Increased DNA methylation contributes to the early ripening of pear fruits during domestication and improvement

Cedar H, Bergman Y. Programming of DNA methylation patterns. Ann Rev Biochem. 2012;81:97–117.

Article  CAS  PubMed  Google Scholar 

He L, Zhao C, Zhang Q, Zinta G, Wang D, Lozano-Durán R, Zhu J-K. Pathway conversion enables a double-lock mechanism to maintain DNA methylation and genome stability. Proc Natl Acad Sci. 2021;118:e2107320118.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhang H, Lang Z, Zhu J-K. Dynamics and function of DNA methylation in plants. Nat Rev Mol Cell Biol. 2018;19:489–506.

Article  CAS  PubMed  Google Scholar 

Lucibelli F, Valoroso MC, Aceto S. Plant DNA methylation: an epigenetic mark in development, environmental interactions, and evolution. Int J Mol Sci. 2022;23:8299.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Xu Q, Wu L, Luo Z, Zhang M, Lai J, Li L, Springer NM, Li Q. DNA demethylation affects imprinted gene expression in maize endosperm. Genome Biol. 2022;23:77.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cheng J, Niu Q, Zhang B, Chen K, Yang R, Zhu J-K, Zhang Y, Lang Z. Downregulation of RdDM during strawberry fruit ripening. Genome Biol. 2018;19:212.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Huang H, Liu R, Niu Q, Tang K, Zhang B, Zhang H, Chen K, Zhu J-K, Lang Z. Global increase in DNA methylation during orange fruit development and ripening. Proc Natl Acad Sci. 2019;116:1430–6.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lister R, O’Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 2008;133:523–36.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SWL, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell. 2006;126:1189–201.

Article  CAS  PubMed  Google Scholar 

Kankel MW, Ramsey DE, Stokes TL, Flowers SK, Haag JR, Jeddeloh JA, Riddle NC, Verbsky ML, Richards EJ. Arabidopsis MET1 cytosine methyltransferase mutants. Genetics. 2003;163:1109–22.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science. 2001;292:2077–80.

Article  CAS  PubMed  Google Scholar 

Bartee L, Malagnac F, Bender J. Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Genes Dev. 2001;15:1753–8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cao X, Jacobsen SE. Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol. 2002;12:1138–44.

Article  CAS  PubMed  Google Scholar 

Stroud H, Do T, Du J, Zhong X, Feng S, Johnson L, Patel DJ, Jacobsen SE. Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nat Struct Mol Biol. 2014;21:64–72.

Article  CAS  PubMed  Google Scholar 

Zemach A, Kim MY, Hsieh P-H, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer SL, Zilberman D. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 2013;153:193–205.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhang H, Zhu J-K. RNA-directed DNA methylation. Curr Opin Plant Biol. 2011;14:142–7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhu J-K. Active DNA demethylation mediated by DNA glycosylases. Ann Rev Genet. 2009;43:143–66.

Article  CAS  PubMed  Google Scholar 

Quinet M, Wesel J-P. Botany and taxonomy of pear. In: Korban SS, editor. The Pear Genome. Cham: Springer International Publishing; 2019. p. 1–33.

Google Scholar 

Wu J, Wang Y, Xu J, Korban SS, Fei Z, Tao S, Ming R, Tai S, Khan AM, Postman JD, et al. Diversification and independent domestication of Asian and European pears. Genome Biol. 2018;19:77.

Article  PubMed  PubMed Central  Google Scholar 

Li J, Zhang M, Li X, Khan A, Kumar S, Allan AC, Lin-Wang K, Espley RV, Wang C, Wang R, et al. Pear genetics: recent advances, new prospects, and a roadmap for the future. Hortic Res. 2022;9:uhab040.

