Skip to main content

Characterization of DNA methylation variations during fruit development and ripening of Vitis vinifera (cv. ‘Fujiminori’)

Abstract

The fruit is the most important economical organ in the grape; accordingly, to investigate the grapevine genomic methylation landscape and examine its functional significance during fruit development, we generated whole genome DNA methylation maps for various developmental stages in the fruit of grapevine. In this study, thirteen DNA methylation-related genes and their expression profiles were identified and analyzed. The methylation levels for mC, mCG, mCHG, and mCHH contexts in 65 days after flowering (65DAF) fruit (véraison stage) were higher than those in 40DAF (green stage) and 90DAF (mature stage) fruits. Relative to methylation in the mC context, methylation levels in the mCHH context were higher than those of mCG and mCHG. The DNA methylation level in the ncRNA regions was significantly higher than that in exon, gene, intron, and mRNA regions. The differentially methylated regions (DMRs) and differentially methylated promoters (DMPs) in 65DAF_vs_40DAF were both higher than those in 90DAF_vs_65DAF and 90DAF_vs_40DAF. Most DMRs (or DMPs) were involved in metabolic processes and cell processes, binding, and catalytic activity. These results indicated that DNA methylation represses gene expression during grape fruit development, and it broadens our understanding of the landscape and function of DNA methylation in grapevine genomes.

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

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Data Archiving Statement

The sequencing datasets were deposited in NCBI database with accession number GSE77066.

Abbreviations

CMT:

Chromomethylase

DAF:

Days after flowering

DME:

Demeter

DML2:

Demethylase 2

DML3:

Demeter-like 3

DMPs:

DNA methylation promoters

DMRs:

DNA methylation regions

DRM:

Domain-rearranged methyltransferases

Gbp:

Giga base pairs

GO:

Gene ontology

Mb:

Megabase

RIN:

Ripening inhibitor

RNA-seq:

RNA-sequencing

ROS1:

Repressor of silencing 1

SBP box-Cnr:

SQUAMOSA promoter binding protein-like-Colorless non-ripening

TAIR:

The Arabidopsis Information Resource

TSS:

Transcription start site

TTS:

Transcription termination sites

WGBS:

Whole-genome bisulfite sequencing

References

  1. Adams S, Cockshull K, Cave C (2001) Effect of temperature on the growth and development of tomato fruits. Ann Bot Lond 88:869–877

    Google Scholar 

  2. Ahmad F, Huang X, Lan HX, Huma T, Bao YM, Huang J, Zhang HS (2014) Comprehensive gene expression analysis of the DNA (cytosine-5) methyltransferase family in rice (Oryza sativa L.). Genet Mol Res 13:5159–5172. https://doi.org/10.4238/2014.July.7.9

    CAS  Article  PubMed  Google Scholar 

  3. Ali M, Howard S, Chen S, Wang Y, Yu O, Kovacs L, Qiu W (2011) Berry skin development in Norton grape: distinct patterns of transcriptional regulation and flavonoid biosynthesis. BMC Plant Biol 11:7

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Alonso C, Pérez R, Bazaga P, Herrera CM (2015) Global DNA cytosine methylation as an evolving trait: phylogenetic signal and correlated evolution with genome size in angiosperms. Front Genet 6:4

    PubMed  PubMed Central  Google Scholar 

  5. Ashapkin VV, Kutueva LI, Vanyushin BF (2016) Plant DNA methyltransferase genes: multiplicity, expression, methylation patterns. Biochemistry (Moscow) 81:141–151. https://doi.org/10.1134/S0006297916020085

    CAS  Article  Google Scholar 

  6. Aufsatz W, Mette MF, Matzke AJM, Matzke M (2004) The role of MET1 in RNA-directed de novo and maintenance methylation of CG dinucleotides. Plant Mol Biol 54:793–804. https://doi.org/10.1007/s11103-004-0179-1

