Skip to main content
SpringerLink
Log in

Epigenetics and Epigenomics of Plants

  • Chapter
  • First Online:
Plant Genetics and Molecular Biology

Part of the book series: Advances in Biochemical Engineering/Biotechnology ((ABE,volume 164))

Abstract

The genetic material DNA in association with histone proteins forms the complex structure called chromatin, which is prone to undergo modification through certain epigenetic mechanisms including cytosine DNA methylation, histone modifications, and small RNA-mediated methylation. Alterations in chromatin structure lead to inaccessibility of genomic DNA to various regulatory proteins such as transcription factors, which eventually modulates gene expression. Advancements in high-throughput sequencing technologies have provided the opportunity to study the epigenetic mechanisms at genome-wide levels. Epigenomic studies using high-throughput technologies will widen the understanding of mechanisms as well as functions of regulatory pathways in plant genomes, which will further help in manipulating these pathways using genetic and biochemical approaches. This technology could be a potential research tool for displaying the systematic associations of genetic and epigenetic variations, especially in terms of cytosine methylation onto the genomic region in a specific cell or tissue. A comprehensive study of plant populations to correlate genotype to epigenotype and to phenotype, and also the study of methyl quantitative trait loci (QTL) or epiGWAS, is possible by using high-throughput sequencing methods, which will further accelerate molecular breeding programs for crop improvement.

Graphical Abstract

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 299.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 379.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 379.99
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

References

  1. Grossniklaus U (2001) From sexuality to apomixis: molecular and genetic approaches. In: Savidan Y, Carman J, Dresselhaus T (eds) Advances in apomixis research. CIMMYT Press, Mexico City, pp 168–211

    Google Scholar 

  2. Lippman Z, Gendrel A, Black M, Vaugn M, Dedhia N, McComble R, Lavine K, Mittal V, May B, Kasschau K, Carrington J, Doerge R, Colot V, Martienssen R (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature 430:471–476

    Article  CAS  PubMed  Google Scholar 

  3. Jablonka E, Lamb MJ (2002) The changing concept of epigenetics. Ann N Y Acad Sci 981:82–96

    Article  PubMed  Google Scholar 

  4. Capuano F, Mulleder M, Kok R, Blom HJ, Ralser M (2014) Cytosine DNA methylation is found in Drosophila melanogaster but absent in Saccharomyces cerevisiae, Schizosaccharomyces pombe, and other yeast species. Anal Chem 86:3697–3702

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  5. Gehring M (2013) Genomic imprinting: insights from plants. Annu Rev Genet 47:187–208

    Article  CAS  PubMed  Google Scholar 

  6. Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE (2001) Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292:2077–2080

    Article  CAS  PubMed  Google Scholar 

  7. 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 U S A 111:10642–10647

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  8. Yamauchi T, Johzuka-Hisatomi Y, Terada R, Nakamura I, Iida S (2014) The MET1b gene encoding a maintenance DNA methyltransferase is indispensable for normal development in rice. Plant Mol Biol 85:219–232

    Article  CAS  PubMed  Google Scholar 

  9. Tompa R, McCallum CM, Delrow J, Henikoff JG, van Steensel B, Henikoff S (2002) Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3. Curr Biol 12:65–68

    Article  CAS  PubMed  Google Scholar 

  10. Chan S, Henderson IR, Jacobsen SE (2005) Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet 6:351–360

    Article  CAS  PubMed  Google Scholar 

  11. Ramsahoye BH, Biniszkiewicz D, Lyko F, Clrk V, Bird AP, Jaenisch R (2000) Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc Natl Acad Sci U S A 97:5237–5242

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  12. Li GF, Bishop KJ, Hall TC (2001) De novo activation of the beta-phaseolin promoter by phosphatase or protein synthesis inhibitors. J Biol Chem 276:2062–2068

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  14. Charron JB, He H, Elling AA, Deng XW (2009) Dynamic landscapes of four histone modifications during de etiolation in Arabidopsis. Plant Cell 21:3732–3748

