Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening

Nature Biotechnology volume 31, pages 154–159 (2013)Cite this article

Subjects

Abstract

Ripening of tomato fruits is triggered by the plant hormone ethylene, but its effect is restricted by an unknown developmental cue to mature fruits containing viable seeds. To determine whether this cue involves epigenetic remodeling, we expose tomatoes to the methyltransferase inhibitor 5-azacytidine and find that they ripen prematurely. We performed whole-genome bisulfite sequencing on fruit in four stages of development, from immature to ripe. We identified 52,095 differentially methylated regions (representing 1% of the genome) in the 90% of the genome covered by our analysis. Furthermore, binding sites for RIN, one of the main ripening transcription factors, are frequently localized in the demethylated regions of the promoters of numerous ripening genes, and binding occurs in concert with demethylation. Our data show that the epigenome is not static during development and may have been selected to ensure the fidelity of developmental processes such as ripening. Crop-improvement strategies could benefit by taking into account not only DNA sequence variation among plant lines, but also the information encoded in the epigenome.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Application of a methylation inhibitor uncouples seed maturation and fruit ripening.
Figure 2: The tomato epigenome.
Figure 3: Tissue and developmental specific epigenetic variation in tomato.
Figure 4: Demethylation of RIN binding sites during ripening.
Figure 5: Model of fruit ripening regulation.

Similar content being viewed by others

Accession codes

Primary accessions

Sequence Read Archive

References

  1. Patterson, G.I., Thorpe, C.J. & Chandler, V.L. Paramutation, an allelic interaction, is associated with a stable and heritable reduction of transcription of the maize b regulatory gene. Genetics 135, 881–894 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Cubas, P., Vincent, C. & Coen, E. An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401, 157–161 (1999).

    Article  CAS  Google Scholar 

  3. Manning, K. et al. A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat. Genet. 38, 948–952 (2006).

    Article  CAS  Google Scholar 

  4. Law, J.A. & Jacobsen, S.E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 11, 204–220 (2010).

    Article  CAS  Google Scholar 

  5. Becker, C. et al. Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 480, 245–249 (2011).

    Article  CAS  Google Scholar 

  6. Schmitz, R.J. et al. Transgenerational epigenetic instability is a source of novel methylation variants. Science 334, 369–373 (2011).

    Article  CAS  Google Scholar 

  7. Cokus, S.J. et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215–219 (2008).

    Article  CAS  Google Scholar 

  8. Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523–536 (2008).

    Article  CAS  Google Scholar 

  9. Zemach, A. et al. Local DNA hypomethylation activates genes in rice endosperm. Proc. Natl. Acad. Sci. USA 107, 18729–18734 (2010).

    Article  CAS  Google Scholar 

  10. The Tomato Genome Consortium. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485, 635–641 (2012).

  11. Klee, H.J. & Giovannoni, J.J. Genetics and control of tomato fruit ripening and quality attributes. Annu. Rev. Genet. 45, 41–59 (2011).

    Article  CAS  Google Scholar 

  12. Burg, S.P. & Burg, E.A. Ethylene action and the ripening of fruits. Science 148, 1190–1196 (1965).

    Article  CAS  Google Scholar 

  13. Hamilton, A.J., Lycett, G.W. & Grierson, D. Antisense gene that inhibits synthesis of the hormone ethylene in transgenic plants. Nature 346, 284–287 (1990).

    Article  CAS  Google Scholar 

  14. Oeller, P.W., Lu, M.W., Taylor, L.P., Pike, D.A. & Theologis, A. Reversible inhibition of tomato fruit senescence by antisense RNA. Science 254, 437–439 (1991).

    Article  CAS  Google Scholar 

  15. Seymour, G., Poole, M., Manning, K. & King, G.J. Genetics and epigenetics of fruit development and ripening. Curr. Opin. Plant Biol. 11, 58–63 (2008).

    Article  CAS  Google Scholar 

  16. Messeguer, R., Ganal, M.W., Steffens, J.C. & Tanksley, S.D. Characterization of the level, target sites and inheritance of cytosine methylation in tomato nuclear DNA. Plant Mol. Biol. 16, 753–770 (1991).

    Article  CAS  Google Scholar 

  17. Vrebalov, J. et al. A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (Rin) locus. Science 296, 343–346 (2002).

    Article  CAS  Google Scholar 

  18. Martel, C., Vrebalov, J., Tafelmeyer, P. & Giovannoni, J.J. The tomato MADS-box transcription factor ripening inhibitor interacts with promoters involved in numerous ripening processes in a colorless nonripening–dependent manner. Plant Physiol. 157, 1568–1579 (2011).

    Article  CAS  Google Scholar 

  19. Ito, Y. et al. DNA-binding specificity, transcriptional activation potential, and the rin mutation effect for the tomato fruit-ripening regulator RIN. Plant J. 55, 212–223 (2008).

    Article  CAS  Google Scholar 

  20. Fujisawa, M., Nakano, T. & Ito, Y. Identification of potential target genes for the tomato fruit-ripening regulator RIN by chromatin immunoprecipitation. BMC Plant Biol. 11, 26 (2011).

    Article  CAS  Google Scholar 

  21. Barry, C.S., Llop-Tous, M.I. & Grierson, D. The regulation of 1-aminocyclopropane-1-carboxylic acid synthase gene expression during the transition from system-1 to system-2 ethylene synthesis in tomato. Plant Physiol. 123, 979–986 (2000).

    Article  CAS  Google Scholar 

  22. Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315–322 (2009).

    Article  CAS  Google Scholar 

  23. Feng, S., Jacobsen, S.E. & Reik, W. Epigenetic reprogramming in plant and animal development. Science 330, 622–627 (2010).

    Article  CAS  Google Scholar 

  24. Deikman, J., Kline, R. & Fischer, R.L. Organization of ripening and ethylene regulatory regions in a fruit-specific promoter from tomato (Lycopersicon esculentum). Plant Physiol. 100, 2013–2017 (1992).

    Article  CAS  Google Scholar 

  25. Nicholass, F.J., Smith, C.J., Schuch, W., Bird, C.R. & Grierson, D. High levels of ripening-specific reporter gene expression directed by tomato fruit polygalacturonase gene-flanking regions. Plant Mol. Biol. 28, 423–435 (1995).

    Article  CAS  Google Scholar 

  26. McMurchie, E.J., McGlasson, W.B. & Eaks, I.L. Treatment of fruit with propylene gives information about the biogenesis of ethylene. Nature 237, 235–236 (1972).

    Article  CAS  Google Scholar 

  27. King, G.N. Artificial parthenocarpy in Lycopersicum esculentum; tissue development. Plant Physiol. 22, 572–581 (1947).

    Article  CAS  Google Scholar 

  28. Wang, H. et al. Regulatory features underlying pollination-dependent and -independent tomato fruit set revealed by transcript and primary metabolite profiling. Plant Cell 21, 1428–1452 (2009).

    Article  CAS  Google Scholar 

  29. Thurman, R.E. et al. The accessible chromatin landscape of the human genome. Nature 489, 75–82 (2012).

    Article  CAS  Google Scholar 

  30. Stadler, M.B. et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480, 490–495 (2011).

    Article  CAS  Google Scholar 

  31. Zhong, S. et al. High-throughput illumina strand-specific RNA sequencing library preparation. Cold Spring Harb. Protoc. 2011, 940–949 (2011).

    Article  Google Scholar 

  32. Chen, Y.R. et al. A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters. Plant Methods 8, 41 (2012).

    Article  CAS  Google Scholar 

  33. Ricardi, M.M., Gonzalez, R.M. & Iusem, N.D. Protocol: fine-tuning of a chromatin immunoprecipitation (ChIP) protocol in tomato. Plant Methods 6, 11 (2010).

    Article  Google Scholar 

  34. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).

    Article  Google Scholar 

  35. Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009).

    Article  CAS  Google Scholar 

  36. Wang, L.K., Feng, Z.X., Wang, X., Wang, X.W. & Zhang, X.G. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26, 136–138 (2010).

    Article  Google Scholar 

  37. Smyth, G.K. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, 3 (2004).

    Article  Google Scholar 

  38. Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate—a practical and powerful approach to multiple testing. J. R. Stat. Soc., B 57, 289–300 (1995).

    Google Scholar 

  39. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).

    Article  Google Scholar 

Download references

Acknowledgements

We thank E. Richards, R. Schmitz and J. Ecker for discussion and thoughtful advice in preparing this manuscript, and R. White, Y. Xu and Z. Li for technical assistance. This project was supported by the United States Department of Agriculture – Agricultural Research Service, National Science Foundation IOS-0606595 and IOS-0923312 to J.J.G. and Z.F., DBI-0820612 to J.J.G., National Natural Science Foundation of China 30900783 and 3090243 to S.Z. and B.L. and the Human Frontier Science Program LTF000076/2009 to S.Z.

Author information

Author notes

  1. Silin Zhong and Zhangjun Fei: These authors contributed equally to this work.

Authors and Affiliations

  1. Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA

    Silin Zhong, Zhangjun Fei, Yun-Ru Chen, Yi Zheng, Mingyun Huang, Julia Vrebalov, Ryan McQuinn, Nigel Gapper & James J Giovannoni

  2. Key Laboratories of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, China

    Silin Zhong & Bao Liu

  3. US Department of Agriculture/Agriculture Research Service, Robert W. Holley Centre for Agriculture and Health, Ithaca, New York, USA

    Zhangjun Fei & James J Giovannoni

  4. Weill Medical College, Genomics Resource Core Facility, Cornell University, New York, New York, USA

    Jenny Xiang & Ying Shao

Authors
  1. Silin Zhong
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zhangjun Fei
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yun-Ru Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yi Zheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Mingyun Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Julia Vrebalov
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Ryan McQuinn
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Nigel Gapper
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Bao Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Jenny Xiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Ying Shao
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. James J Giovannoni
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

J.J.G., Z.F. and S.Z. devised the project and wrote the manuscript. Z.F. and S.Z. led the bioinformatic and experimental teams, respectively. Y.-R.C., J.V., R.M. and N.G. performed the experiments. Y.Z., Z.F., M.H., B.L., Y.S., J.X. and J.J.G. analyzed and interpreted the data.

Corresponding authors

Correspondence to Silin Zhong, Zhangjun Fei or James J Giovannoni.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–11 (PDF 2185 kb)

Supplementary Tables

Supplementary Tables 1–12 (XLSX 4924 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zhong, S., Fei, Z., Chen, YR. et al. Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat Biotechnol 31, 154–159 (2013). https://doi.org/10.1038/nbt.2462

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt.2462

This article is cited by

Search

Advanced search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research