    CAS  Article  PubMed  Google Scholar 

  7. Bartee L, Malagnac F, Bender J (2001) Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Gene Dev 15:1753–1758. https://doi.org/10.1101/gad.905701

    CAS  Article  PubMed  Google Scholar 

  8. Barter MJ, Bui C, Young DA (2012) Epigenetic mechanisms in cartilage and osteoarthritis: DNA methylation, histone modifications and microRNAs. Osteoarthr Cartill 20:339–349. https://doi.org/10.1016/j.joca.2011.12.012

    CAS  Article  Google Scholar 

  9. Bender J (2004) DNA methylation and epigenetics. Annu Rev Plant Biol 55:41–68

    CAS  PubMed  Google Scholar 

  10. Bennetzen JL, SanMiguel P, Chen M, Tikhonov A, Francki M, Avramova Z (1998) Grass genomes. Proc Natl Acad Sci USA 95:1975–1978

    CAS  PubMed  Google Scholar 

  11. Bernacchia G, Primo A, Giorgetti L, Pitto L, Cella R (1998) Carrot DNA-methyltransferase is encoded by two classes of genes with differing patterns of expression. Plant J 13:317–329

    CAS  PubMed  Google Scholar 

  12. Bird A (2002) DNA methylation patterns and epigenetic memory. Gene Dev 16:6–21. https://doi.org/10.1101/gad.947102

    CAS  Article  PubMed  Google Scholar 

  13. Bird A (2007) Perceptions of epigenetics. Nature 447:396–398. https://doi.org/10.1038/nature05913

    CAS  Article  PubMed  Google Scholar 

  14. Burn J, Bagnall D, Metzger J, Dennis E, Peacock W (1993) DNA methylation, vernalization, and the initiation of flowering. Proc Natl Acad Sci USA 90:287–291

    CAS  PubMed  Google Scholar 

  15. Cao X, Jacobsen SE (2002) Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol 12:1138–1144

    CAS  PubMed  Google Scholar 

  16. 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 13:2212–2217. https://doi.org/10.1016/j.cub.2003.11.052

    CAS  Article  PubMed  Google Scholar 

  17. Cao D et al (2014) Genome-wide identification of cytosine-5 DNA methyltransferases and demethylases in Solanum lycopersicum. Gene 550:230–237

    CAS  PubMed  Google Scholar 

  18. Cokus SJ et al (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452:215–219. https://doi.org/10.1038/nature06745

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  19. Dai Y, Ni Z, Dai J, Zhao T, Sun Q (2005) Isolation and expression analysis of genes encoding DNA methyltransferase in wheat. Biochim Biophys Acta BBA Gene Struct Expr 1729:118–125

    CAS  Google Scholar 

  20. Dokoozlian N, Kliewer W (1996) Influence of light on grape berry growth and composition varies during fruit development. J Am Soc Hortic Sci 121:869–874

    Google Scholar 

  21. Du Z, Zhou X, Ling Y, Zhang Z, Su Z (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38:w64

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Eichten SR et al (2013) Epigenetic and genetic influences on DNA methylation variation in maize populations. Plant Cell 25:2783–2797

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Fedoroff NV (2012) Transposable elements, epigenetics, and genome evolution. Science 338:758–767

    CAS  PubMed  Google Scholar 

  24. Finn RD et al (2006) Pfam: clans, web tools and services. Nucleic Acids Res 34:D247–D251

    CAS  PubMed  Google Scholar 

  25. Gehring M, Henikoff S (2007) DNA methylation dynamics in plant genomes. Biochim Biophys Acta 1769:276–286

    CAS  PubMed  Google Scholar 

  26. Goff SA et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100

    CAS  PubMed  Google Scholar 

  27. Goll MG, Bestor TH (2005) Eukaryotic cytosine methyltransferases. Annu Rev Biochem 74:481–514. https://doi.org/10.1146/annurev.biochem.74.010904.153721

