An operational definition of epigenetics. Genes Dev 23:781–783

    CAS  PubMed  Google Scholar 

  15. Jaenisch R, Bird A (2003) Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 33:S245–S254

    Google Scholar 

  16. Bird A (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16:6–21

    CAS  PubMed  Google Scholar 

  17. Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M (2007) What is a gene, post-ENCODE? History and updated definition. Genome Res 17:669–681

    CAS  PubMed  Google Scholar 

  18. Hauser M-T, Aufsatz W, Jonak C, Luschnig C (2011) Transgenerational epigenetic inheritance in plants. Biochim Biophys Acta 1809:459–468

    CAS  PubMed  Google Scholar 

  19. Kakutani T, Jeddeloh JA, Flowers SK, Munakata K, Richards EJ (1996) Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proc Natl Acad Sci U S A 93:12406–12411

    CAS  PubMed Central  PubMed  Google Scholar 

  20. Soppe WJJ, Jacobsen SE, Alonso-Blanco C, Jackson JP, Kakutani T, Koornneef M, Peeters AJM (2000) The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene. Mol Cell 6:791–802

    CAS  PubMed  Google Scholar 

  21. Rangwala SH, Elumalai R, Vanier C, Ozkan H, Galbraith DW, Richards EJ (2006) Meiotically stable natural epialleles of Sadhu, a novel Arabidopsis retroposon. PLoS Genet 2:e36

    PubMed Central  PubMed  Google Scholar 

  22. Johannes F, Porcher E, Teixeira FK, Saliba-Colombani V, Simon M, Agier N, Bulski A, Albuisson J, Heredia F, Audigier P, Bouchez D, Dillmann C, Guerche P, Hospital F, Colot V (2009) Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet 5:e1000530

    PubMed Central  PubMed  Google Scholar 

  23. Janoušek B, Široký J, Vyskot B (1996) Epigenetic control of sexual phenotype in a dioecious plant, Melandrium album. Mol Gen Genet 250:483–490

    PubMed  Google Scholar 

  24. Pecinka A, Mittelsten Scheid O (2012) Stress-induced chromatin changes: a critical view on their heritability. Plant Cell Physiol 53:801–808

    CAS  PubMed  Google Scholar 

  25. Rapp RA, Wendel JF (2005) Epigenetics and plant evolution. New Phytol 168:81–91

    CAS  PubMed  Google Scholar 

  26. Goldberg AD, Allis CD, Bernstein E (2007) Epigenetics: a landscape takes shape. Cell 128:635–638

    CAS  PubMed  Google Scholar 

  27. Chase CD (2007) Cytoplasmic male sterility: a window to the world of plant mitochondrial–nuclear interactions. Trends Genet 23:81–90

    CAS  PubMed  Google Scholar 

  28. Deaton AM, Bird A (2011) CpG islands and the regulation of transcription. Genes Dev 25:1010–1022

    CAS  PubMed  Google Scholar 

  29. Bird AP (1986) CpG-rich islands and the function of DNA methylation. Nature 321:209–213

    CAS  PubMed  Google Scholar 

  30. Doerfler W (1983) DNA methylation and gene activity. Annu Rev Biochem 52:93–124

    CAS  PubMed  Google Scholar 

  31. Wigler MH (1981) The inheritance of methylation patterns in vertebrates. Cell 24:285–286

    CAS  PubMed  Google Scholar 

  32. Bestor TH, Verdine GL (1994) DNA methyltransferases. Curr Opin Cell Biol 6:380–389

    CAS  PubMed  Google Scholar 

  33. Youngson NA, Chong S, Whitelaw E (2011) Gene silencing is an ancient means of producing multiple phenotypes from the same genotype. Bioessays 33:95–99

    PubMed  Google Scholar 

  34. Gruenbaum Y, Navehmany T, Cedar H, Razin A (1981) Sequence specificity of methylation in higher plant DNA. Nature 292:860–862

    CAS  PubMed  Google Scholar 

  35. Lahmy S, Bies-Etheve N, Lagrange T (2010) Plant-specific multisubunit RNA polymerase in gene silencing. Epigenetics 5:4–8

    CAS  PubMed  Google Scholar 

  36. Waterborg JH (1990) Sequence analysis of acetylation and methylation in two histone H3 variants of alfalfa. J Biol Chem 265:17157–17161