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  15. Offermann S, Danker T, Dreymuller D, Kalamajka R, Topsch S, Weyand K, Peterhansel C (2006) Illumination is necessary and sufficient to induce histone acetylation independent of transcriptional activity at the C4-specific phosphoenolpyruvate carboxylase promoter in maize. Plant Physiol 141:1078–1088

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  16. Ding Y, Avramova Z, Fromm M (2011) The Arabidopsis trithorax-like factor ATX1 functions in dehydration stress responses via ABA-dependent and ABA-independent pathways. Plant J 66:735–744

    Article  CAS  PubMed  Google Scholar 

  17. Song Y, Ji D, Li S, Wang P, Li Q, Xiang F (2012) The dynamic changes of DNA methylation and histone modifications of salt responsive transcription factor genes in soybean. PLoS One 7:e41274

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  18. Kwon CS, Lee D, Choi G, Chung WI (2009) Histone occupancy-dependent and - independent removal of H3K27 trimethylation at cold-responsive genes in Arabidopsis. Plant J 60:112–121

    Article  CAS  PubMed  Google Scholar 

  19. Folsom JJ, Begcy K, Hao X, Wang D, Walia H (2014) Rice fertilization-independent endosperm1 regulates seed size under heat stress by controlling early endosperm development. Plant Physiol 165:238–248

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  20. Köhler C, Makarevich G (2006) Epigenetic mechanisms governing seed development in plants. EMBO Rep 7:1223–1227

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  21. Rodrigues JCM, Johnson S, Okada T, Koltunow AMG (2006) In: Proc. of 8th international congress of plant molecular biology (Apomixis Workshop), Adelaide, Australia

    Google Scholar 

  22. Wassenegger M, Heimes S, Riedel L, Sanger HL (1994) RNA-directed de novo methylation of genomic sequences in plants. Cell 76:567–576

    Article  CAS  PubMed  Google Scholar 

  23. Pikaard CS, Haag JR, Pontes OM, Blevins T, Cocklin R (2012) A transcription fork model for Pol IV and Pol V-dependent RNA-directed DNA methylation. Cold Spring Harb Symp Quant Biol 77:205–212

    Article  CAS  PubMed  Google Scholar 

  24. Gao ZH et al (2010) An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature 465:106–109

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  25. Buermans HPJ, den Dunnen JT (2014) Next generation sequencing technology: advance and applications. Biochem Biophys Acta 1842:1932–1941

    CAS  PubMed  Google Scholar 

  26. Eichten SR, Springer NM (2015) Minimal evidence for consistent changes in maize DNA methylation patterns following environmental stress. Front Plant Sci 6(308)

    Google Scholar 

  27. Bilichak A, Ilnystkyy Y, Hollunder J, Kovalchuk I (2012) The progeny of Arabidopsis thaliana plants exposed to salt exhibit changes in DNA methylation, histone modifications and gene expression. PLoS One 7:e30515

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  28. Li Q et al (2014) Genetic perturbation of the maize methylome. Plant Cell 26:4602–4616

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  29. Zhao L et al (2014) Transcriptional regulation of cell cycle genes in response to abiotic stresses correlates with dynamic changes in histone modifications in maize. PLoS One 9:e106070

    Article  PubMed  PubMed Central  Google Scholar 

  30. Roy D, Paul A, Roy A, Ghosh R, Ganguly P, Chaudhuri S (2014) Differential acetylation of histone H3 at the regulatory region of OsDREB1b promoter facilitates chromatin remodelling and transcription activation during cold stress. PLoS One 9:e100343

    Article  PubMed  PubMed Central  Google Scholar 

  31. Hu Y, Zhang L, Zhao L, Li J, He S, Zhou K, Yang F, Huang M, Jiang L, Li L (2011) Trichostatin, A selectively suppresses the cold-induced transcription of the ZmDREB1 gene in maize. PLoS One 6:e22132

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  32. Migicovsky Z, Yao Y, Kovalchuk I (2014) Transgenerational phenotypic and epigenetic changes in response to heat stress in Arabidopsis thaliana. Plant Signal Behav 9:e27971

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  33. Sani E, Herzyk P, Perrella G, Colot V, Amtmann A (2013) Hyperosmotic priming of Arabidopsisseedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome. Genome Biol 14:R59