Li X, Liu L, Ming M, Hu H, Zhang M, Fan J, Song B, Zhang S, Wu J. Comparative transcriptomic analysis provides insight into the domestication and improvement of pear (P. pyrifolia) fruit. Plant Physiol. 2019;180:435–52.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Moore LD, Le T, Fan G. DNA methylation and its basic function. Neuropsychopharmacology. 2013;38:23–38.

Article  CAS  PubMed  Google Scholar 

He L, Huang H, Bradai M, Zhao C, You Y, Ma J, Zhao L, Lozano-Durán R, Zhu J-K. DNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development. Nat Commun. 2022;13:1335.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Xu G, Lyu J, Li Q, Liu H, Wang D, Zhang M, Springer NM, Ross-Ibarra J, Yang J. Evolutionary and functional genomics of DNA methylation in maize domestication and improvement. Nat Commun. 2020;11:5539.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Guo H, Cao P, Wang C, Lai J, Deng Y, Li C, Hao Y, Wu Z, Chen R, Qiang Q, et al. Population analysis reveals the roles of DNA methylation in tomato domestication and metabolic diversity. Sci China Life Sci. 2023;66:1888–902.

Article  CAS  PubMed  Google Scholar 

Jühling F, Kretzmer H, Bernhart SH, Otto C, Stadler PF, Hoffmann S. Metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data. Genome Res. 2016;26:256–62.

Article  PubMed  PubMed Central  Google Scholar 

McRae AF, Powell JE, Henders AK, Bowdler L, Hemani G, Shah S, Painter JN, Martin NG, Visscher PM, Montgomery GW. Contribution of genetic variation to transgenerational inheritance of DNA methylation. Genome Biol. 2014;15:R73.

Article  PubMed  PubMed Central  Google Scholar 

Nie H, Zhao C, Wu G, Wu Y, Chen Y, Tang D. SR1, a calmodulin-binding transcription factor, modulates plant defense and ethylene-induced senescence by directly regulating NDR1 and EIN3. Plant Physiol. 2012;158:1847–59.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Taylor SM, Jones PA. Mechanism of action of eukaryotic DNA methyltransferase: use of 5-azacytosine-containing DNA. J Mol Biol. 1982;162:679–92.

Article  CAS  PubMed  Google Scholar 

Zhong S, Fei Z, Chen Y-R, Zheng Y, Huang M, Vrebalov J, McQuinn R, Gapper N, Liu B, Xiang J, et al. Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat Biotechnol. 2013;31:154–9.

Article  CAS  PubMed  Google Scholar 

Lang Z, Wang Y, Tang K, Tang D, Datsenka T, Cheng J, Zhang Y, Handa AK, Zhu J-K. Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit. Proc Natl Acad Sci. 2017;114:E4511–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yuan L, Wang D, Cao L, Yu N, Liu K, Guo Y, Gan S, Chen L. Regulation of leaf longevity by DML3-mediated DNA demethylation. Mol Plant. 2020;13:1149–61.

Article  CAS  PubMed  Google Scholar 

Cao S, Chen K, Lu K, Chen S, Zhang X, Shen C, Zhu S, Niu Y, Fan L, Chen ZJ, et al. Asymmetric variation in DNA methylation during domestication and de-domestication of rice. Plant Cell. 2023;35:3429–43.

Zhang Y, Liu C, Cheng H, Tian S, Liu Y, Wang S, Zhang H, Saqib M, Wei H, Wei Z. DNA methylation and its effects on gene expression during primary to secondary growth in poplar stems. BMC Genomics. 2020;21:498.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lippman Z, Gendrel A-V, Black M, Vaughn MW, Dedhia N, Richard McCombie W, Lavine K, Mittal V, May B, Kasschau KD, et al. Role of transposable elements in heterochromatin and epigenetic control. Nature. 2004;430:471–6.

Article  CAS  PubMed  Google Scholar 

Ma K, Song Y, Yang X, Zhang Z, Zhang D. Variation in genomic methylation in natural populations of Chinese white poplar. PLOS One. 2013;8:e63977.

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