    CAS  PubMed  Google Scholar 

  37. Finnegan EJ, Peacock WJ, Dennis ES (1996) Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc Natl Acad Sci U S A 93:8449–8454

    CAS  PubMed Central  PubMed  Google Scholar 

  38. Li E, Bestor TH, Jaenisch R (1992) Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69:915–926

    CAS  PubMed  Google Scholar 

  39. Lisch D (2012) How important are transposons for plant evolution? Nat Rev Genet 14:49–61

    Google Scholar 

  40. Shimotohno K, Mizutani S, Temin HM (1980) Sequence of retrovirus provirus resembles that of bacterial transposable elements. Nature 285:550–554

    CAS  PubMed  Google Scholar 

  41. Coen ES, Carpenter R, Martin C (1986) Transposable elements generate novel spatial patterns of gene expression in Antirrhinum majus. Cell 47:285–296

    CAS  PubMed  Google Scholar 

  42. Bennetzen JL (2005) Transposable elements, gene creation and genome rearrangement in flowering plants. Curr Opin Genet Dev 15:621–627

    CAS  PubMed  Google Scholar 

  43. McDonald JF (1995) Transposable elements: possible catalysts of organismic evolution. Trends Ecol Evol 10:123–126

    CAS  PubMed  Google Scholar 

  44. Lippman Z, Gendrel A-V, Black M, Vaughn MW, Dedhia N, Richard McCombie W, Lavine K, Mittal V, May B, Kasschau KD, Carrington JC, Doerge RW, Colot V, Martienssen R (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature 430:471–476

    CAS  PubMed  Google Scholar 

  45. Parisod C, Salmon A, Zerjal T, Tenaillon M, Grandbastien M-A, Ainouche M (2009) Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in Spartina. New Phytol 184:1003–1015

    CAS  PubMed  Google Scholar 

  46. Hirochika H, Okamoto H, Kakutani T (2000) Silencing of retrotransposons in Arabidopsis and reactivation by the ddm1 mutation. Plant Cell 12:357–368

    CAS  PubMed Central  PubMed  Google Scholar 

  47. Okamoto H, Hirochika H (2001) Silencing of transposable elements in plants. Trends Plant Sci 6:527–534

    CAS  PubMed  Google Scholar 

  48. Reinders J, Wulff BBH, Mirouze M, Marí-Ordóñez A, Dapp M, Rozhon W, Bucher E, Theiler G, Paszkowski J (2009) Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes. Genes Dev 23:939–950

    CAS  PubMed  Google Scholar 

  49. Lisch D (2009) Epigenetic regulation of transposable elements in plants. Annu Rev Plant Biol 60:43–66

    CAS  PubMed  Google Scholar 

  50. Cui X, Jin P, Gu L, Lu Z, Xue Y, Wei L, Qi J, Song X, Luo M (2013) Control of transposon activity by a histone H3K4 demethylase in rice. Proc Natl Acad Sci U S A 110:1953–1958

    CAS  PubMed Central  PubMed  Google Scholar 

  51. Bots M, Maughan S, Nieuwland J (2006) RNAi Nobel ignores vital groundwork on plants. Nature 443:906

    CAS  PubMed  Google Scholar 

  52. Jorgensen R (2006) Plants, RNAi, and the Nobel prize. Science 314:1242–1243

    CAS  PubMed  Google Scholar 

  53. Matzke M, Matzke AJM (2006) Plants, RNAi, and the Nobel prize. Science 314:1242

    CAS  PubMed  Google Scholar 

  54. Cibrián-Jaramillo A, Martienssen RA (2009) Darwin’s “abominable mystery”: the role of RNA interference in the evolution of flowering plants. Cold Spring Harb Symp Quant Biol 74:267–273

    PubMed  Google Scholar 

  55. Green PJ, Pines O, Inouye M (1986) The role of antisense RNA in gene regulation. Annu Rev Biochem 55:569–597

    CAS  PubMed  Google Scholar 

  56. Rosenberg UB, Preiss A, Seifert E, Jäckle H, Knipple DC (1985) Production of phenocopies by Krüppel antisense RNA injection into drosophila embryos. Nature 313:703

    CAS  PubMed  Google Scholar 

  57. Harland R, Weintraub H (1985) Translation of mRNA injected into Xenopus oocytes is specifically inhibited by antisense RNA. J Cell Biol 101:1094–1099

