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Characteristics of cytosine methylation status and methyltransferase genes in the early development stage of cauliflower (Brassica oleracea L. var. botrytis)

  • Hui Li
  • Meijuan Geng
  • Qian Liu
  • Chuan Jin
  • Qingli Zhang
  • Chengbin Chen
  • Wenqin Song
  • Chunguo WangEmail author
Original Paper

Abstract

DNA methylation is one of the most important epigenetic modifications involved in the development and differentiation in plants. Hypocotyl and cotyledon are the two major tissues of cauliflower (Brassica oleracea L. var. botrytis) seedlings. Both tissues show significantly different tissue specificity and regenerative abilities in vitro. However, the characteristics of DNA methylation modification and its roles in regulating the organ development in cauliflower remain largely unknown. In the present study, the DNA methylation status between the hypocotyl and cotyledon of cauliflower seedlings were analyzed. The results indicated that although the hypocotyl and cotyledon of cauliflower seedlings share the same genome, the genomic DNA methylation levels and patterns at CCGG sites were different. Compared with the cotyledon, the hypocotyl showed higher DNA methylation level, and more loci showing methylation pattern adjustments were also discovered. Twelve loci with changes of DNA methylation patterns were further explored. The quantitative expression analysis indicated that eight out of twelve sequenced fragments showed differential expression between the hypocotyl and cotyledon, of which the expression of six sequences was identified to be negative correlation with their DNA methylation status. In addition, three main DNA methyltransferase genes MET1, CMT3 and DRM were first explored in cauliflower. The results indicated that the expression of these three genes was closely associated with the different DNA methylation status in the hypocotyl and cotyledon. These findings provided more information to further explore the roles of DNA methylation modification in tissue differentiation and development of cauliflower.

Keywords

DNA methylation DNA methyltransferase genes Cauliflower (Brassica oleracea L. var. botrytisHypocotyl Cotyledon 

Notes

Acknowledgments

We greatly thank Dr. Deling Sun at Tianjin Kernel Vegetable Research Institute, China for kindly providing the cauliflower seeds. This work was performed with financial support from The Natural Science Foundation from The National Natural Science Foundation of China (No. 31100234) and Tianjin (No. 10JCZDJC17900).

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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Supplementary material 1 (DOC 34 kb)
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Supplementary material 2 (DOC 48 kb)
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Supplementary material 3 (DOC 53 kb)
11240_2014_432_MOESM4_ESM.doc (338 kb)
Supplementary material 4 (DOC 338 kb)

