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Gibberellin A3 as an epigenetic determinant of global DNA hypo-methylation in tobacco

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Biologia Plantarum

Abstract

Gibberellins (GAs) are a large family of tetracyclic diterpenoids, controlling important aspects of growth and development throughout the plant life cycle. To explore the possibility that gibberellin A3 (GA3) signalling induces epigenetic alteration(s), we carried out a field experiment study using Nicotiana tabacum as a model system. The GA3 application on leaves resulted in increased plant-height, foliage density, leaf cell area, and trichome density. The plants exposed to GA3 also exhibited: 1) increased chromatin de-condensation, 2) reduced global DNA methylation, 3) reduced DNA methyltransferases (NtDNMTs) activities accompanied by decreased amounts of NtMET1 and NtCMT3 transcripts, and 4) partial restoration of phenotype and expression of epigenetically silenced reporter transgene. Based on these observations, we propose that GA3 application induces complex epigenetic re-programming, which may lead to distinct developmental phenotypes. These results could provide an important insight for future studies on epigenetic mechanism(s) in other important crops.

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Abbreviations

Ado-Met:

S-adenosyl-methionine

5-AZA -C:

5-azacytidine

DNMT:

DNA methyltransferase

DSMO:

dimethyl sulfoxide

GA3 :

gibberellin A3

Gen:

genistein

PTGS:

post-transcriptional gene silencing

TGS:

transcriptional gene silencing

TSA:

trichostatin A

References

  • Ahmad, F., Huang, X., Lan, H.X., Huma, T., Bao, Y.M., Huang, J., Zhang, H.S.: Comprehensive gene expression analysis of the DNA (cytosine-5) methyltransferase family in rice (Oryza sativa L.). — Genet. mol. Res. 13: 5159–5172, 2014.

    Article  CAS  PubMed  Google Scholar 

  • Akimoto, K., Katakami, H., Kim, H.J., Ogawa, E., Sano, C.M., Wada, Y., Sano, H.: Epigenetic inheritance in rice plants. — Ann. Bot. 100: 205–217, 2007.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Atzorn, R., Weiler, E.W.: The role of endogenous gibberellins in the formation of α-amylase by aleurone layers of germinating barley caryopses. — Planta 159: 289–299, 1983.

    Article  CAS  PubMed  Google Scholar 

  • Bar, M., Ori, N.: Leaf development and morphogenesis. — Development 141: 4219–4230, 2014.

    Article  CAS  PubMed  Google Scholar 

  • Baylin, S.B., Herman, J.G.: DNA hypermethylation in tumorigenesis: epigenetics joins genetics. — Trends Genet. 16: 168–174, 2000.

    Article  CAS  PubMed  Google Scholar 

  • Bird, A.: DNA methylation patterns and epigenetic memory. — Genes Dev. 16: 6–21, 2002.

    Article  CAS  PubMed  Google Scholar 

  • Brautigam, K., Vining, K.J., Lafon-Placette, C., Fossdal, C.G., Mirouze, M., Marcos, J.G., Fluch, S., Fraga, M.F., Guevara, M.A., Abarca, D., Johnsen, O., Maury, S., Strauss, S.H., Campbell, M.M., Rohde, A., Diaz-Sala, C., Cervera, M.T.: Epigenetic regulation of adaptive responses of forest tree species to the environment. — Ecol. Evol. 3: 399–415, 2013.

    Article  PubMed  PubMed Central  Google Scholar 

  • Chinnusamy, V., Gong, Z., Zhu, J.K.: Abscisic acid-mediated epigenetic processes in plant development and stress responses. — J. Integ. Plant. Biol. 50: 1187–1195, 2008.

    Article  CAS  Google Scholar 

  • Choi, C.S., Sano, H.: Abiotic-stress induces demethylation and transcriptional activation of a gene encoding a glycerophosphodiesterase-like protein in tobacco plants. — Mol. Genet. Genom. 277: 589–600, 2007.

    Article  CAS  Google Scholar 

  • Clement, G., Benhattar, J.: A methylation sensitive dot blot assay (MS-DBA) for the quantitative analysis of DNA methylation in clinical samples. — J. clin. Pathol. 58: 155–158, 2005.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Colot, V., Rossignol, J.L.: Eukaryotic DNA methylation as an evolutionary device. — Bioessays 21: 402–411, 1999.

    Article  CAS  PubMed  Google Scholar 

  • Fajkus, J., Vyskot, B., Bezdĕk, M.: Changes in chromatin structure due to hypomethylation induced with 5-azacytidine or DL-ethionine. — FEBS Lett. 314: 13–16, 1992.

    Article  CAS  PubMed  Google Scholar 

  • Finnegan, E.J., Dennis, E.S.: Isolation and identification by sequence homology of a putative cytosine methyltransferase from Arabidopsis thaliana. — Nucl. Acids Res. 21: 2383–2388, 1993.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Finnegan, E.J., Kovac, K.A.: Plant DNA methyltransferases. — Plant mol. Biol. 43: 189–201, 2000.

    Article  CAS  PubMed  Google Scholar 

  • Fojtová, M., Van Houdt, H., Depicker, A., Kovařík, A.: Epigenetic switch from posttranscriptional to transcriptional silencing is correlated with promoter hypermethylation. — Plant Physiol. 133: 1240–1250, 2003.

    Article  PubMed  PubMed Central  Google Scholar 

  • Fulnecek, J., Matyasek, R., Votruba, I., Holy, A., Krizova, K., Kovařík, A.: Inhibition of SAH-hydrolase activity during seed germination leads to deregulation of flowering genes and altered flower morphology in tobacco. — Mol. Genet. Genom. 285: 225–236, 2011.

    Article  CAS  Google Scholar 

  • Hedden, P., Phillips, A.L.: Gibberellin metabolism: new insights revealed by the genes. — Trends Plant Sci. 5: 523–530, 2000.

    Article  CAS  PubMed  Google Scholar 

  • Karagiannis, C.S., Pappelis, A.J.: Effect of abscisic acid, gibberellic acid, indole acetic acid, and kinetin on selective ribosomal cistron regulation in quiescent and senescent onion leaf base tissue. — Mech. Ageing Dev. 76: 145–155, 1994.

    Article  CAS  PubMed  Google Scholar 

  • Koukalova, B., Moraes, A.P., Renny-Byfield, S., Matyasek, R., Leitch, A.R., Kovařík, A.: Fall and rise of satellite repeats in allopolyploids of Nicotiana over c. 5 million years. — New Phytol. 186: 148–160, 2010.

    Article  CAS  PubMed  Google Scholar 

  • Kovařík, A., Koukalová, B., Bezděk, M., Opatrný, Z.: Hypermethylation of tobacco heterochromatic loci in response to osmotic stress. — Theor. appl. Genet. 95: 301–306, 1997.

    Article  Google Scholar 

  • Kovařík, A., Van Houdt, H., Holý, A., Depicker, A.: Drug-induced hypomethylation of a posttranscriptionally silenced transgene locus of tobacco leads to partial release of silencing. — FEBS Lett. 467: 47–51, 2000.

    Article  PubMed  Google Scholar 

  • Lee, H.S., Chen, Z.J.: Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. — Proc. nat. Acad. Sci. USA 98: 6753–6758, 2001.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lewis, J., Bird, A.: DNA methylation and chromatin structure. — FEBS Lett. 285: 155–159, 1991.

    Article  CAS  PubMed  Google Scholar 

  • Lim, K.Y., Kovařík, A., Matyasek, R., Bezděk, M., Lichtenstein, C.P., Leitch, A.R.: Gene conversion of ribosomal DNA in Nicotiana tabacum is associated with undermethylated, decondensed and probably active gene units. — Chromosoma 109: 161–172, 2000.

    Article  CAS  PubMed  Google Scholar 

  • Lin, Y.T., Wei, H.M., Lu, H.Y., Lee, Y.I., Fu, S.F.: Developmental-and tissue-specific expression of NbCMT3-2 encoding a chromomethylase in Nicotiana benthamiana. — Plant Cell Physiol. 56: 1124–1143, 2015.

    Article  CAS  PubMed  Google Scholar 

  • Liu, B., Wendel, J.F.: Epigenetic phenomena and the evolution of plant allopolyploids. — Mol. Phylogenet. Evol. 29: 365–379, 2003.

    Article  CAS  PubMed  Google Scholar 

  • Meilan, L., Qiaomei, W., Zhujun, Z., Guangwen, Z.: Studies on the changes of DNA methylation level, GA content and protein in non-heading Chinese cabbage during vernalization. — Acta hort. sin. 29: 353–357, 2002.

    Google Scholar 

  • Meng, F.R., Li, Y.C., Yin, J., Liu, H., Chen, X.J., Ni, Z.F., Sun, Q.X.: Analysis of DNA methylation during the germination of wheat seeds. — Biol. Plant. 56: 269–275, 2012.

    Article  CAS  Google Scholar 

  • Michalak, M., Barciszewska, M.Z., Barciszewski, J., Plitta, B.P., Chmielarz, P.: Global changes in DNA methylation in seeds and seedlings of Pyrus communis after seed desiccation and storage. — PLoS ONE 8: e70693, 2013.

    Article  Google Scholar 

  • Mutasa-Gottgens, E., Hedden, P.: Gibberellin as a factor in floral regulatory networks. — J. exp. Bot. 60: 1979–1989, 2009.

    Article  PubMed  Google Scholar 

  • Nakano, Y., Steward, N., Sekine, M., Kusano, T., Sano, H.: A tobacco NtMET1 cDNA encoding a DNA methyltransferase: molecular characterization and abnormal phenotypes of transgenic tobacco plants. — Plant Cell Physiol. 41: 448–457, 2000.

    Article  CAS  PubMed  Google Scholar 

  • Nonogaki, H.: Seed dormancy and germination-emerging mechanisms and new hypotheses. — Front. Plant. Sci. 5: 233, 2014.

    Article  PubMed  PubMed Central  Google Scholar 

  • Olszewski, N., Sun, T.P., Gubler, F.: Gibberellin signaling: biosynthesis, catabolism, and response pathways. — Plant Cell 14: S61–S80, 2002.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pavlopoulou, A., Kossida, S.: Plant cytosine-5 DNA methyltransferases: structure, function, and molecular evolution. — Genomics 90: 530–541, 2007.

    Article  CAS  PubMed  Google Scholar 

  • Razin, A., Cedar, H.: Distribution of 5-methylcytosine in chromatin. — Proc. nat. Acad. Sci. USA 74: 2725–2728, 1977.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Razin, A., Cedar, H.: DNA methylation and gene expression. — Microbiol. Rev. 55: 451–458, 1991.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Reinders, J., Wulff, B.B., Mirouze, M., Mari-Ordonez, A., Dapp, M., Rozhon, W., Bucher, E., Theiler, G., Paszkowski, J.: Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes. — Genes Dev. 23: 939–950, 2009.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Richards, D.E., King, K.E., Ait-Ali, T., Harberd, N.P.: How gibberellin regulates plant growth and development: a molecular genetic analysis of gibberellin signaling. — Annu. Rev. Plant Physiol. Plant mol. Biol. 52: 67–88, 2001.

    Article  CAS  PubMed  Google Scholar 

  • Santamaria, M.E., Hasbun, R., Valera, M.J., Meijon, M., Valledor, L., Rodriguez, J.L., Toorop, P.E., Canal, M.J., Rodriguez, R.: Acetylated H4 histone and genomic DNA methylation patterns during bud set and bud burst in Castanea sativa. — J. Plant Physiol. 166: 1360–1369, 2009.

    Article  CAS  PubMed  Google Scholar 

  • Sharma, R., Mohan Singh, R.K., Malik, G., Deveshwar, P., Tyagi, A.K., Kapoor, S., Kapoor, M.: Rice cytosine DNA methyltransferases–gene expression profiling during reproductive development and abiotic stress. — FEBS J. 276: 6301–6311, 2009.

    Article  CAS  PubMed  Google Scholar 

  • Thomas, S.G., Sun, T.P.: Update on gibberellin signaling. A tale of the tall and the short. — Plant Physiol. 135: 668–676, 2004.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Valledor, L., Hasbún, R., Meijón, M., Rodríguez, J.L., Santamaria, E., Viejo, M., Berdasco, M., Feito, I., Fraga, M., Cañal, M.J., Rodríguez, R.: Involvement of DNA methylation in tree development and micropropagation. — Plant Cell Tissue Organ Cult. 91: 75–86, 2007.

    Article  CAS  Google Scholar 

  • Van Houdt, H., Kovařík, A., Van Montagu, M., Depicker, A.: Cross-talk between post-transcriptionally silenced neomycin phosphotransferase II transgenes. — FEBS Lett. 467: 41–46, 2000.

    Article  PubMed  Google Scholar 

  • Vanyushin, B.F., Ashapkin, V.V.: DNA methylation in higher plants: past, present and future. — Biochim. biophys. Acta 1809: 360–368, 2011.

    Article  CAS  PubMed  Google Scholar 

  • Vlasova, T.I., Demidenko, Z.N., Kirnos, M.D., Vanyushin, B.F.: In vitro DNA methylation by wheat nuclear cytosine DNA methyltransferase: effect of phytohormones. — Gene 157: 279–281, 1995.

    Article  CAS  PubMed  Google Scholar 

  • Wada, Y., Ohya, H., Yamaguchi, Y., Koizumi, N., Sano, H.: Preferential de novo methylation of cytosine residues in non-CpG sequences by a domains rearranged DNA methyltransferase from tobacco plants. — J. biol. Chem. 278: 42386–42393, 2003.

    Article  CAS  PubMed  Google Scholar 

  • Wang, T., Pan, Q., Lin, L., Szulwach, K.E., Song, C.X., He, C., Wu, H., Warren, S.T., Jin, P., Duan, R., Li, X.: Genomewide DNA hydroxymethylation changes are associated with neurodevelopmental genes in the developing human cerebellum. — Human mol. Genet. 21: 5500–5510, 2012.

    Article  CAS  Google Scholar 

  • Wierzbicki, A.T., Jerzmanowski, A.: Suppression of histone H1 genes in Arabidopsis results in heritable developmental defects and stochastic changes in DNA methylation. — Genetics 169: 997–1008, 2005.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wuyts, N., Palauqui, J.C., Conejero, G., Verdeil, J.L., Granier, C., Massonnet, C.: High-contrast three-dimensional imaging of the Arabidopsis leaf enables the analysis of cell dimensions in the epidermis and mesophyll. — Plant Methods 6: 17, 2010.

    Article  PubMed  PubMed Central  Google Scholar 

  • Zajączkowska, U., Kucharski, S., Guzek, D.: Are trichomes involved in the biomechanical systems of Cucurbita leaf petioles? — Planta 242: 1453–1465, 2015.

    Article  PubMed  PubMed Central  Google Scholar 

  • Zemach, A., Grafi, G.: Methyl-CpG-binding domain proteins in plants: interpreters of DNA methylation. — Trends Plant Sci. 12: 80–85, 2007.

    Article  CAS  PubMed  Google Scholar 

  • Zhang, J., Ruf, S., Hasse, C., Childs, L., Scharff, L.B., Bock, R.: Identification of cis-elements conferring high levels of gene expression in non-green plastids. — Plant J. 72: 115–128, 2012.

    Article  CAS  PubMed  Google Scholar 

  • Zhao, J., Morozova, N., Williams, L., Libs, L., Avivi, Y., Grafi, G.: Two phases of chromatin decondensation during dedifferentiation of plant cells: distinction between competence for cell fate switch and a commitment for S phase. — J. biol. Chem. 276: 22772–22778, 2001.

    Article  CAS  PubMed  Google Scholar 

  • Zilberman, D., Gehring, M., Tran, R.K., Ballinger, T., Henikoff, S.: Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. — Nat. Genet. 39: 61–69, 2007.

    Article  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. ITC Life Science and Technology Centre, Peenya Industrial Area, Bengaluru, 560058, Karnataka, India

    R. Manoharlal, G. V. S. Saiprasad & C. Ullagaddi

  2. Institute of Biophysics, Academy of Sciences of the Czech Republic, CZ-61265, Brno, Czech Republic

    A. Kovařík

Authors
  1. R. Manoharlal
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  2. G. V. S. Saiprasad
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  3. C. Ullagaddi
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  4. A. Kovařík
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Corresponding author

Correspondence to R. Manoharlal.

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Acknowledgments: We would like to acknowledge Dr. C.C. Lakshmanan (Head), Mr. Ramaswamy [Corporate R&D, ITC Limited, ITC Life Science and Technology Centre (LSTC)] and Czech Science Foundation project (P501/12/G090) for their consistent support. Prof. Ales Kovařík’s laboratory members are duly acknowledged for their support in reporter transgene assays. We would also like to gratefully acknowledge Dr. Ganesh Chowthi Thimmegowda (LSTC-ITC) for his valuable initiative in DNA methylation studies. Our appreciation is also extended to field-workers at Northern Light Soil (NLS) region, Rajahmundry, Andhra Pradesh (A.P.), India, for providing their help and support during field experiments and sample collections.

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Manoharlal, R., Saiprasad, G.V.S., Ullagaddi, C. et al. Gibberellin A3 as an epigenetic determinant of global DNA hypo-methylation in tobacco. Biol Plant 62, 11–23 (2018). https://doi.org/10.1007/s10535-017-0738-3

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  • DOI: https://doi.org/10.1007/s10535-017-0738-3

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