    CAS  PubMed  Google Scholar 

  58. Crowley TE, Nellen W, Gomer RH, Firtel RA (1985) Phenocopy of discoidin I-minus mutants by antisense transformation in Dictyostelium. Cell 43:633

    CAS  PubMed  Google Scholar 

  59. Cornehssen M, Vandewiele M (1989) Both RNA level and translation efficiency are reduced by anti-sense RNA in transgenic tobacco. Nucleic Acids Res 17:833–843

    Google Scholar 

  60. Lee JT, Davidow LS, Warshawsky D (1999) Tsix, a gene antisense to Xist at the X-inactivation centre. Nat Genet 21:400–404

    CAS  PubMed  Google Scholar 

  61. Izant JG, Weintraub H (1984) Inhibition of thymidine kinase gene-expression by anti-sense RNA—a molecular approach to genetic-analysis. Cell 36:1007–1015

    CAS  PubMed  Google Scholar 

  62. Guo S, Kemphues KJ (1995) par-1, a gene required for establishing polarity in C. elegans embryos, encodes a putative Ser/Thr kinase that is asymmetrically distributed. Cell 81:611–620

    CAS  PubMed  Google Scholar 

  63. Grishok A, Mello CC (2002) RNAi (nematodes: Caenorhabditis elegans). Adv Genet 46:339–360

    CAS  PubMed  Google Scholar 

  64. Fire A, Xu SQ, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806–811

    CAS  PubMed  Google Scholar 

  65. Napoli C, Lemieux C, Jorgensen R (1990) Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans. Plant Cell 2:279–289

    CAS  PubMed Central  PubMed  Google Scholar 

  66. Abel PP, Nelson RS, De B, Hoffmann N, Rogers SG, Fraley RT, Beachy RN (1986) Delay of disease development in transgenic plants that express the tobacco mosaic virus coat protein gene. Science 232:738

    CAS  PubMed  Google Scholar 

  67. Kassanis B, White RF (1972) Interference between two satellite viruses of tobacco necrosis virus. J Gen Virol 17:177–183

    CAS  PubMed  Google Scholar 

  68. Lindbo JA, Dougherty WG (2005) Plant pathology and RNAi: a brief history. Annu Rev Phytopathol 43:191–204

    CAS  PubMed  Google Scholar 

  69. Sanford JC, Johnston SA (1985) The concept of parasite-derived resistance—deriving resistance genes from the parasites own genome. J Theor Biol 113:395–405

    Google Scholar 

  70. Lindbo JA, Silva-Rosales L, Proebsting WM, Dougherty WG (1993) Induction of a highly specific antiviral state in transgenic plants: implications for regulation of gene expression and virus resistance. Plant Cell 5:1749–1759

    CAS  PubMed Central  PubMed  Google Scholar 

  71. Smith HA, Swaney SL, Parks TD, Wernsman EA, Dougherty WG (1994) Transgenic plant virus resistance mediated by untranslatable sense RNAs: expression, regulation, and fate of nonessential RNAs. Plant Cell 6:1441–1453

    CAS  PubMed Central  PubMed  Google Scholar 

  72. Mueller E, Gilbert J, Davenport G, Brigneti G, Baulcombe DC (2002) Homology-dependent resistance: transgenic virus resistance in plants related to homology-dependent gene silencing. Plant J 7:1001–1013

    Google Scholar 

  73. English JJ, Mueller E, Baulcombe DC (1996) Suppression of virus accumulation in transgenic plants exhibiting silencing of nuclear genes. Plant Cell 8:179–188

    CAS  PubMed Central  PubMed  Google Scholar 

  74. Montgomery MK, Fire A (1998) Double-stranded RNA as a mediator in sequence-specific genetic silencing and co-suppression. Trends Genet 14:255–258

    CAS  PubMed  Google Scholar 

  75. Metzlaff M, O’dell M, Cluster PD, Flavell RB (1997) RNA-mediated RNA degradation and chalcone synthase A silencing in petunia. Cell 88:845–854

    CAS  PubMed  Google Scholar 

  76. Dalmay T, Hamilton A, Rudd S, Angell S, Baulcombe DC (2000) An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell 101:543–553

    CAS  PubMed  Google Scholar 

  77. Dougherty WG, Parks TD (1995) Transgenes and gene suppression—telling us something new. Curr Opin Cell Biol 7:399–405