    CAS  Article  PubMed  Google Scholar 

  28. Gu T, Ren S, Wang Y, Han Y, Li Y (2016) Characterization of DNA methyltransferase and demethylase genes in Fragaria vesca. Mol Genet Genom 291:1333–1345. https://doi.org/10.1007/s00438-016-1187-y

    CAS  Article  Google Scholar 

  29. Hasbun R et al (2005) In vitro proliferation and genome DNA methylation in adult chestnuts. Acta Hortic 693:333–340

    CAS  Google Scholar 

  30. Hayatsu H, Tsuji K, Negishi K (2006) Does urea promote the bisulfite-mediated deamination of cytosine in DNA? Investigation aiming at speeding-up the procedure for DNA methylation analysis. Nucleic Acids Symp Ser (Oxf) 50:69

    Google Scholar 

  31. Jaillon O et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463–465. https://doi.org/10.1038/nature06148

    CAS  Article  PubMed  Google Scholar 

  32. Jones PA (2012) Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 13:484–492. https://doi.org/10.1038/nrg3230

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  33. Kawanabe T et al (2016) Role of DNA methylation in hybrid vigor in Arabidopsis thaliana. Proc Natl Acad Sci USA 113:E6704–E6711

    CAS  PubMed  Google Scholar 

  34. Khan AR, Enjalbert J, Marsollier A-C, Rousselet A, Goldringer I, Vitte C (2013) Vernalization treatment induces site-specific DNA hypermethylation at the VERNALIZATION-A1 (VRN-A1) locus in hexaploid winter wheat. BMC Plant Biol 13:1

    Google Scholar 

  35. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:1

    Google Scholar 

  36. Kumar G, Rattan UK, Singh AK (2016) Chilling-mediated DNA methylation changes during dormancy and its release reveal the importance of epigenetic regulation during winter dormancy in apple (Malus x domestica Borkh.). PLoS ONE 11:e0149934

    PubMed  PubMed Central  Google Scholar 

  37. Laird PW (2010) Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet 11:191–203. https://doi.org/10.1038/nrg2732

    CAS  Article  PubMed  Google Scholar 

  38. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Lechner M, Marz M, Ihling C, Sinz A, Stadler PF, Krauss V (2013) The correlation of genome size and DNA methylation rate in metazoans. Theory Biosci 132:47–60. https://doi.org/10.1007/s12064-012-0167-y

    CAS  Article  PubMed  Google Scholar 

  40. Li S, Huguet J, Schoch P, Orlando P (1989) Response of peach tree growth and cropping to soil water deficit at various phenological stages of fruit development. J Hortic Sci 64:541–552

    Google Scholar 

  41. Li H et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079

    PubMed  PubMed Central  Google Scholar 

  42. Li X et al (2012) Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression. BMC Genom 13:300

    CAS  Google Scholar 

  43. Liang D et al (2014) Single-base-resolution methylomes of populus trichocarpa reveal the association between DNA methylation and drought stress. BMC Genet 15:S9

    PubMed  PubMed Central  Google Scholar 

  44. 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. https://doi.org/10.1016/j.cell.2008.03.029

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  45. Lister R et al (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462:315

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Liu R et al (2015a) A DEMETER-like DNA demethylase governs tomato fruit ripening. Proc Natl Acad Sci USA 112:10804–10809

    CAS  PubMed  Google Scholar 

  47. Liu W et al (2015b) IBS: an illustrator for the presentation and visualization of biological sequences. Bioinformatics 31:3359–3361

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Liu C, Li H, Lin J, Wang Y, Xu X, Cheng ZM, Chang Y (2018) Genome-wide characterization of DNA demethylase genes and their association with salt response in Pyrus. Genes (Basel). https://doi.org/10.3390/genes9080398

    Article  PubMed  PubMed Central  Google Scholar 

  49. Manning K et al (2006) A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat Genet 38:948–952. https://doi.org/10.1038/ng1841

    CAS  Article  PubMed  Google Scholar 

  50. Messeguer R, Ganal MW, Steffens JC, Tanksley SD (1991) Characterization of the level, target sites and inheritance of cytosine methylation in tomato nuclear-DNA. Plant Mol Biol 16:753–770. https://doi.org/10.1007/Bf00015069

    CAS  Article  PubMed  Google Scholar 

  51. Moglia A, Gianoglio S, Acquadro A, Valentino D, Milani AM, Lanteri S, Comino C (2019) Identification of DNA methyltransferases and demethylases. PLoS ONE 14:e0223581. https://doi.org/10.1371/journal.pone.0223581

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  52. Pilati S et al (2007) Genome-wide transcriptional analysis of grapevine berry ripening reveals a set of genes similarly modulated during three seasons and the occurrence of an oxidative burst at veraison. BMC Genom 8:428

    Google Scholar 

  53. Popp C et al (2010) Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature 463:1101–1105

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005) InterProScan: protein domains identifier. Nucleic Acids Res 33:W116–W120

    CAS  PubMed  PubMed Central  Google Scholar 

  55. Rabinowicz PD, Palmer LE, May BP, Hemann MT, Lowe SW, McCombie WR, Martienssen RA (2003) Genes and transposons are differentially methylated in plants, but not in mammals. Genome Res 13:2658–2664

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Raddatz G et al (2013) Aging is associated with highly defined epigenetic changes in the human epidermis. Epigenet Chromatin 6:36

    CAS  Google Scholar 

  57. Ren F, Yang L, Su L, Gong L, Wang P, Wang Y (2017) Genome-wide identification and analysis of DNA methyltransferases in grape. Agric Sci Technol 18:1781–1794

    Google Scholar 

  58. Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140

    CAS  PubMed  PubMed Central  Google Scholar 

  59. SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20:43–45

    CAS  PubMed  Google Scholar 

  60. Shangguan L et al (2013) Evaluation of genome sequencing quality in selected plant species using expressed sequence tags. PLoS ONE 8:e69890. https://doi.org/10.1371/journal.pone.0069890

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  61. Shangguan L et al (2017) RNA-Sequencing reveals biological networks during table grapevine (‘Fujiminori’) fruit development. PLoS ONE 12:e0170571

    PubMed  PubMed Central  Google Scholar 

  62. Shen H et al (2012) Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids. Plant Cell 24:875–892

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Song Q-X et al (2013a) Genome-wide analysis of DNA methylation in soybean. Mol Plant 6:1961–1974

    CAS  PubMed  Google Scholar 

  64. Song Y, Ma K, Ci D, Chen Q, Tian J, Zhang D (2013b) Sexual dimorphic floral development in dioecious plants revealed by transcriptome, phytohormone, and DNA methylation analysis in Populus tomentosa. Plant Mol Biol 83:559–576

    CAS  PubMed  Google Scholar 

  65. Stroud H, Greenberg MV, Feng S, Bernatavichute YV, Jacobsen SE (2013) Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell 152:352–364. https://doi.org/10.1016/j.cell.2012.10.054

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  66. Suzuki MM, Bird A (2008) DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 9:465–476. https://doi.org/10.1038/nrg2341

    CAS  Article  PubMed  Google Scholar 

  67. Sweetman C, Wong DC, Ford CM, Drew DP (2012) Transcriptome analysis at four developmental stages of grape berry (Vitis vinifera cv. Shiraz) provides insights into regulated and coordinated gene expression. BMC Genom 13:691

    CAS  Google Scholar 

  68. Tang J, Bassham DC (2018) Autophagy in crop plants: what’s new beyond Arabidopsis? Open Biol. https://doi.org/10.1098/rsob.180162

    Article  PubMed  PubMed Central  Google Scholar 

  69. Team D (2009) R: A language and environment for statistical computing. Computing 14:12–21

    Google Scholar 

  70. Teyssier E, Bernacchia G, Maury S, Kit AH, Stammitti-Bert L, Rolin D, Gallusci P (2008) Tissue dependent variations of DNA methylation and endoreduplication levels during tomato fruit development and ripening. Planta 228:391–399. https://doi.org/10.1007/s00425-008-0743-z

    CAS  Article  PubMed  Google Scholar 

  71. Trapnell C et al (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7:562–578

    CAS  PubMed  PubMed Central  Google Scholar 

  72. Tuskan GA et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:1596–1604

    CAS  PubMed  Google Scholar 

  73. Vaughn MW et al (2007) Epigenetic natural variation in Arabidopsis thaliana. PLoS Biol 5:e174

    PubMed  PubMed Central  Google Scholar 

  74. Velasco R et al (2007) A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE 2:e1326. https://doi.org/10.1371/journal.pone.0001326

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  75. Wang H et al (2015a) CG gene body DNA methylation changes and evolution of duplicated genes in cassava. Proc Natl Acad Sci USA 112:13729–13734

    CAS  PubMed  Google Scholar 

  76. Wang P et al (2015b) Genome-wide high-resolution mapping of DNA methylation identifies epigenetic variation across embryo and endosperm in maize (Zea may). BMC Genom 16:1

    Google Scholar 

  77. Wickham H (2009) ggplot2: elegant graphics for data analysis. Springer, New York

    Google Scholar 

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

    Google Scholar 

  79. Xie W et al (2013) Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153:1134–1148. https://doi.org/10.1016/j.cell.2013.04.022

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  80. Xu W, Yang T, Dong X, Li D-Z, Liu A (2016) Genomic DNA methylation analyses reveal the distinct profiles in castor bean seeds with persistent endosperms. Plant Physiol 171:1242–1258

    CAS  PubMed  PubMed Central  Google Scholar 

  81. Yang H et al (2015) Whole-genome DNA methylation patterns and complex associations with gene structure and expression during flower development in Arabidopsis. Plant J 81:268–281

    CAS  PubMed  Google Scholar 

  82. Zenoni S et al (2010) Characterization of transcriptional complexity during berry development in Vitis vinifera using RNA-Seq. Plant Physiol 152:1787–1795

    CAS  PubMed  PubMed Central  Google Scholar 

  83. Zhang XY et al (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126:1189–1201. https://doi.org/10.1016/j.cell.2006.08.003

    CAS  Article  PubMed  Google Scholar 

  84. Zhang B et al (2016) Chilling-induced tomato flavor loss is associated with altered volatile synthesis and transient changes in DNA methylation. Proc Natl Acad Sci USA 113:12580–12585

    CAS  PubMed  Google Scholar 

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

    CAS  Article  PubMed  Google Scholar 

  86. Zilberman D, Cao XF, Johansen LK, Xie ZX, Carrington JC, Jacobsen SE (2004) Role of arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Curr Biol 14:1214–1220. https://doi.org/10.1016/j.cub.2004.06.055

    CAS  Article  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by grants from the Natural Science Foundation of China (NSFC) (No. 31772283), and Key R&D projects in Jiangsu Province (BE2018389). We thank Novogene for helping the joint analysis of RNA sequencing and Methylation sequencing data.

Author information

Affiliations

Authors

Contributions

LFSG and JGF conceived and designed the experiments. LFSG, XF, and KKZ analyzed the data. LFSG and HFJ, helped in manuscript write-up. LFSG, MXC and JGF revised the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Lingfei Shangguan.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (XLSX 46 kb)

Supplementary material 2 (DOCX 22010 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Shangguan, L., Fang, X., Jia, H. et al. Characterization of DNA methylation variations during fruit development and ripening of Vitis vinifera (cv. ‘Fujiminori’). Physiol Mol Biol Plants 26, 617–637 (2020). https://doi.org/10.1007/s12298-020-00759-5

Download citation

Keywords

  • Grapevine
  • DNA methylation
  • Fruit development
  • Epigenetics
  • Gene expression