A DEMETER-like DNA demethylase governs tomato fruit ripening

Proceedings of the National Academy of Sciences of the United States of America

Volumn 112, Issue 34, 2015, Pages 10804-10809

  Liu, Ruie ^a   How Kit, Alexandre ^b   Stammitti, Linda ^a   Teyssier, Emeline ^a   Rolin, Dominique ^a   Mortain Bertrand, Anne ^a   Halle, Stefanie ^a   Liu, Mingchun ^c,d   Kong, Junhua ^e   Wu, Chaoqun ^e   Degraeve Guibault, Charlotte ^a   Chapman, Natalie H ^f   Maucourt, Mickael ^a   Hodgman, T Charlie ^f   Tost, Jörg ^b,g   Bouzayen, Mondher ^c,d   Hong, Yiguo ^e,h   Seymour, Graham B ^g   Giovannoni, James J ⁱ   Gallusci, Philippe ^a  

^a UNIVERSITÉ DE BORDEAUX   (France)

^b Fondation Jean Dausset   (France)

^c Centre National de la Recherche Scientifique   (France)

^d CEMAGREF   (France)

^e HANGZHOU NORMAL UNIVERSITY   (China)

^f UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^g CENTRE NATIONAL DE GÉNOTYPAGE   (France)

^h UNIVERSITY OF WARWICK   (United Kingdom)

ⁱ United States Department of Agriculture Agricultural Research Service and Boyce Thompson Institute for Plant Research   (United States)

Author keywords

Active DNA demethylation; DNA glycosylase lyase; Epigenetic; Fruit ripening; Tomato

Indexed keywords

CAROTENOID; DNA GLYCOSYLTRANSFERASE; PLANT DNA; TRANSCRIPTION FACTOR; VEGETABLE PROTEIN;

ARTICLE; BIOCHEMISTRY; CONTROLLED STUDY; DEMETHYLATION; DNA METHYLATION; FRUIT RIPENING; GENE EXPRESSION; NONHUMAN; PERICARP; PLANT CELL; PRIORITY JOURNAL; TOMATO; ENZYMOLOGY; FRUIT; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; PHYSIOLOGY; PLANT GENE; RNA INTERFERENCE; TRANSGENIC PLANT;

DNA GLYCOSYLASES; DNA METHYLATION; DNA, PLANT; FRUIT; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; LYCOPERSICON ESCULENTUM; PLANT PROTEINS; PLANTS, GENETICALLY MODIFIED; RNA INTERFERENCE;

EID: 84940536894     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1503362112     Document Type: Article

References (32)

1. Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11(3):204-220.
2. Saze H, Tsugane K, Kanno T, Nishimura T (2012) DNA methylation in plants: Relationship to small RNAs and histone modifications, and functions in transposon inactivation. Plant Cell Physiol 53(5):766-784.
3. Chan SW, Henderson IR, Jacobsen SE (2005) Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet 6(5):351-360.
4. Mirouze M, et al. (2012) Loss of DNA methylation affects the recombination landscape in Arabidopsis. Proc Natl Acad Sci USA 109(15):5880-5885.
5. Zhang M, Kimatu JN, Xu K, Liu B (2010) DNA cytosine methylation in plant development. J Genet Genomics 37(1):1-12.
6. Bender J (2004) DNA methylation and epigenetics. Annu Rev Plant Biol 55(1):41-68.
7. Finnegan EJ, Kovac KA (2000) Plant DNA methyltransferases. Plant Mol Biol 43(2-3): 189-201.
8. Hsieh T-F, et al. (2009) Genome-wide demethylation of Arabidopsis endosperm. Science 324(5933):1451-1454.
9. Gong Z, et al. (2002) ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 111(6):803-814.
10. Zhu J-K (2009) Active DNA demethylation mediated by DNA glycosylases. Annu Rev Genet 43(1):143-166.
11. Wu SC, Zhang Y (2010) Active DNA demethylation: Many roads lead to Rome. Nat Rev Mol Cell Biol 11(9):607-620.
12. Choi Y, et al. (2002) DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in arabidopsis. Cell 110(1):33-42.
13. Zhu J, Kapoor A, Sridhar VV, Agius F, Zhu J-K (2007) The DNA glycosylase/lyase ROS1 functions in pruning DNA methylation patterns in Arabidopsis. Curr Biol 17(1):54-59.
14. Gehring M, Bubb KL, Henikoff S (2009) Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324(5933): 1447-1451.
15. Yu A, et al. (2013) Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense. Proc Natl Acad Sci USA 110(6):2389-2394.
16. Yamamuro C, et al. (2014) Overproduction of stomatal lineage cells in Arabidopsis mutants defective in active DNA demethylation. Nat Commun 5:4062.
17. Penterman J, et al. (2007) DNA demethylation in the Arabidopsis genome. Proc Natl Acad Sci USA 104(16):6752-6757.
18. Gehring M, Henikoff S (2007) DNA methylation dynamics in plant genomes. Biochim Biophys Acta 1769(5-6):276-286.
19. Bhutani N, Burns DM, Blau HM (2011) DNA Demethylation Dynamics. Cell 146(6): 866-872.
20. Zhong S, et al. (2013) Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat Biotechnol 31(2): 154-159.
21. 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(8): 948-952.
22. Teyssier E, et al. (2008) Tissue dependent variations of DNA methylation and endoreduplication levels during tomato fruit development and ripening. Planta 228(3): 391-399.
23. Mok YG, et al. (2010) Domain structure of the DEMETER 5-methylcytosine DNA glycosylase. Proc Natl Acad Sci USA 107(45):19225-19230.
24. Vrebalov J, et al. (2002) A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus. Science 296(5566):343-346.
25. Giovannoni JJ (2004) Genetic regulation of fruit development and ripening. Plant Cell 16(Suppl):S170-S180.
26. Bartley GE, Viitanen PV, Bacot KO, Scolnik PA (1992) A tomato gene expressed during fruit ripening encodes an enzyme of the carotenoid biosynthesis pathway. J Biol Chem 267(8):5036-5039.
27. Ray J, et al. (1992) Cloning and characterization of a gene involved in phytoene synthesis from tomato. Plant Mol Biol 19(3):401-404.
28. How-Kit A, et al. (2015) Accurate CpG and non-CpG cytosine methylation analysis by high-throughput locus-specific pyrosequencing in plants. Plant Mol Biol 88(4-5): 471-485.
29. Chen W, et al. (2015) Requirement of CHROMOMETHYLASE3 for somatic inheritance of the spontaneous tomato epimutation Colourless non-ripening. Sci Rep 5:9192.
30. Lin T, et al. (2014) Genomic analyses provide insights into the history of tomato breeding. Nat Genet 46(11):1220-1226.
31. Telias A, et al. (2011) Apple skin patterning is associated with differential expression of MYB10. BMC Plant Biol 11(1):93.
32. Wang Z, et al. (2013) The methylation of the PcMYB10 promoter is associated with green-skinned sport in Max Red Bartlett pear. Plant Physiol 162(2):885-896.