    CAS  PubMed  Google Scholar 

  78. Sen GL, Blau HM (2006) A brief history of RNAi: the silence of the genes. FASEB J 20:1293–1299

    CAS  PubMed  Google Scholar 

  79. Baulcombe D (2004) RNA silencing in plants. Nature 431:356–363

    CAS  PubMed  Google Scholar 

  80. Ito H, Gaubert H, Bucher E, Mirouze M, Vaillant I, Paszkowski J (2011) An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress. Nature 472:115–119

    CAS  PubMed  Google Scholar 

  81. Staiger D, Korneli C, Lummer M, Navarro L (2012) Emerging role for RNA-based regulation in plant immunity. New Phytol 197(2):394–404

    PubMed  Google Scholar 

  82. Brink RA (1973) Paramutation. Annu Rev Genet 7:129–152

    CAS  PubMed  Google Scholar 

  83. Chandler VL, Stam M (2004) Chromatin conversations: mechanisms and implications of paramutation. Nat Rev Genet 5:532–544

    CAS  PubMed  Google Scholar 

  84. Meyer P, Heidmann I, Niedenhof I (1993) Differences in DNA methylation are associated with a paramutation phenomenon in transgenic Petunia. Plant J 4:89–100

    CAS  PubMed  Google Scholar 

  85. Coe EH (1966) Properties origin and mechanism of conversion-type inheritance at b locus in maize. Genetics 53:1035–1063

    CAS  PubMed  Google Scholar 

  86. Mittelsten Scheid O, Afsar K, Paszkowski J (2003) Formation of stable epialleles and their paramutation-like interaction in tetraploid Arabidopsis thaliana. Nat Genet 34:450–454

    CAS  PubMed  Google Scholar 

  87. Alleman M, Sidorenko L, McGinnis K, Seshadri V, Dorweiler JE, White J, Sikkink K, Chandler VL (2006) An RNA-dependent RNA polymerase is required for paramutation in maize. Nature 442:295–298

    CAS  PubMed  Google Scholar 

  88. Erhard KF Jr, Stonaker JL, Parkinson SE, Lim JP, Hale CJ, Hollick JB (2009) RNA polymerase IV functions in paramutation in Zea mays. Science 323:1201–1205

    CAS  PubMed  Google Scholar 

  89. Stam M, Belele C, Dorweiler JE, Chandler VL (2002) Differential chromatin structure within a tandem array 100 kb upstream of the maize b1 locus is associated with paramutation. Genes Dev 16:1906–1918

    CAS  PubMed  Google Scholar 

  90. Matzke M, Kanno T, Huettel B, Daxinger L, Matzke AJM (2006) RNA-directed DNA methylation and pol IVb in Arabidopsis. Cold Spring Harb Symp Quant Biol 71:449–459

    CAS  PubMed  Google Scholar 

  91. Chandler VL, Eggleston WB, Dorweiler JE (2000) Paramutation in maize. Plant Mol Biol 43:121–145

    CAS  PubMed  Google Scholar 

  92. Suter CM, Martin DIK (2010) Paramutation: the tip of an epigenetic iceberg? Trends Genet 26:9–14

    CAS  PubMed Central  PubMed  Google Scholar 

  93. Hollick JB (2010) Paramutation and development. Annu Rev Cell Dev Biol 26:557–579

    CAS  PubMed  Google Scholar 

  94. Rassoulzadegan M, Grandjean V, Gounon P, Vincent S, Gillot I, Cuzin F (2006) RNA-mediated non-Mendelian inheritance of an epigenetic change in the mouse. Nature 441:469–474

    CAS  PubMed  Google Scholar 

  95. Chandler VL (2007) Paramutation: from maize to mice. Cell 128:641–645

    CAS  PubMed  Google Scholar 

  96. Cuzin F, Grandjean V, Rassoulzadegan M (2008) Inherited variation at the epigenetic level: paramutation from the plant to the mouse. Curr Opin Genet Dev 18:193–196

    CAS  PubMed  Google Scholar 

  97. de Vanssay A, Bougé AL, Boivin A, Hermant C, Teysset L, Delmarre V, Antoniewski C, Ronsseray S (2012) Paramutation in drosophila linked to emergence of a piRNA-producing locus. Nature 490:112–115