References

  1. Akimoto K, Katakami H, Kim HJ, Ogawa E, Sano CM, Wada Y, Sano H (2007) Epigenetic inheritance in rice plant. Ann Bot 100:205–217PubMedCentralPubMedCrossRefGoogle Scholar
  2. Alvarez ME, Nota F, Cambiagno DA (2010) Epigenetic control of plant immunity. Mol Plant Pathol 11:563–576PubMedCrossRefGoogle Scholar
  3. Andika IB, Kondo H, Rahim MD, Tamada T (2006) Lower levels of transgene silencing in roots is associated with reduced DNA methylation levels at non-symmetrical sites but not at symmetrical sites. Plant Mol Biol 60:423–435PubMedCrossRefGoogle Scholar
  4. Baránek M, Křižan B, Ondrušíková E, Pidra M (2010) DNA-methylation changes in grapevine somaclones following in vitro culture and thermotherapy. Plant Cell Tissue Organ Cult 101:11–22CrossRefGoogle Scholar
  5. Bardini M, Labra M, Winfield M, Sala F (2003) Antibiotic-induced DNA methylation changes in calluses of Arabidopsis thaliana. Plant Cell Tissue Organ Cult 72:157–162CrossRefGoogle Scholar
  6. Bender J (2004) DNA methylation and epigenetics. Annu Rev Plant Biol 55:41–68PubMedCrossRefGoogle Scholar
  7. Brabbs TR, He Z, Hogg K, Kamenski A, Li Y, Paszkiewicz KH, Moore KA, O’Toole P, Graham IA, Jones L (2013) The stochastic silencing phenotype of Arabidopsis morc6 mutants reveals a role in efficient RNA-directed DNA methylation. Plant J 75:835–846Google Scholar
  8. Braszewska-Zalewska AJ, Wolny EA, Smialek L, Hasterok R (2013) Tissue-specific epigenetic modifications in root apical meristem cells of Hordeum vulgare. PLoS One 8:e69204PubMedCentralPubMedCrossRefGoogle Scholar
  9. Cao X, Jacobsen SE (2002) Role of the arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol 12:1138–1144PubMedCrossRefGoogle Scholar
  10. Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, Matzke M, Jacobsen SE (2003) Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Curr Biol 13:2212–2217PubMedCrossRefGoogle Scholar
  11. Chalhoub BA, Thibault S, Laucou V, Rameau C, Höfte H, Cousin R (1997) Silver staining and recovery of AFLP amplification products on large denaturing polyacrylamide gels. Biotechniques 22:216–220PubMedGoogle Scholar
  12. Chan SW, Henderson IR, Jacobsen SE (2005) Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet 6:351–360PubMedCrossRefGoogle Scholar
  13. Chang S, Pikaard CS (2005) Transcript profiling in Arabidopsis reveals complex responses to global inhibition of DNA methylation and histone deacetylation. J Biol Chem 280:796–804PubMedGoogle Scholar
  14. 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 11:2124–2136PubMedCentralPubMedCrossRefGoogle Scholar
  15. Dong ZY, Wang YM, Zhang ZJ, Shen Y, Lin XY, Ou XF, Han FP, Liu B (2006) Extent and pattern of DNA methylation alteration in rice lines derived from introgressive hybridization of rice and Zizania latifolia Griseb. Theor Appl Genet 113:196–205PubMedCrossRefGoogle Scholar
  16. Finnegan EJ, Kovac KA (2000) Plant DNA methyltransferases. Plant Mol Biol 43:189–201PubMedCrossRefGoogle Scholar
  17. Finnegan EJ, Peacock WJ, Dennis ES (1996) Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc Natl Acad Sci USA 93:8449–8454PubMedCentralPubMedCrossRefGoogle Scholar
  18. Fu C, Li L, Wu W, Li M, Yu X, Yu L (2012) Assessment of genetic and epigenetic variation during long-term Taxus cell culture. Plant Cell Rep 31:1321–1331PubMedCrossRefGoogle Scholar
  19. Gehring M, Henikoff S (2007) DNA methylation dynamics in plant genomes. Biochim Biophys Acta 1769:276–286PubMedCrossRefGoogle Scholar
