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Indian Journal of Plant Physiology

, Volume 23, Issue 3, pp 543–556 | Cite as

Analysis of DNA methylome and transcriptome profiling following Gibberellin A3 (GA3) foliar application in Nicotiana tabacum L.

  • Raman ManoharlalEmail author
  • G. V. S. Saiprasad
  • Vinay Kaikala
  • R. Suresh Kumar
  • Ales Kovařík
Original Article
  • 49 Downloads

Abstract

The present work investigated a comprehensive genome-wide landscape of DNA methylome and its relationship with transcriptome upon gibberellin A3 (GA3) foliar application under practical field conditions in solanaceae model, Nicotiana tabacum L. Methylated DNA Immunoprecipitation-Sequencing (MeDIP-Seq) analysis uncovered over 82% (18,456) of differential methylated regions (DMRs) in intergenic-region. Within protein-coding region, 2339 and 1685 of identified DMRs were observed in genebody- and promoter-region, respectively. Microarray study revealed 7032 differential expressed genes (DEGs) with 3507 and 3525 genes displaying up- and down-regulation, respectively. Integration analysis revealed 520 unique non-redundant annotated DMRs overlapping with DEGs. Our results indicated that GA3 induced DNA hypo- as well as hyper-methylation were associated with both gene-silencing and -activation. No complete biasness or correlation was observed in either of the promoter- or genebody-regions, which otherwise showed an overall trend towards GA3 induced global DNA hypo-methylation. Taken together, our results suggested that differential DNA methylation mediated by GA3 may only play a permissive role in regulating the gene expression.

Keywords

Nicotiana tabacum GA3 Microarray DNA methylation and MeDIP-Seq 

Abbreviations

CGIs

CpG islands

DEGs

Differential Expressed Genes

DMRs

Differential Methylated Regions

MeDIP

Methylated DNA Immunoprecipitation

Notes

Acknowledgements

We would like to acknowledge Dr. C.C. Lakshmanan [Head, Corporate R&D, ITC Limited, ITC Life Science and Technology Centre (LSTC)] for his consistent support. Our appreciation is extended to Prof. Sanjeev Galande [Head, Centre of Excellence in Epigenetics, Indian Institute of Science Education and Research (IISER), Pune, India] for providing his valuable inputs on MeDIP-Seq experiment. Nucleome Informatics Private Limited, Hyderabad, India and Genotypic Technology Private Limited, Bengaluru, India are acknowledged for performing the MeDIP-Seq and microarray processing and data analysis, respectively. We would also like to acknowledge EpigenDx Hopkinton, MA, USA for carrying out tNGBS assays. Editorial and useful tips from the in-house manuscript committee of LSTC-ITC are well appreciated. Overall support from team Agriscience, ITC-LSTC is greatly acknowledged. We also acknowledge the field-workers at Northern Light Soil (NLS) region, Rajahmundry, Andhra Pradesh (A.P.), India for providing their consistent help and support during field experiments and sample collections.

Compliance with ethical standards

Conflict of interest

The authors declare that there are no conflict of interest. The content of this manuscript does not necessarily reflect the views or policies of the ITC-LSTC.

Supplementary material

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References

  1. Aran, D., Toperoff, G., Rosenberg, M., & Hellman, A. (2011). Replication timing-related and gene body-specific methylation of active human genes. Human Molecular Genetics, 20(4), 670–680.  https://doi.org/10.1093/hmg/ddq513.CrossRefPubMedGoogle Scholar
  2. Ashikawa, I. (2001). Gene-associated CpG islands in plants as revealed by analyses of genomic sequences. The Plant Journal, 26(6), 617–625.CrossRefGoogle Scholar
  3. Bird, A. (2002). DNA methylation patterns and epigenetic memory. Genes & Development, 16(1), 6–21.  https://doi.org/10.1101/gad.947102.CrossRefGoogle Scholar
  4. Bujnicki, J. M., Feder, M., Radlinska, M., & Rychlewski, L. (2001). mRNA:guanine-N7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships. BMC Bioinformatics, 2, 2.CrossRefGoogle Scholar
  5. Chan, S. W., Henderson, I. R., & Jacobsen, S. E. (2005). Gardening the genome: DNA methylation in Arabidopsis thaliana. Nature Reviews Genetics, 6(5), 351–360.  https://doi.org/10.1038/nrg1601.CrossRefPubMedGoogle Scholar
  6. da Huang, W., Sherman, B. T., & Lempicki, R. A. (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols, 4(1), 44–57.  https://doi.org/10.1038/nprot.2008.211.CrossRefGoogle Scholar
  7. Desikan, R. S. A. H.-M., Hancock, J. T., & Neill, S. J. (2001). Regulation of the Arabidopsis transcriptome by oxidative stress. Plant Physiology, 127(1), 159–172.CrossRefGoogle Scholar
  8. Edwards, R., Dixon, D. P., & Walbot, V. (2000). Plant glutathione S-transferases: enzymes with multiple functions in sickness and in health. Trends in Plant Science, 5(5), 193–198.CrossRefGoogle Scholar
  9. Exner, V., Taranto, P., Schonrock, N., Gruissem, W., & Hennig, L. (2006). Chromatin assembly factor CAF-1 is required for cellular differentiation during plant development. Development, 133(21), 4163–4172.  https://doi.org/10.1242/dev.02599.CrossRefPubMedGoogle Scholar
  10. Gao, M., Huang, Q., Chu, Y., Ding, C., Zhang, B., & Su, X. (2014). Analysis of the leaf methylomes of parents and their hybrids provides new insight into hybrid vigor in Populus deltoides. BMC Genetics, 15(Suppl 1), S8.  https://doi.org/10.1186/1471-2156-15-S1-S8.CrossRefPubMedPubMedCentralGoogle Scholar
  11. Hardcastle, T. J. (2013). High-throughput sequencing of cytosine methylation in plant DNA. Plant Methods, 9(1), 16.  https://doi.org/10.1186/1746-4811-9-16.CrossRefPubMedPubMedCentralGoogle Scholar
  12. Illingworth, R., Kerr, A., Desousa, D., Jorgensen, H., Ellis, P., Stalker, J., et al. (2008). A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biology, 6(1), e22.  https://doi.org/10.1371/journal.pbio.0060022.CrossRefPubMedPubMedCentralGoogle Scholar
  13. Kass, S. U., Landsberger, N., & Wolffe, A. P. (1997). DNA methylation directs a time-dependent repression of transcription initiation. Current Biology, 7(3), 157–165.CrossRefGoogle Scholar
  14. Kliebenstein, D. J., Lim, J. E., Landry, L. G., & Last, R. L. (2002). Arabidopsis UVR8 regulates ultraviolet-B signal transduction and tolerance and contains sequence similarity to human regulator of chromatin condensation 1. Plant Physiology, 130(1), 234–243.  https://doi.org/10.1104/pp.005041.CrossRefPubMedPubMedCentralGoogle Scholar
  15. Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9(4), 357–359.  https://doi.org/10.1038/nmeth.1923.CrossRefPubMedPubMedCentralGoogle Scholar
  16. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., et al. (2009). The sequence alignment/map format and SAMtools. Bioinformatics, 25(16), 2078–2079.  https://doi.org/10.1093/bioinformatics/btp352.CrossRefPubMedPubMedCentralGoogle Scholar
  17. Li, X., Zhu, J., Hu, F., Ge, S., Ye, M., Xiang, H., et al. (2012). Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression. BMC Genomics, 13, 300.  https://doi.org/10.1186/1471-2164-13-300.CrossRefPubMedPubMedCentralGoogle Scholar
  18. Lorincz, M. C., Dickerson, D. R., Schmitt, M., & Groudine, M. (2004). Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nature Structural & Molecular Biology, 11(11), 1068–1075.  https://doi.org/10.1038/nsmb840.CrossRefGoogle Scholar
  19. Manoharlal, R., Saiprasad, G. V. S., Thambrahalli, A., & Madhavakrishna, K. (2018a). Dissecting the transcriptional networks underlying the gibberellin response in Nicotiana tabacum. Biologia Plantarum, 62, 647–662.CrossRefGoogle Scholar
  20. Manoharlal, R., Saiprasad, G. V. S., Ullagaddi, C., & Kovařík, A. (2018b). Gibberellin A3 (GA3) as an epigenetic determinant of global DNA hypo-methylation in tobacco. Biologia Plantarum, 62, 11–23.CrossRefGoogle Scholar
  21. Martienssen, R. A., & Colot, V. (2001). DNA methylation and epigenetic inheritance in plants and filamentous fungi. Science, 293(5532), 1070–1074.  https://doi.org/10.1126/science.293.5532.1070.CrossRefPubMedGoogle Scholar
  22. Pai, A. A., Bell, J. T., Marioni, J. C., Pritchard, J. K., & Gilad, Y. (2011). A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues. PLoS Genetics, 7(2), e1001316.  https://doi.org/10.1371/journal.pgen.1001316.CrossRefPubMedPubMedCentralGoogle Scholar
  23. Parkin, I. A., Koh, C., Tang, H., Robinson, S. J., Kagale, S., Clarke, W. E., et al. (2014). Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biology, 15(6), R77.  https://doi.org/10.1186/gb-2014-15-6-r77.CrossRefPubMedPubMedCentralGoogle Scholar
  24. Ramiro, A. R., & Barreto, V. M. (2015). Activation-induced cytidine deaminase and active cytidine demethylation. Trends in Biochemical Sciences, 40(3), 172–181.  https://doi.org/10.1016/j.tibs.2015.01.006.CrossRefPubMedGoogle Scholar
  25. Rountree, M. R., & Selker, E. U. (1997). DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa. Genes & Development, 11(18), 2383–2395.CrossRefGoogle Scholar
  26. Schumacher, K., & Krebs, M. (2010). The V-ATPase: small cargo, large effects. Current Opinion in Plant Biology, 13(6), 724–730.  https://doi.org/10.1016/j.pbi.2010.07.003.CrossRefPubMedGoogle Scholar
  27. Vierstra, R. D. (2012). The expanding universe of ubiquitin and ubiquitin-like modifiers. Plant Physiology, 160(1), 2–14.  https://doi.org/10.1104/pp.112.200667.CrossRefPubMedPubMedCentralGoogle Scholar
  28. Yuan, Y., Qi, L., Yu, J., Wang, X., & Huang, L. (2015). Transcriptome-wide analysis of SAMe superfamily to novelty phosphoethanolamine N-methyltransferase copy in Lonicera japonica. International Journal of Molecular Sciences, 16(1), 521–534.  https://doi.org/10.3390/ijms16010521.CrossRefGoogle Scholar
  29. Zemach, A., McDaniel, I. E., Silva, P., & Zilberman, D. (2010). Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science, 328(5980), 916–919.  https://doi.org/10.1126/science.1186366.CrossRefGoogle Scholar
  30. Zhang, M., Kimatu, J. N., Xu, K., & Liu, B. (2010). DNA cytosine methylation in plant development. J Genet Genomics, 37(1), 1–12.  https://doi.org/10.1016/S1673-8527(09)60020-5.CrossRefPubMedGoogle Scholar
  31. Zhang, M., Xie, S., Dong, X., Zhao, X., Zeng, B., Chen, J., et al. (2014). Genome-wide high resolution parental-specific DNA and histone methylation maps uncover patterns of imprinting regulation in maize. Genome Research, 24(1), 167–176.  https://doi.org/10.1101/gr.155879.113.CrossRefPubMedPubMedCentralGoogle Scholar
  32. Zhang, X., Yazaki, J., Sundaresan, A., Cokus, S., Chan, S. W., Chen, H., et al. (2006). Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell, 126(6), 1189–1201.  https://doi.org/10.1016/j.cell.2006.08.003.CrossRefGoogle Scholar
  33. Zilberman, D., Gehring, M., Tran, R. K., Ballinger, T., & Henikoff, S. (2007). Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature Genetics, 39(1), 61–69.  https://doi.org/10.1038/ng1929.CrossRefPubMedGoogle Scholar

Copyright information

© Indian Society for Plant Physiology 2018

Authors and Affiliations

  1. 1.Corporate R&D (Agrisciences), ITC Limited, ITC Life Science and Technology Centre (LSTC)BengaluruIndia
  2. 2.Academy of Sciences of the Czech Republic, Institute of Biophysics, v.v.iBrnoCzech Republic

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