    PubMed  Google Scholar 

  98. Cuzin F, Rassoulzadegan M (2010) Non-Mendelian epigenetic heredity: gametic RNAs as epigenetic regulators and transgenerational signals. Essays Biochem 48:101–106

    CAS  PubMed  Google Scholar 

  99. Parkinson SE, Gross SM, Hollick JB (2007) Maize sex determination and abaxial leaf fates are canalized by a factor that maintains repressed epigenetic states. Dev Biol 308:462–473

    CAS  PubMed  Google Scholar 

  100. Garnier O, Laoueille-Duprat S, Spillane C (2008) Genomic imprinting in plants. Epigenetics 3:14–20

    PubMed  Google Scholar 

  101. Bauer MJ, Fischer RL (2011) Genome demethylation and imprinting in the endosperm. Curr Opin Genet Dev 14:162–167

    CAS  Google Scholar 

  102. Goday C, Esteban MR (2001) Chromosome elimination in sciarid flies. Bioessays 23:242–250

    CAS  PubMed  Google Scholar 

  103. Kermicle JL (1970) Dependence of the R-mottled aleurone phenotype in maize on mode of sexual transmission. Genetics 66:69

    CAS  PubMed  Google Scholar 

  104. McGrath J, Solter D (1984) Completion of mouse embryogenesis requires both the maternal and paternal genomes. Cell 37:179–183

    CAS  PubMed  Google Scholar 

  105. Surani MAH, Barton SC, Norris ML (1984) Development of reconstituted mouse eggs suggests imprinting of the genome during gametogenesis. Nature 308:548–550

    CAS  PubMed  Google Scholar 

  106. Hirasawa R, Feil R (2010) Genomic imprinting and human disease. Essays Biochem 48:187–200

    CAS  PubMed  Google Scholar 

  107. Köhler C, Wolff P, Spillane C (2012) Epigenetic mechanisms underlying genomic imprinting in plants. Annu Rev Plant Biol 63:331–352

    PubMed  Google Scholar 

  108. Bauer MJ, Fischer RL (2011) Genome demethylation and imprinting in the endosperm. Curr Opin Plant Biol 14:162–167

    CAS  PubMed Central  PubMed  Google Scholar 

  109. Raissig MT, Baroux C, Grossniklaus U (2011) Regulation and flexibility of genomic imprinting during seed development. Plant Cell 23:16–26

    CAS  PubMed Central  PubMed  Google Scholar 

  110. Grossniklaus U, Vielle-Calzada J-P, Hoeppner MA, Gagliano WB (1998) Maternal control of embryogenesis by MEDEA, a Polycomb group gene in Arabidopsis. Science 280:446–450

    CAS  PubMed  Google Scholar 

  111. Josefsson C, Dilkes B, Comai L (2006) Parent-dependent loss of gene silencing during interspecies hybridization. Curr Biol 16:1322–1328

    CAS  PubMed  Google Scholar 

  112. Luo M, Taylor JM, Spriggs A, Zhang H, Wu X, Russell S, Singh M, Koltunow A (2011) A genome-wide survey of imprinted genes in rice seeds reveals imprinting primarily occurs in the endosperm. PLoS Genet 7:e1002125

    CAS  PubMed Central  PubMed  Google Scholar 

  113. Waters AJ, Makarevitch I, Eichten SR, Swanson-Wagner RA, Yeh C-T, Xu W, Schnable PS, Vaughn MW, Gehring M, Springer NM (2011) Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm. Plant Cell 23:4221–4233

    CAS  PubMed Central  PubMed  Google Scholar 

  114. McKeown PC, Laouielle-Duprat S, Prins P, Wolff P, Schmid MW, Donoghue MT, Fort A, Duszynska D, Comte A, Lao NT, Wennblom TJ, Smant G, Kohler C, Grossniklaus U, Spillane C (2011) Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds. BMC Plant Biol 11:113

    CAS  PubMed Central  PubMed  Google Scholar 

  115. Hsieh T-F, Shin J, Uzawa R, Silva P, Cohen S, Bauer MJ, Hashimoto M, Kirkbride RC, Harada JJ, Zilberman D, Fischer RL (2011) Regulation of imprinted gene expression in Arabidopsis endosperm. Proc Natl Acad Sci U S A 108:1755–1762

    CAS  PubMed Central  PubMed  Google Scholar 

  116. Wolff P, Weinhofer I, Seguin J, Roszak P, Beisel C, Donoghue MTA, Spillane C, Nordborg M, Rehmsmeier M, Köhler C (2011) High-resolution analysis of parent-of-origin allelic expression in the Arabidopsis endosperm. PLoS Genet 7:e1002126

    CAS  PubMed Central  PubMed  Google Scholar 

  117. Moore T, Haig D (1991) Genomic imprinting in mammalian development—a parental tug-of-war. Trends Genet 7:45–49

    CAS  PubMed  Google Scholar 

  118. Tucker S, Vitins A, Pikaard CS (2010) Nucleolar dominance and ribosomal RNA gene silencing. Curr Opin Cell Biol 22:351–356

    CAS  PubMed Central  PubMed  Google Scholar 

  119. McClintock B (1934) The relation of a particular chromosomal element to the development of the nucleoli in Zea mays. Cell Tissue Res 21:294–326

    Google Scholar 

  120. Pikaard CS (2000) The epigenetics of nucleolar dominance. Trends Genet 16:495–500

    CAS  PubMed  Google Scholar 

  121. Honjo T, Reeder RH (1973) Preferential transcription of Xenopus laevis ribosomal RNA in interspecies hybrids between Xenopus laevis and Xenopus mulleri. J Mol Biol 80:217–228

    CAS  PubMed  Google Scholar 

  122. McStay B (2006) Nucleolar dominance: a model for rRNA gene silencing. Genes Dev 20:1207–1214

    CAS  PubMed  Google Scholar 

  123. McStay B, Grummt I (2008) The epigenetics of rRNA genes: from molecular to chromosome biology. Annu Rev Cell Dev Biol 24:131–157

    CAS  PubMed  Google Scholar 

  124. Flavell RB, Odell M, Thompson WF (1988) Regulation of cytosine methylation in ribosomal RNA and nucleolus organizer expression in wheat. J Mol Biol 204:523–534

    CAS  PubMed  Google Scholar 

  125. Chen ZJ, Pikaard CS (1997) Epigenetic silencing of RNA polymerase I transcription: a role for DNA methylation and histone modification in nucleolar dominance. Genes Dev 11:2124–2136

    CAS  PubMed  Google Scholar 

  126. Conconi A, Widmer RM, Koller T, Sogo JM (1989) Two different chromatin structures coexist in ribosomal RNA genes throughout the cell cycle. Cell 57:753–761

    CAS  PubMed  Google Scholar 

  127. Pontes O, Lawrence RJ, Neves N, Silva M, Lee JH, Chen ZJ, Viegas W, Pikaard CS (2003) Natural variation in nucleolar dominance reveals the relationship between nucleolus organizer chromatin topology and rRNA gene transcription in Arabidopsis. Proc Natl Acad Sci U S A 100:11418–11423

    CAS  PubMed Central  PubMed  Google Scholar 

  128. Liu X, Yu C-W, Duan J, Luo M, Wang K, Tian G, Cui Y, Wu K (2012) HDA6 directly interacts with DNA methyltransferase MET1 and maintains transposable element silencing in Arabidopsis. Plant Physiol 158:119–129

    CAS  PubMed Central  PubMed  Google Scholar 

  129. Lawrence RJ, Earley K, Pontes O, Silva M, Chen ZJ, Neves N, Viegas W, Pikaard CS (2004) A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance. Mol Cell 13:599–609

    CAS  PubMed  Google Scholar 

  130. McKeown PC, Shaw P (2009) Chromatin: linking structure and function in the nucleolus. Chromosoma 118:11–23

    PubMed  Google Scholar 

  131. Pontes O, Li CF, Nunes PC, Haag J, Ream T, Vitins A, Jacobsen SE, Pikaard CS (2006) The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center. Cell 126:79–92

    CAS  PubMed  Google Scholar 

  132. Kim D-H, Doyle MR, Sung S, Amasino RM (2009) Vernalization: winter and the timing of flowering in plants. Annu Rev Cell Dev Biol 25:277–299

    CAS  PubMed  Google Scholar 

  133. Andrés F, Coupland G (2012) The genetic basis of flowering responses to seasonal cues. Nat Rev Genet 13:627–639

    PubMed  Google Scholar 

  134. Whyte RO, Hudson PS (1933) Vernalization or Lyssenko’s method for the pre-treatment of seed. Imp Bur Plant Genet 27:1

    Google Scholar 

  135. Amasino R (2004) Vernalization, competence, and the epigenetic memory of winter. Plant Cell 16:2553–2559

    CAS  PubMed Central  PubMed  Google Scholar 

  136. Chouard P (1960) Vernalization and its relations to dormancy. Annu Rev Plant Physiol 11:191–238

    CAS  Google Scholar 

  137. Caspari EW, Marshak RE (1965) Rise and fall of Lysenko. Science 149:275–278

    CAS  PubMed  Google Scholar 

  138. Sung SB, Amasino RM (2004) Vernalization and epigenetics: how plants remember winter. Curr Opin Plant Biol 7:4–10

    CAS  PubMed  Google Scholar 

  139. He Y (2009) Control of the transition to flowering by chromatin modifications. Mol Plant 2:554–564

    CAS  PubMed  Google Scholar 

  140. Ahmad A, Zhang Y, Cao X-F (2010) Decoding the epigenetic language of plant development. Mol Plant 3:719–728

    CAS  PubMed  Google Scholar 

  141. Sung SB, Amasino RM (2004) Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature 427:159–164

    CAS  PubMed  Google Scholar 

  142. Swiezewski S, Liu F, Magusin A, Dean C (2009) Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature 462:799–802

    CAS  PubMed  Google Scholar 

  143. Sicard A, Lenhard M (2011) The selfing syndrome: a model for studying the genetic and evolutionary basis of morphological adaptation in plants. Ann Bot 107:1433–1443

    PubMed  Google Scholar 

  144. Winn AA, Elle E, Kalisz S, Cheptou P-O, Eckert CG, Goodwillie C, Johnston MO, Moeller DA, Ree RH, Sargent RD, Vallejo-Marín M (2011) Analysis of inbreeding depression in mixed-mating plants provides evidence for selective interferences and stable mixed mating. Evolution 65:3339–3359

    PubMed  Google Scholar 

  145. Pennisi E (2011) Epigenetics linked to inbreeding depression. Science 333:1563

    PubMed  Google Scholar 

  146. Biemont C (2010) Inbreeding effects in the epigenetic era. Nat Rev Genet 11:234

    CAS  PubMed  Google Scholar 

  147. Springer NM, Stupar RM (2007) Allelic variation and heterosis in maize: how do two halves make more than a whole? Genome Res 17:264–275

    CAS  PubMed  Google Scholar 

  148. Duszynska D, McKeown PC, Juenger TE, Pietraszewska-Bogiel A, Geelen D, Spillane C (2013) Gamete fertility and ovule number variation in selfed reciprocal F1 hybrid triploid plants are heritable and display epigenetic parent-of-origin effects. New Phytol 198:71–81

    PubMed  Google Scholar 

  149. Yao H, Gray AD, Auger DL, Birchler JA (2013) Genomic dosage effects on heterosis in triploid maize. Proc Natl Acad Sci U S A 110:2665–2669

    CAS  PubMed Central  PubMed  Google Scholar 

  150. Kaplan Z, Fehrer J (2007) Molecular evidence for a natural primary triple hybrid in plants revealed from direct sequencing. Ann Bot 99:1213–1222

    CAS  PubMed  Google Scholar 

  151. Crow JF (1999) Anecdotal, historical and critical commentaries on genetics. Genetics 152:821–825

    CAS  PubMed  Google Scholar 

  152. He G, Zhu X, Elling AA, Chen L, Wang X, Guo L, Liang M, He H, Zhang H, Chen F, Qi Y, Chen R, Deng X-W (2010) Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell 22:17–33

    CAS  PubMed Central  PubMed  Google Scholar 

  153. Chodavarapu RK, Feng S, Ding B, Simon SA, Lopez D, Jia Y, Wang GL, Meyers BC, Jacobsen SE, Pellegrini M (2012) Transcriptome and methylome interactions in rice hybrids. Proc Natl Acad Sci U S A 109:12040–12045

    CAS  PubMed Central  PubMed  Google Scholar 

  154. Groszmann M, Greaves IK, Albertyn ZI, Scofield GN, Peacock WJ, Dennis ES (2011) Changes in 24-nt siRNA levels in Arabidopsis hybrids suggest an epigenetic contribution to hybrid vigor. Proc Natl Acad Sci U S A 108:2617–2622