  20. Gohlke J, Scholz CJ, Kneitz S, Weber D, Fuchs J, Hedrich R, Deeken R (2013) DNA methylation mediated control of gene expression is critical for development of crown gall tumors. PLoS Genet 9:e1003267PubMedCentralPubMedCrossRefGoogle Scholar
  21. Grossniklaus U, Spillane C, Page DR, Köhler C (2001) Genomic imprinting and seed development: endosperm formation with and without sex. Curr Opin Plant Biol 4:21–27PubMedCrossRefGoogle Scholar
  22. Henderson IR, Jacobsen SE (2007) Epigenetic inheritance in plants. Nature 447:418–424PubMedCrossRefGoogle Scholar
  23. Huang LC, Hsiao LJ, Pu SY, Kuo CI, Huang BL, Tseng TC, Huang HJ, Chen YT (2012) DNA methylation and genome rearrangement characteristics of phase change in cultured shoots of Sequoia sempervirens. Physiol Plant 145:360–368PubMedCrossRefGoogle Scholar
  24. Hudson K, Luo S, Hagemann N, Preuss D (2011) Changes in global gene expression in response to chemical and genetic perturbation of chromatin structure. PLoS One 6:e20587PubMedCentralPubMedCrossRefGoogle Scholar
  25. Ito T, Sakai H, Meyerowitz EM (2003) Whorl-specific expression of the SUPERMAN gene of Arabidopsis is mediated by cis elements in the transcribed region. Curr Biol 13:1524–1530PubMedCrossRefGoogle Scholar
  26. Iwasaki M, Takahashi H, Iwakawa H, Nakagawa A, Ishikawa T, Tanaka H, Matsumura Y, Pekker I, Eshed Y, Vial-Pradel S, Ito T, Watanabe Y, Ueno Y, Fukazawa H, Kojima S, Machida Y, Machida C (2013) Dual regulation of ETTIN (ARF3) gene expression by AS1-AS2, which maintains the DNA methylation level, is involved in stabilization of leaf adaxial–abaxial partitioning in Arabidopsis. Development 140:1958–1969PubMedCrossRefGoogle Scholar
  27. Jin X, Pang Y, Jia F, Xiao G, Li Q, Zhu Y (2013) A potential role for CHH DNA methylation in cotton fiber growth patterns. PLoS One 8:e60547PubMedCentralPubMedCrossRefGoogle Scholar
  28. Jullien PE, Susaki D, Yelagandula R, Higashiyama T, Berger F (2012) DNA methylation dynamics during sexual reproduction in Arabidopsis thaliana. Curr Biol 22:1825–1830PubMedCrossRefGoogle Scholar
  29. Kankel MW, Ramsey DE, Stokes TL, Flowers SK, Haag JR, Jeddeloh JA, Riddle NC, Verbsky ML, Richards EJ (2003) Arabidopsis MET1 cytosine methyltransferase mutants. Genetics 163:1109–1122PubMedCentralPubMedGoogle Scholar
  30. 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:e40203PubMedCentralPubMedCrossRefGoogle Scholar
  31. Kidwell KK, Osborn TC (1992) Simple plant DNA isolation procedures. In: Beckmann JS, Osborn TC (eds) Plant genomes: methods for genetic and physical mapping. Kluwer Academic Publishers, Dordrecht, pp 1–13Google Scholar
  32. Kiselev KV, Tyunin AP, Zhuravlev YN (2013) Involvement of DNA methylation in the regulation of STS10 gene expression in Vitis amurensis. Planta 237:933–941PubMedCrossRefGoogle Scholar
  33. Kubis SE, Castilho AM, Vershinin AV, Heslop-Harrison JS (2003) Retroelements, transposons and methylation status in the genome of oil palm (Elaeis guineensis) and the relationship to somaclonal variation. Plant Mol Biol 52:69–79PubMedCrossRefGoogle Scholar
  34. Li X, Zhu J, Hu F, Ge S, Ye M, Xiang H, Zhang G, Zheng X, Zhang H, Zhang S, Li Q, Luo R, Yu C, Yu J, Sun J, Zou X, Cao X, Xie X, Wang J, Wang W (2012) Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression. BMC Genom 13:300CrossRefGoogle Scholar
  35. Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE (2001) Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292:2077–2080PubMedCrossRefGoogle Scholar
  36. Malik G, Dangwal M, Kapoor S, Kapoor M (2012) Role of DNA methylation in growth and differentiation in Physcomitrella patens and characterization of cytosine DNA methyltransferases. FEBS J 279:4081–4094PubMedCrossRefGoogle Scholar
  37. Matthes M, Singh R, Cheah S-C, Karp A (2001) Variation in oil palm (Eleais guineensis Jacq.) tissue culture-derived regenerants revealed by AFLPs with methylation-sensitive enzymes. Theor Appl Genet 102:971–979CrossRefGoogle Scholar
  38. Pillot M, Autran D, Leblanc O, Grimanelli D (2010) A role for CHROMOMETHYLASE3 in mediating transposon and euchromatin silencing during egg cell reprogramming in Arabidopsis. Plant Signal Behav 5:1167–1170PubMedCentralPubMedCrossRefGoogle Scholar
  39. Ronemus MJ, Galbiati M, Ticknor C, Chen J, Dellaporta SL (1996) Demethylation-induced developmental pleiotropy in Arabidopsis. Science 273:654–657PubMedCrossRefGoogle Scholar
  40. Ruiz-Ferrer V, Voinnet O (2009) Roles of plant small RNAs in biotic stress responses. Annu Rev Plant Biol 60:485–510PubMedCrossRefGoogle Scholar
  41. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  42. Sha AH, Lin XH, Huang JB, Zhang DP (2005) Analysis of DNA methylation related to rice adult plant resistance to bacterial blight based on methylation-sensitive AFLP (MSAP) analysis. Mol Genet Genomics 273:484–490PubMedCrossRefGoogle Scholar
  43. Sieburth LE, Meyerowitz EM (1997) Molecular dissection of the AGAMOUS control region shows that cis elements for spatial regulation are located intragenically. Plant Cell 9:355–365PubMedCentralPubMedGoogle Scholar
  44. 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:e41274PubMedCentralPubMedCrossRefGoogle Scholar
  45. Steward N, Kusano T, Sano H (2000) Expression of ZmMET1, a gene encoding a DNA methyltransferase from maize, is associated not only with DNA replication in actively proliferating cells, but also with altered DNA methylation status in cold-stressed quiescent cells. Nucleic Acids Res 28:3250–3259PubMedCentralPubMedCrossRefGoogle Scholar
  46. Steward N, Ito M, Yamaguchi Y, Koizumi N, Sano H (2002) Periodic DNA methylation in maize nucleosomes and demethylation by environmental stress. J Biol Chem 277:37741–37746PubMedCrossRefGoogle Scholar
  47. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599PubMedCrossRefGoogle Scholar
  48. 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 48:21–26PubMedCrossRefGoogle Scholar
  49. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680PubMedCentralPubMedCrossRefGoogle Scholar
  50. Tsukahara S, Kobayashi A, Kawabe A, Mathieu O, Miura A, Kakutani T (2009) Bursts of retrotransposition reproduced in Arabidopsis. Nature 461:423–426PubMedCrossRefGoogle Scholar
  51. Tyunin AP, Kiselev KV, Zhuravlev YN (2012) Effects of 5-azacytidine induced DNA demethylation on methyltransferase gene expression and resveratrol production in cell cultures of Vitis amurensis. Plant Cell Tissue Organ Cult 111:91–100CrossRefGoogle Scholar
  52. Verhoeven KJ, Jansen JJ, van Dijk PJ, Biere A (2010) Stress-induced DNA methylation changes and their heritability in asexual dandelions. New Phytol 185:1108–1118PubMedCrossRefGoogle Scholar
  53. Viejo M, Santamaría ME, Rodríguez JL, Valledor L, Meijón M, Pérez M, Pascual J, Hasbún R, Fernández Fraga M, Berdasco M, Toorop PE, Cañal MJ, Rodríguez Fernández R (2012) Epigenetics, the role of DNA methylation in tree development. Methods Mol Biol 877:277–301PubMedCrossRefGoogle Scholar
  54. Vining K, Pomraning KR, Wilhelm LJ, Ma C, Pellegrini M, Di Y, Mockler TC, Freitag M, Strauss SH (2013) Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa. BMC Plant Biol 13:92PubMedCentralPubMedCrossRefGoogle Scholar
  55. Wang CG, Chen XQ, Li H, Song WS (2007) RNA editing analysis of mitochondrial nad3/rps12 genes in cytoplasmic male sterility and fertile cauliflower (Brassica oleracea var. botrytis) by cDNA-SSCP. Bot Stud 48:13–23Google Scholar
  56. Wang CG, Li H, Xue ZY, Chen CB, Gu Y, Sun DL, Song WQ (2009) Marker-based analysis of genomic structure and DNA methylation in a watermelon (Citrullus lanatus) ploidy series. Bot Stud 50:389–402Google Scholar
  57. Wang X, Wu R, Lin X, Bai Y, Song C, Yu X, Xu C, Zhao N, Dong Y, Liu B (2013a) Tissue culture-induced genetic and epigenetic alterations in rice pure-lines, F1 hybrids and polyploids. BMC Plant Biol 13:77PubMedCentralPubMedCrossRefGoogle Scholar
  58. Wang Y, Wang X, Lee TH, Mansoor S, Paterson AH (2013b) Gene body methylation shows distinct patterns associated with different gene origins and duplication modes and has a heterogeneous relationship with gene expression in Oryza sativa (rice). New Phytol 198:274–283PubMedCrossRefGoogle Scholar
  59. Weinhold A, Kallenbach M, Baldwin IT (2013) Progressive 35S promoter methylation increases rapidly during vegetative development in transgenic Nicotiana attenuata plants. BMC Plant Biol 13:99PubMedCentralPubMedCrossRefGoogle Scholar
  60. Xiao W, Custard KD, Brown RC, Lemmon BE, Harada JJ, Goldberg RB, Fischer RL (2006) DNA methylation is critical for Arabidopsis embryogenesis and seed viability. Plant Cell 18:805–814PubMedCentralPubMedCrossRefGoogle Scholar
  61. Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC (2004) Genetic and functional diversification of small RNA pathways in plants. PLoS Biol 2:e104PubMedCentralPubMedCrossRefGoogle Scholar
  62. Xiong LZ, Xu CG, Saghai Maroof MA, Zhang Q (1999) Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique. Mol Gen Genet 261:439–446PubMedCrossRefGoogle Scholar
  63. Yoshida H, Akimoto H, Yamaguchi M, Shibata M, Habu Y, Iida S, Ozeki Y (2004) Alteration of methylation profiles in distinct cell lineages of the layers during vegetative propagation in carnations (Dianthus caryophyllus). Euphytica 135:247–253CrossRefGoogle Scholar
  64. Yu A, Lepère G, Jay F, Wang J, Bapaume L, Wang Y, Abraham AL, Penterman J, Fischer RL, Voinnet O, Navarro L (2013a) Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense. Proc Natl Acad Sci USA 110:2389–2394PubMedCentralPubMedCrossRefGoogle Scholar
  65. Yu Y, Yang X, Wang H, Shi F, Liu Y, Liu J, Li L, Wang D, Liu B (2013b) Cytosine methylation alteration in natural populations of Leymus chinensis induced by multiple abiotic stresses. PLoS One 8:e55772PubMedCentralPubMedCrossRefGoogle Scholar
  66. Zhao Y, Yu S, Xing C, Fan S, Song M (2008) Analysis of DNA methylation in cotton hybrids and their parents. Mol Biol 42:195–205CrossRefGoogle Scholar
  67. 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 31:154–159PubMedCrossRefGoogle Scholar
  68. Zubko E, Gentry M, Kunova A, Meyer P (2012) De novo DNA methylation activity of methyltransferase 1 (MET1) partially restores body methylation in Arabidopsis thaliana. Plant J 71:1029–1037PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Hui Li
    • 2
  • Meijuan Geng
    • 1
  • Qian Liu
    • 1
  • Chuan Jin
    • 1
  • Qingli Zhang
    • 1
  • Chengbin Chen
    • 1
  • Wenqin Song
    • 1
  • Chunguo Wang
    • 1
    Email author
  1. 1.College of Life SciencesNankai UniversityTianjinChina
  2. 2.Department of HorticultureTianjin Agricultural UniversityTianjinChina

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