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  34. Widiez T, Symeonidi A, Luo C, Lam E, Lawton M, Rensing SA (2014) The chromatin landscape of the moss Physcomitrella patens and its dynamics during development and drought stress. Plant J 79:67–81

    Article  CAS  PubMed  Google Scholar 

  35. Zong W, Zhong X, You J, Xiong L (2013) Genome-wide profiling of histone H3K4-tri-methylation and gene expression in rice under drought stress. Plant Mol Biol 81:175–188

    Article  CAS  PubMed  Google Scholar 

  36. Schneeberger K et al (2011) Reference-guided assembly of four diverse Arabidopsis thaliana genomes. Proc Natl Acad Sci U S A 108:10249–10254

    Article  PubMed  PubMed Central  Google Scholar 

  37. González RM, Ricardi MM, Iusem ND (2013) Epigenetic marks in an adaptive water stress-responsive gene in tomato roots under normal and drought conditions. Epigenetics 8:864–872

    Article  PubMed  PubMed Central  Google Scholar 

  38. Gent JI, Ellis NA, Guo L, Harkess AE, Yao Y, Zhang X et al (2013) CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize. Genome Res 23:628–637

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  39. Stroud H, Ding B, Simon SA, Feng S, Bellizzi M, Pellegrini M, Wang G-L, Meyers BC, Jacobsen SE (2013) Plants regenerated from tissue culture contain stable epigenome changes in rice. eLife 2:e00354

    Article  PubMed  PubMed Central  Google Scholar 

  40. Schmitz RJ, He Y, Valdés-López O, Khan SM, Joshi T, Urich MA, Nery JR, Diers B, Xu D, Stacey G, Ecker JR (2013) Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Res 23:1663–1674

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  41. Takuno S, Gaut BS (2013) Gene body methylation is conserved between plant orthologs and is of evolutionary consequence. Proc Natl Acad Sci U S A 110:1797–1802

    Article  PubMed  PubMed Central  Google Scholar 

  42. 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:e1004785

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  43. Karan R, DeLeon T, Biradar H, Subudhi PK (2012) Salt stress induced variation in DNA methylation pattern and its influence on gene expression in contrasting rice genotypes. PLoS One 7:e40203

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  44. Wang W, Zhao X, Pan Y, Zhu L, Fu B, Li Z (2011) DNA methylation changes detected by methylation-sensitive amplified polymorphism in two contrasting rice genotypes under salt stress. J Genet Genomics 38:419–424

    Article  CAS  PubMed  Google Scholar 

  45. Wang WS, Pan YJ, Zhao XQ, Dwivedi D, Zhu LH, Ali J, Fu BY, Li ZK (2011) Drought-induced site-specific DNA methylation and its association with drought tolerance in rice (Oryza sativa L.) J Exp Bot 62:1951–1960

    Article  CAS  PubMed  Google Scholar 

  46. Zhong L, Xu Y, Wang J (2009) DNA-methylation changes induced bysalt stress in wheat Triticum aestivum. Afr J Biotechnol 8:6201–6207

    Article  CAS  Google Scholar 

  47. Tan MP (2010) Analysis of DNA methylation of maize in response to osmotic and salt stress based on methylation-sensitive amplified polymorphism. Plant Physiol Biochem 48:21–26

    Article  CAS  PubMed  Google Scholar 

  48. Marconi G, Pace R, Traini A, Raggi L, Lutts S, Chiusano M, Guiducci M, Falcinelli M, Benincasa P, Albertini E (2013) Use of MSAP markers to analyse the effects of salt stress on DNA methylation in rapeseed (Brassica napusvar. oleifera). PLoS One 8:e75597

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  49. Zheng X, Chen L, Li M, Lou Q, Xia H, Wang P, Li T, Liu H, Luo L (2013) Transgenerational variations in DNA methylation induced by drought stress in two rice varieties with distinguished difference to drought resistance. PLoS One 8:e80253

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  50. Gayacharan A, Joel AJ (2013) Epigenetic responses to drought stress in rice (Oryza sativa L.) Physiol Mol Biol Plants 19:379–387

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  51. Gao G, Li J, Li H, Li F, Xu K, Yan G, Chen B, Qiao J, Wu X (2014) Comparison of the heat stress induced variations in DNA methylation between heat-tolerant and heat-sensitive rapeseed seedlings. Breed Sci 64:125–133

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  52. Baranek M, Cechova J, Raddova J, Holleinova V, Ondrusikova E, Pidra M (2015) Dynamics and reversibility of the DNA methylation landscape of grapevine plants (Vitis vinifera) stressed by in vitro cultivation and thermotherapy. PLoS One 10:e0126638

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  53. Ou X, Zhang Y, Xu C (2012) Transgenerational inheritance of modified DNA methylation patterns and enhanced tolerance induced by heavy metal stress in rice (Oryza sativa L.) PLoS One 7:e41143

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  54. Cicatelli A, Todeschini V, Lingua G, Biondi S, Torrigiani P, Castiglione S (2014) Epigenetic control of heavy metal stress response in mycorrhizal versus non-mycorrhizal poplar plants. Environ Sci Pollut Res Int 21:1723–1737

    Article  CAS  PubMed  Google Scholar 

  55. Greco M, Chiappetta A, Bruno L, Bitonti MB (2012) In Posidoniaoceanica cadmium induces changes in DNA methylation and chromatin patterning. J Exp Bot 63:695–709

    Article  CAS  PubMed  Google Scholar 

  56. Yang JL, Liu LW, Gong YQ, Huang DQ, Wang F, He LL (2007) Analysis of genomic DNA methylation level in radish under cadmium stress by methylation-sensitive amplified polymorphism technique. J Exp Bot 33:219–226

    CAS  Google Scholar 

  57. Filek M, Keskinen R, Hartikainen H, Szarejko I, Janiak A, Miszalski Z, Golda A (2008) The protective role of selenium in rape seedlings subjected to cadmium stress. J Plant Physiol 165:833–844

    Article  CAS  PubMed  Google Scholar 

  58. Rakei A, Maali-Amiri R, Zeinali H, Ranjbar M (2015) DNA methylation and physio-biochemical analysis of chickpea in response to cold stress. Protoplasma 253:61–76

    Article  CAS  PubMed  Google Scholar 

  59. Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD et al (2014) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452:215–219

    Article  CAS  Google Scholar 

  60. 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 133:523–536

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  61. Eichten SR et al (2011) Heritable epigenetic variation among maize inbreds. PLoS Genet 7:e1002372

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  62. Li Q, Gent JI, Zynda G, Song J, Makarevitch I, Hirsch CD, Hirsch CN, Dawe RK, Madzima TF, McGinnis KM, Lisch D, Schmitz RJ, Vaughn MW, Springer NM (2015) RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome. Proc Natl Acad Sci U S A 112:14728–14733

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  63. Takuno S, Ran JH, Gaut BS (2016) Evolutionary patterns of genic DNA methylation vary across land plants. Nat Plants 2:15222

    Article  CAS  PubMed  Google Scholar 

  64. Zemach A, McDaniel IE, Silva P, Zilberman D (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328:916–919

    Article  CAS  PubMed  Google Scholar 

  65. Zhong S, Fei Z, Chen YR, Zheng Y, Huang M, Vrebalov J, McQuinn R, Gapper N, Liu B, Xiang J, Shao Y, Giovannoni JJ (2013) Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat Biotechnol 31:154–159

    Article  CAS  PubMed  Google Scholar 

  66. Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A et al (2008) Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454:766–770

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  67. Chen X, Ge X, Wang J, Tan C, King GJ, Liu K (2015) Genome-wide DNA methylation profiling by modified reduced representation bisulfite sequencing in Brassica rapa suggests that epigenetic modifications play a key role in polyploid genome evolution. Front Plant Sci 6:836

    PubMed Central  PubMed  Google Scholar 

  68. Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, Mason CE (2012) methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol 13:R87

    Article  PubMed  PubMed Central  Google Scholar 

  69. Jiang P, Sun K, Lun FMF, Guo AM, Wang H, Chan KCA et al (2014) Methy-pipe: an integrated bioinformatics pipeline for whole genome bisulfite sequencing data analysis. PLoS One 9:e100360

    Article  PubMed  PubMed Central  Google Scholar 

  70. Krueger F, Andrews SR (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27:1571–1572

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  71. Chen PY, Cokus SJ, Pellegrini M (2010) BS Seeker: precise mapping for bisulfite sequencing. BMC Bioinformatics 11:203–208

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  72. Lim JQ, Tennakoon C, Li G, Wong E, Ruan Y et al (2012) BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation. Genome Biol 13:R82

    Article  PubMed  PubMed Central  Google Scholar 

  73. Xi Y, Li W (2009) BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics 10:232

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  74. Benoukraf T, Wongphayak S, Hadi LH, Wu M, Soong R (2013) GBSA: a comprehensive software for analysing whole genome bisulfite sequencing data. Nucleic Acids Res 41:e55

    Article  CAS  PubMed  Google Scholar 

  75. Hansen KD, Langmead B, Irizarry RA (2012) BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol 13:R83

    Article  PubMed  PubMed Central  Google Scholar 

  76. Zhang R et al (2014) PEAR: a fast and accurate Illumina Paired-End reAd merge. Bioinformatics 30:614–620

    Article  PubMed  CAS  Google Scholar 

  77. Peters TJ, Buckley MJ, Statham AL, Pidsley R, Samaras K, Lord RV, Clark SJ, Molloy PL (2015) De novo identification of differentially methylated regions in the human genome. Epigenetics Chromatin 8:6

    PubMed Central  PubMed  Google Scholar 

  78. Song Q, Decato B, Hong E, Zhou M, Fang F, Qu J, Garvin T, Kessler M, Zhou J, Smith AD (2013) A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics. PLoS One 8:e81148

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  79. Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA (2014) Minfi: a flexible and comprehensive bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics 30:1363–1369

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  80. Akman K (2014) BEAT: BEAT - BS-Seq epimutation analysis toolkit. R package version 1.8.0

    Google Scholar 

  81. Martin TC, Yet I, Tsai PC, Bell JT (2015) coMET: visualisation of regional epigenome-wide association scan results and DNA co-methylation patterns. BMC Bioinformatics 16:131

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  82. Statham AL, Strbenac D, Coolen MW, Stirzaker C, Clark SJ, Robinson MD (2010) Repitools: an R package for the analysis of enrichment-based epigenomic data. Bioinformatics 26:1659

    Article  CAS  Google Scholar 

  83. Kishore K, de Pretis S, Lister R, Morelli MJ, Bianchi V, Amati B, Ecker JR, Pelizzola M (2015) methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data. BMC Bioinformatics 16:313–324

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  84. Klein H, Schaefer M, Porse BT, Hasemann MS, Ickstadt K, Dugas M (2014) Integrative analysis of histone ChIP-seq and transcription data using Bayesian mixture models. Bioinformatics 30:1154–1162

    Article  CAS  PubMed  Google Scholar 

  85. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS (2008) Model based analysis of ChIP-Seq (MACS). Genome Biol 9:R137

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  86. Schweikert G (2012) MMDiff: statistical testing for ChIP-Seq data sets. R package version 1.10.0

    Google Scholar 

  87. Choi CS, Sano H (2007) Abiotic-stress induces demethylation and transcriptional activation of a gene encoding a glycerophosphodiesterase-like protein in tobacco plants. Mol Genet Genomics 277:589–600

    Article  CAS  PubMed  Google Scholar 

  88. Ocaña J, Walter B, Schellenbaum P (2013) Stable MSAP markers for the distinction of Vitis vinifera cv Pinot Noir Clones. Mol Biotechnol 55:236–248

    Article  CAS  PubMed  Google Scholar 

  89. Danker T (2008) Developmental information but not promoter activity controls the methylation state of histone H3 lysine 4 on two photosynthetic genes in maize. Plant J 53:465–474

    Article  CAS  PubMed  Google Scholar 

  90. Jaskiewicz M (2011) Chromatin modification acts as a memory for systemic acquired resistance in the plant stress response. EMBO Rep 12:50–55

    Article  CAS  PubMed  Google Scholar 

  91. Zhang X, Bernatavichute YV, Cokus S, Pellegrini M, Jacobsen SE (2009) Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol 10:R62

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  92. van Dijk K, Ding Y, Malkaram S, Riethoven JJM, Liu R, Yang J, Laczko P, Chen H, Xia Y, Ladunga I et al (2010) Dynamic changes in genome-wide histone H3 lysine 4 methylation patterns in response to dehydration stress in Arabidopsis thaliana. BMC Plant Biol 10:238

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  93. Mosquna A, Katz A, Decker EL, Rensing SA, Reski R, Ohad N (2009) Regulation of stem cell maintenance by the Polycomb protein FIE has been conserved during land plant evolution. Development 136:2433–2444

    Article  CAS  PubMed  Google Scholar 

  94. Okano Y, Aono N, Hiwatashi Y, Murata T, Nishiyama T, Ishikawa T, Kubo M, Hasebe M (2009) A Polycomb repressive complex 2 gene regulates apogamy and gives evolutionary insights into early land plant evolution. Proc Natl Acad Sci U S A 106:16321–16326

    Article  PubMed  PubMed Central  Google Scholar 

  95. Schramke V, Allshire R (2003) Hairpin RNAs and retrotransposon LTRs effect RNAi and chromatin-based gene silencing. Science 301:1069–1074

    Article  CAS  PubMed  Google Scholar 

  96. Durán-Figueroa N, Vielle-Calzada JP (2010) ARGONAUTE9-dependent silencing of transposable elements in pericentromeric regions of Arabidopsis. Plant Signal Behav 6:5

    Google Scholar 

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

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  98. Boyko A, Kovalchuk I (2008) Epigenetic control of plant stress response. Environ Mol Mutagen 49:61–72

    Article  CAS  PubMed  Google Scholar 

  99. Chinnusamy V, Zhu JK (2009) Epigenetic regulation of stress responses in plants. Curr Opin Plant Biol 12:1–7

    Article  CAS  Google Scholar 

  100. Zhu J, Jeong JC, Zhu Y, Sokolchik I, Miyazaki S, Zhu JK, Hasegawa PM, Bohnert HJ, Shi H, Yun DJ et al (2008) Involvement of Arabidopsis HOS15 in histone deacetylation and cold tolerance. Proc Natl Acad Sci U S A 105:4945–4950

    Article  PubMed  PubMed Central  Google Scholar 

  101. Sokol A, Kwiathowska A, Jerzmanowski A, Prymakowska-Bosak M (2007) Up-regulation of stress-inducible genes in tobacco and Arabidopsis cells in response to abiotic stresses and ABA treatment correlates with dynamic changes in histone H3 and H4 modifications. Planta 227:245–254

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

C.B.Y. acknowledges the Science and Engineering Research Board, Department of Science and Technology, Govt. of India, India for providing a Young Scientist Research Grant (File No. YSS/2015/000287). Ms. Garima Pandey and Mr. Mehanathan Muthamilarasan thank the University Grants Commission for Research Fellowship.

Author information

Authors and Affiliations

  1. National Institute of Plant Genome Research (NIPGR), New Delhi, India

    Chandra Bhan Yadav, Garima Pandey, Mehanathan Muthamilarasan & Manoj Prasad

Authors
  1. Chandra Bhan Yadav
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Garima Pandey
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Mehanathan Muthamilarasan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Manoj Prasad
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Manoj Prasad .

Editor information

Editors and Affiliations

  1. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India

    Rajeev K. Varshney

  2. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India

    Manish K. Pandey

  3. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India

    Annapurna Chitikineni

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer International Publishing AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Yadav, C.B., Pandey, G., Muthamilarasan, M., Prasad, M. (2018). Epigenetics and Epigenomics of Plants. In: Varshney, R., Pandey, M., Chitikineni, A. (eds) Plant Genetics and Molecular Biology. Advances in Biochemical Engineering/Biotechnology, vol 164. Springer, Cham. https://doi.org/10.1007/10_2017_51

Download citation

Publish with us

Policies and ethics

Search

Navigation