    CAS  PubMed Central  PubMed  Google Scholar 

  155. Comai L (2000) Genetic and epigenetic interactions in allopolyploid plants. Plant Mol Biol 43:387–399

    CAS  PubMed  Google Scholar 

  156. Gaeta RT, Pires JC (2010) Homoeologous recombination in allopolyploids: the polyploid ratchet. New Phytol 186:18–28

    CAS  PubMed  Google Scholar 

  157. Liu B, Wendel JF (2003) Epigenetic phenomena and the evolution of plant allopolyploids. Mol Phylogenet Evol 29:365–379

    CAS  PubMed  Google Scholar 

  158. Parisod C, Holderegger R, Brochmann C (2010) Evolutionary consequences of autopolyploidy. New Phytol 186:5–17

    CAS  PubMed  Google Scholar 

  159. Paun O, Forest F, Fay MF, Chase MW (2009) Hybrid speciation in angiosperms: parental divergence drives ploidy. New Phytol 182:507–518

    PubMed Central  PubMed  Google Scholar 

  160. Soltis PS, Soltis DE (2009) The role of hybridization in plant speciation. Annu Rev Plant Biol 60:561–588

    CAS  PubMed  Google Scholar 

  161. Hegarty MJ, Hiscock SJ (2008) Genomic clues to the evolutionary success of review polyploid plants. Curr Biol 18:R435–R444

    CAS  PubMed  Google Scholar 

  162. Donoghue MTA, Fort A, Clifton R, Zhang X, McKeown PC, Voigt-Zielinski ML, Borevitz JO, Spillane C (2013) CmCGG methylation-independent parent-of-origin effects on genome-wide transcript levels in isogenic reciprocal F1 triploid plants. DNA Research doi:10.1093/dnares/dst046

    Google Scholar 

  163. McKeown PC, Fort A, Duszynska D, Sulpice R, Spillane C. (2013) Emerging molecular mechanisms for biotechnological harnessing of heterosis in crops. Trends Biotechnol 31:549–551

    Google Scholar 

  164. Birchler JA, Yao H, Chudalayandi S (2006) Unraveling the genetic basis of hybrid vigor. Proc Natl Acad Sci U S A 103:12957–12958

    CAS  PubMed Central  PubMed  Google Scholar 

  165. Groszmann M, Greaves IK, Albert N, Fujimoto R, Helliwell CA, Dennis ES, Peacock WJ (2011) Epigenetics in plants—vernalisation and hybrid vigour. Biochim Biophys Acta 1809:427–437

    CAS  PubMed  Google Scholar 

  166. Thudi M, Li Y, Jackson SA, May GD, Varshney RK (2012) Current state-of-art of sequencing technologies for plant genomics research. Brief Funct Genomics 11:3–11

    CAS  PubMed  Google Scholar 

  167. Schmitz RJ, Zhang X (2011) High-throughput approaches for plant epigenomic studies. Curr Opin Plant Biol 14:130–136

    CAS  PubMed Central  PubMed  Google Scholar 

  168. ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57–74

    Google Scholar 

  169. Hawkins RD, Hon GC, Ren B (2010) Next-generation genomics: an integrative approach. Nat Rev Genet 11:476–486

    CAS  PubMed Central  PubMed  Google Scholar 

  170. Shen W-H, Xu L (2009) Chromatin remodeling in stem cell maintenance in Arabidopsis thaliana. Mol Plant 2:600–609

    CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Genetics & Biotechnology Lab, Plant & Agribiosciences Centre (PABC), School of Natural Sciences, National University of Ireland, Galway (NUI Galway), Ireland

    Peter C. McKeown & Charles Spillane

Authors
  1. Peter C. McKeown
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Charles Spillane
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Genetics & Biotechnology Lab,Plant & Agribiosciences Centre (PABC),School of Natural Sciences,National University of Ireland, Galway, Ireland

    Charles Spillane

  2. Genetics & Biotechnology Lab,Plant & Agribiosciences Centre (PABC),School of Natural Sciences,National University of Ireland, Galway, Ireland

    Peter C. McKeown

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media, New York

About this protocol

Cite this protocol

McKeown, P.C., Spillane, C. (2014). Landscaping Plant Epigenetics. In: Spillane, C., McKeown, P. (eds) Plant Epigenetics and Epigenomics. Methods in Molecular Biology, vol 1112. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-773-0_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-773-0_1

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-772-3

  • Online ISBN: 978-1-62703-773-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation