Skip to main content

An Overview of Current Research in Plant Epigenetic and Epigenomic Phenomena

  • Protocol
  • First Online:
Plant Epigenetics and Epigenomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2093))

Abstract

Biological phenomena defined as having an “epigenetic” component (according to various definitions) have been extensively studied in plant systems and illuminated many mechanisms by which gene expression is regulated and patterns of expression inherited through cell divisions. This second volume of Plant Epigenetics and Epigenomics: Methods in Molecular Biology builds on the work of its predecessor to describe cutting-edge tools for plant epigenetic and epigenomic research, and embrace crop and forestry species as well as natural populations and further insights from model species. In this chapter, the historical background to plant epigenetic and epigenomic research is summarized, and key considerations for the interpretation of current data are outlined.

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

Access this chapter

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 99.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 129.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
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. Spillane C, McKeown PC (eds) (2014) Plant epigenetics and epigenomics: methods and protocols, Methods in molecular biology, vol 1112. Springer Science+Business Media, New York

    Google Scholar 

  2. McKeown PC, Spillane C (2014) Landscaping plant epigenetics. In: Plant epigenetics and epigenomics. Springer, New York, pp 1–24

    Google Scholar 

  3. Greally JM (2018) A user’s guide to the ambiguous word ‘epigenetics’. Nat Rev Mol Cell Biol 19(4):207–208

    Article  CAS  PubMed  Google Scholar 

  4. Lappalainen T, Greally JM (2017) Associating cellular epigenetic models with human phenotypes. Nat Rev Genet 18:441. https://doi.org/10.1038/nrg.2017.32

    Article  CAS  PubMed  Google Scholar 

  5. Gayon J (2016) From Mendel to epigenetics: history of genetics. C R Biol 339(7–8):225–230

    Article  PubMed  Google Scholar 

  6. Felsenfeld G (2014) A brief history of epigenetics. Cold Spring Harb Perspect Biol 6(1):a018200

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  7. Haig D (2004) The (dual) origin of epigenetics. Cold Spring Harb Symp Quant Biol 69:67–70. https://doi.org/10.1101/sqb.2004.69.67

    Article  CAS  PubMed  Google Scholar 

  8. Huang S (2012) The molecular and mathematical basis of Waddington’s epigenetic landscape: a framework for post-Darwinian biology? BioEssays 34(2):149–157. https://doi.org/10.1002/bies.201100031

    Article  CAS  PubMed  Google Scholar 

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

    Google Scholar 

  10. Waddington CH (1942) Canalization of development and the inheritance of acquired characters. Nature 150(3811):563–565

    Article  Google Scholar 

  11. Bird A (2007) Perceptions of epigenetics. Nature 447(7143):396–398

    Article  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. Richards EJ (2006) Inherited epigenetic variation—revisiting soft inheritance. Nat Rev Genet 7(5):395–401. https://doi.org/10.1038/nrg1834

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Vongs A, Kakutani T, Martienssen RA, Richards EJ (1993) Arabidopsis thaliana DNA methylation mutants. Science 260:1926–1928

    Article  CAS  PubMed  Google Scholar 

  16. Verhoeven KJ, Vonholdt BM, Sork VL (2016) Epigenetics in ecology and evolution: what we know and what we need to know. Mol Ecol 25(8):1631–1638

    Article  PubMed  Google Scholar 

  17. Quadrana L, Colot V (2016) Plant transgenerational epigenetics. Annu Rev Genet 50:467–491

    Article  CAS  PubMed  Google Scholar 

  18. Henikoff S, Greally JM (2016) Epigenetics, cellular memory and gene regulation. Curr Biol 26(14):R644–R648

    Article  CAS  PubMed  Google Scholar 

  19. 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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  20. Richards EJ (2011) Natural epigenetic variation in plant species: a view from the field. Curr Opin Plant Biol 14(2):204–209

    Article  CAS  PubMed  Google Scholar 

  21. He L, Wu W, Zinta G, Yang L, Wang D, Liu R, Zhang H, Zheng Z, Huang H, Zhang Q (2018) A naturally occurring epiallele associates with leaf senescence and local climate adaptation in Arabidopsis accessions. Nat Commun 9(1):460

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  22. Bird A (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16(1):6–21. https://doi.org/10.1101/gad.947102

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  24. Berger SL, Kouzarides T, Shiekhattar R, Shilatifard A (2009) An operational definition of epigenetics. Genes Dev 23(7):781–783. https://doi.org/10.1101/gad.1787609

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Bird AP (1986) CpG-rich islands and the function of DNA methylation. Nature 321(6067):209–213

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  27. Wigler MH (1981) The inheritance of methylation patterns in vertebrates. Cell 24(2):285–286

    Article  CAS  PubMed  Google Scholar 

  28. Bestor TH, Verdine GL (1994) DNA methyltransferases. Curr Opin Cell Biol 6(3):380–389

    Article  CAS  PubMed  Google Scholar 

  29. Youngson NA, Chong S, Whitelaw E (2011) Gene silencing is an ancient means of producing multiple phenotypes from the same genotype. BioEssays 33(2):95–99. https://doi.org/10.1002/bies.201000122

    Article  PubMed  Google Scholar 

  30. Gruenbaum Y, Navehmany T, Cedar H, Razin A (1981) Sequence specificity of methylation in higher plant DNA. Nature 292(5826):860–862. https://doi.org/10.1038/292860a0

    Article  CAS  PubMed  Google Scholar 

  31. Lahmy S, Bies-Etheve N, Lagrange T (2010) Plant-specific multisubunit RNA polymerase in gene silencing. Epigenetics 5(1):4–8

    Article  CAS  PubMed  Google Scholar 

  32. Waterborg JH (1990) Sequence analysis of acetylation and methylation in two histone H3 variants of alfalfa. J Biol Chem 265(28):17157–17161

    CAS  PubMed  Google Scholar 

  33. 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(16):8449–8454

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Goldberg AD, Allis CD, Bernstein E (2007) Epigenetics: a landscape takes shape. Cell 128(4):635–638

    Article  CAS  PubMed  Google Scholar 

  35. Chase CD (2007) Cytoplasmic male sterility: a window to the world of plant mitochondrial–nuclear interactions. Trends Genet 23(2):81–90

    Article  CAS  PubMed  Google Scholar 

  36. Kim D-H, Sung SB (2014) Genetic and epigenetic mechanisms underlying vernalization. Arabidopsis Book 12:e0171

    Article  PubMed  PubMed Central  Google Scholar 

  37. Auge G, Blair L, Neville H, Donohue K (2017) Maternal vernalization and vernalization-pathway genes influence progeny seed germination. New Phytol 216:388–400

    Article  CAS  PubMed  Google Scholar 

  38. Lämke J, Bäurle I (2017) Epigenetic and chromatin-based mechanisms in environmental stress adaptation and stress memory in plants. Genome Biol 18(1):124

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  39. Johannes F, Schmitz RJ (2019) Spontaneous epimutations in plants. New Phytol 221(3):1253–1259

    Article  PubMed  Google Scholar 

  40. Coe EH (1966) Properties origin and mechanism of conversion-type inheritance at b locus in maize. Genetics 53(6):1035

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Chandler VL, Stam M (2004) Chromatin conversations: mechanisms and implications of paramutation. Nat Rev Genet 5(7):532–544. https://doi.org/10.1038/nrg1378

    Article  CAS  PubMed  Google Scholar 

  42. Meyer P, Heidmann I, Niedenhof I (1993) Differences in DNA methylation are associated with a paramutation phenomenon in transgenic Petunia. Plant J 4(1):89–100. https://doi.org/10.1046/j.1365-313X.1993.04010089.x

    Article  CAS  PubMed  Google Scholar 

  43. Köhler C, Wolff P, Spillane C (2012) Epigenetic mechanisms underlying genomic imprinting in plants. Annu Rev Plant Biol 63(1):331. https://doi.org/10.1146/annurev-arplant-042811-105514

    Article  CAS  PubMed  Google Scholar 

  44. McKeown PC, Fort A, Spillane C (2013) Genomic imprinting: parental control of gene expression in higher plants. In: Polyploid hybrid genomics. Wiley, New York, p 257

    Chapter  Google Scholar 

  45. Gehring M, Bubb KL, Henikoff S (2009) Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324(5933):1447–1451. https://doi.org/10.1126/science.1171609

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Tuteja R, McKeown PC, Ryan P, Morgan CC, Donoghue MTA, Downing T, O’Connell MJ, Spillane C (2019) Paternally expressed imprinted genes under positive Darwinian selection in Arabidopsis thaliana. Mol Biol Evol 36(6):1239–1253. https://doi.org/10.1093/molbev/msz063

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Costa Liliana M, Yuan J, Rouster J, Paul W, Dickinson H, Gutierrez-Marcos Jose F (2012) Maternal control of nutrient allocation in plant seeds by genomic imprinting. Curr Biol 22(2):160–165

    Article  CAS  PubMed  Google Scholar 

  48. Haig D (2000) The kinship theory of genomic imprinting. Annu Rev Ecol Syst 31(1):9–32

    Article  Google Scholar 

  49. Kradolfer D, Wolff P, Hua J, Siretskiy A, Köhler C (2013) An imprinted gene underlies postzygotic reproductive isolation in Arabidopsis thaliana. Dev Cell 26:525–535

    Article  CAS  PubMed  Google Scholar 

  50. Dickinson H, Scholten S (2013) And baby makes three: genomic imprinting in plant embryos. PLoS Genet 9(12):e1003981

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  51. 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(8):939–950. https://doi.org/10.1101/gad.524609

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Lindbo JA, Dougherty WG (2005) Plant pathology and RNAi: a brief history. Annu Rev Phytopathol 43:191–204. https://doi.org/10.1146/annurev.phyto.43.040204.140228

    Article  CAS  PubMed  Google Scholar 

  53. Sanford JC, Johnston SA (1985) The concept of parasite-derived resistance—deriving resistance genes from the parasites own genome. J Theor Biol 113(2):395–405. https://doi.org/10.1016/s0022-5193(85)80234-4

    Article  Google Scholar 

  54. Dougherty WG, Parks TD (1995) Transgenes and gene suppression—telling us something new. Curr Opin Cell Biol 7(3):399–405. https://doi.org/10.1016/0955-0674(95)80096-4

    Article  CAS  PubMed  Google Scholar 

  55. Sen GL, Blau HM (2006) A brief history of RNAi: the silence of the genes. FASEB J 20(9):1293–1299. https://doi.org/10.1096/fj.06-6014rev

    Article  CAS  PubMed  Google Scholar 

  56. Mirouze M, Reinders J, Bucher E, Nishimura T, Schneeberger K, Ossowski S, Cao J, Weigel D, Paszkowski J, Mathieu O (2009) Selective epigenetic control of retrotransposition in Arabidopsis. Nature 461(7262):427

    Article  CAS  PubMed  Google Scholar 

  57. Zhang Y-Y, Latzel V, Fischer M, Bossdorf O (2018) Understanding the evolutionary potential of epigenetic variation: a comparison of heritable phenotypic variation in epiRILs, RILs, and natural ecotypes of Arabidopsis thaliana. Heredity 121(3):257–265

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Catoni M, Cortijo S (2018) EpiRILs: lessons from arabidopsis. Plant epigenetics coming of age for breeding applications, vol 88, pp 87–116

    Google Scholar 

  59. Springer NM, Stupar RM (2007) Allelic variation and heterosis in maize: how do two halves make more than a whole? Genome Res 17(3):264–275. https://doi.org/10.1101/gr.5347007

    Article  CAS  PubMed  Google Scholar 

  60. Crow JF (1999) Anecdotal, historical and critical commentaries on genetics. Genetics 152(3):821–825

    CAS  PubMed  PubMed Central  Google Scholar 

  61. McKeown PC, Fort A, Duszynska D, Sulpice R, Spillane C (2013) Emerging molecular mechanisms for biotechnological harnessing of heterosis in crops. Trends Biotechnol 31(10):549–551

    Article  CAS  PubMed  Google Scholar 

  62. Fort A, Ryder P, McKeown PC, Wijnen C, Aarts MG, Sulpice R, Spillane C (2016) Disaggregating polyploidy, parental genome dosage and hybridity contributions to heterosis in Arabidopsis thaliana. New Phytol 209(2):590–599

    Article  CAS  PubMed  Google Scholar 

  63. Groszmann M, Greaves IK, Fujimoto R, Peacock WJ, Dennis ES (2013) The role of epigenetics in hybrid vigour. Trends Genet 29(12):684–690

    Article  CAS  PubMed  Google Scholar 

  64. Lauss K, Wardenaar R, Oka R, van Hulten MH, Guryev V, Keurentjes JJ, Stam M, Johannes F (2018) Parental DNA methylation states are associated with heterosis in epigenetic hybrids. Plant Physiol 176(2):1627–1645

    Article  CAS  PubMed  Google Scholar 

  65. Dapp M, Reinders J, Bediee A, Balsera C, Bucher E, Theiler G, Granier C, Paszkowski J (2015) Heterosis and inbreeding depression of epigenetic Arabidopsis hybrids. Nat Plants 1(7):15092

    Article  CAS  PubMed  Google Scholar 

  66. Chen ZJ (2013) Genomic and epigenetic insights into the molecular bases of heterosis. Nat Rev Genet 14(7):471

    Article  CAS  PubMed  Google Scholar 

  67. Ryder P, McKeown PC, Fort A, Spillane C (2019) Epigenetics and heterosis in crop plants. In: Epigenetics in plants of agronomic importance: fundamentals and applications. Springer, Cham, pp 129–147

    Chapter  Google Scholar 

  68. 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(16):2124–2136. https://doi.org/10.1101/gad.11.16.2124

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Huang HR, Liu JJ, Xu Y, Lascoux M, Ge XJ, Wright SI (2018) Homeologue-specific expression divergence in the recently formed tetraploid Capsella bursa-pastoris (Brassicaceae). New Phytol 220(2):624–635

    Article  CAS  PubMed  Google Scholar 

  70. Wolf JB, Wade MJ (2009) What are maternal effects (and what are they not)? Philos Trans R Soc B 364(1520):1107–1115. https://doi.org/10.1098/rstb.2008.0238

    Article  Google Scholar 

  71. Donohue K (2009) Completing the cycle: maternal effects as the missing link in plant life histories. Philos Trans R Soc B 364(1520):1059–1074. https://doi.org/10.1098/rstb.2008.0291

    Article  CAS  Google Scholar 

  72. Forsthoefel NR, Vernon DM (2011) Effect of sporophytic PIRL9 genotype on post-meiotic expression of the Arabidopsis pirl1;pirl9 mutant pollen phenotype. Planta 233(2):423–431. https://doi.org/10.1007/s00425-010-1324-5

    Article  CAS  PubMed  Google Scholar 

  73. 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(1):71–81

    Article  PubMed  Google Scholar 

  74. Charlesworth D (2012) Plant sex chromosome evolution. J Exp Bot 64(2):405–420

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Peter McKeown .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

McKeown, P., Spillane, C. (2020). An Overview of Current Research in Plant Epigenetic and Epigenomic Phenomena. In: Spillane, C., McKeown, P. (eds) Plant Epigenetics and Epigenomics . Methods in Molecular Biology, vol 2093. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0179-2_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-0179-2_1

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0178-5

  • Online ISBN: 978-1-0716-0179-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics