메뉴 건너뛰기




Volumn 114, Issue 22, 2017, Pages E4511-E4519

Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit

Author keywords

5 mC DNA glycosylase; DNA demethylase; DNA methylation; Epigenetic regulation; Gene silencing

Indexed keywords

DNA; DNA DEMETHYLASE; DNA GLYCOSYLTRANSFERASE; GENOMIC DNA; PROTEIN; SLDML2 PROTEIN; UNCLASSIFIED DRUG; HISTONE DEMETHYLASE; NUCLEAR PROTEIN; PLANT PROTEIN;

EID: 85019987594     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1705233114     Document Type: Article
Times cited : (368)

References (46)
  • 1
    • 79952535972 scopus 로고    scopus 로고
    • Regulation and function of DNA methylation in plants and animals
    • He X-J, Chen T, Zhu J-K (2011) Regulation and function of DNA methylation in plants and animals. Cell Res 21:442-465.
    • (2011) Cell Res , vol.21 , pp. 442-465
    • He, X.-J.1    Chen, T.2    Zhu, J.-K.3
  • 2
    • 77249170184 scopus 로고    scopus 로고
    • Establishing, maintaining and modifying DNA methylation patterns in plants and animals
    • Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11:204-220.
    • (2010) Nat Rev Genet , vol.11 , pp. 204-220
    • Law, J.A.1    Jacobsen, S.E.2
  • 3
    • 73349104113 scopus 로고    scopus 로고
    • Active DNA demethylation mediated by DNA glycosylases
    • Zhu J-K (2009) Active DNA demethylation mediated by DNA glycosylases. Annu Rev Genet 43:143-166.
    • (2009) Annu Rev Genet , vol.43 , pp. 143-166
    • Zhu, J.-K.1
  • 4
    • 84901041535 scopus 로고    scopus 로고
    • RNA-directed DNA methylation: An epigenetic pathway of increasing complexity
    • Matzke MA, Mosher RA (2014) RNA-directed DNA methylation: An epigenetic pathway of increasing complexity. Nat Rev Genet 15:394-408.
    • (2014) Nat Rev Genet , vol.15 , pp. 394-408
    • Matzke, M.A.1    Mosher, R.A.2
  • 5
    • 84875741680 scopus 로고    scopus 로고
    • The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin
    • Zemach A, et al. (2013) The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell 153:193-205.
    • (2013) Cell , vol.153 , pp. 193-205
    • Zemach, A.1
  • 6
  • 7
    • 0037074009 scopus 로고    scopus 로고
    • ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase
    • Gong Z, et al. (2002) ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 111:803-814.
    • (2002) Cell , vol.111 , pp. 803-814
    • Gong, Z.1
  • 8
    • 32044470027 scopus 로고    scopus 로고
    • DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation
    • Gehring M, et al. (2006) DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation. Cell 124:495-506.
    • (2006) Cell , vol.124 , pp. 495-506
    • Gehring, M.1
  • 9
    • 84930382619 scopus 로고    scopus 로고
    • A DNA ligase required for active DNA demethylation and genomic imprinting in Arabidopsis
    • Li Y, Duan C-G, Zhu X, Qian W, Zhu J-K (2015) A DNA ligase required for active DNA demethylation and genomic imprinting in Arabidopsis. Cell Res 25:757-760.
    • (2015) Cell Res , vol.25 , pp. 757-760
    • Li, Y.1    Duan, C.-G.2    Zhu, X.3    Qian, W.4    Zhu, J.-K.5
  • 11
    • 85020028428 scopus 로고    scopus 로고
    • PLoS Genet 11: E1004905.
    • PLoS Genet , vol.11 , pp. E1004905
  • 12
    • 84863036797 scopus 로고    scopus 로고
    • A DNA 3 phosphatase functions in active DNA demethylation in Arabidopsis
    • Martínez-Maciás MI, et al. (2012) A DNA 3 phosphatase functions in active DNA demethylation in Arabidopsis. Mol Cell 45:357-370.
    • (2012) Mol Cell , vol.45 , pp. 357-370
    • Martínez-Maciás, M.I.1
  • 13
    • 33746807366 scopus 로고    scopus 로고
    • Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation
    • Agius F, Kapoor A, Zhu J-K (2006) Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation. Proc Natl Acad Sci USA 103:11796-11801.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 11796-11801
    • Agius, F.1    Kapoor, A.2    Zhu, J.-K.3
  • 14
    • 33646473818 scopus 로고    scopus 로고
    • DEMETER and REPRESSOR of SILENCING 1 encode 5-methylcytosine DNA glycosylases
    • Morales-Ruiz T, et al. (2006) DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases. Proc Natl Acad Sci USA 103:6853-6858.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 6853-6858
    • Morales-Ruiz, T.1
  • 15
    • 84862298246 scopus 로고    scopus 로고
    • A histone acetyltransferase regulates active DNA demethylation in Arabidopsis
    • Qian W, et al. (2012) A histone acetyltransferase regulates active DNA demethylation in Arabidopsis. Science 336:1445-1448.
    • (2012) Science , vol.336 , pp. 1445-1448
    • Qian, W.1
  • 16
    • 84906101577 scopus 로고    scopus 로고
    • Regulation of active DNA demethylation by an-crystallin domain protein in Arabidopsis
    • Qian W, et al. (2014) Regulation of active DNA demethylation by an-crystallin domain protein in Arabidopsis. Mol Cell 55:361-371.
    • (2014) Mol Cell , vol.55 , pp. 361-371
    • Qian, W.1
  • 17
    • 84925261224 scopus 로고    scopus 로고
    • The methyl-CpG-binding protein MBD7 facilitates active DNA demethylation to limit DNA hyper-methylation and transcriptional gene silencing
    • Lang Z, et al. (2015) The methyl-CpG-binding protein MBD7 facilitates active DNA demethylation to limit DNA hyper-methylation and transcriptional gene silencing. Mol Cell 57:971-983.
    • (2015) Mol Cell , vol.57 , pp. 971-983
    • Lang, Z.1
  • 18
    • 85004098353 scopus 로고    scopus 로고
    • A pair of transposon-derived proteins function in a histone acetyltransferase complex for active DNA demethylation
    • Duan CG, et al. (2017) A pair of transposon-derived proteins function in a histone acetyltransferase complex for active DNA demethylation. Cell Res 27:226-240.
    • (2017) Cell Res , vol.27 , pp. 226-240
    • Duan, C.G.1
  • 19
    • 84923650135 scopus 로고    scopus 로고
    • Methyl-CpG-binding domain protein MBD7 is required for active DNA demethylation in Arabidopsis
    • Wang C, et al. (2015) Methyl-CpG-binding domain protein MBD7 is required for active DNA demethylation in Arabidopsis. Plant Physiol 167:905-914.
    • (2015) Plant Physiol , vol.167 , pp. 905-914
    • Wang, C.1
  • 20
    • 33845866061 scopus 로고    scopus 로고
    • The DNA glycosylase/lyase ROS1 functions in pruning DNA methylation patterns in Arabidopsis
    • 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: 54-59.
    • (2007) Curr Biol , vol.17 , pp. 54-59
    • Zhu, J.1    Kapoor, A.2    Sridhar, V.V.3    Agius, F.4    Zhu, J.-K.5
  • 21
    • 84993983959 scopus 로고    scopus 로고
    • The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications
    • Tang K, Lang Z, Zhang H, Zhu JK (2016) The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications. Nat Plants 2:16169.
    • (2016) Nat Plants , vol.2 , pp. 16169
    • Tang, K.1    Lang, Z.2    Zhang, H.3    Zhu, J.K.4
  • 22
    • 84902124512 scopus 로고    scopus 로고
    • Overproduction of stomatal lineage cells in Arabidopsis mutants defective in active DNA demethylation
    • Yamamuro C, et al. (2014) Overproduction of stomatal lineage cells in Arabidopsis mutants defective in active DNA demethylation. Nat Commun 5:4062.
    • (2014) Nat Commun , vol.5 , pp. 4062
    • Yamamuro, C.1
  • 23
    • 85003049029 scopus 로고    scopus 로고
    • DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis
    • Le T-N, et al. (2014) DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis. Genome Biol 15:458.
    • (2014) Genome Biol , vol.15 , pp. 458
    • Le, T.-N.1
  • 24
    • 80755169485 scopus 로고    scopus 로고
    • Genetics and control of tomato fruit ripening and quality attributes
    • Klee HJ, Giovannoni JJ (2011) Genetics and control of tomato fruit ripening and quality attributes. Annu Rev Genet 45:41-59.
    • (2011) Annu Rev Genet , vol.45 , pp. 41-59
    • Klee, H.J.1    Giovannoni, J.J.2
  • 25
    • 0037066465 scopus 로고    scopus 로고
    • A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus
    • Vrebalov J, et al. (2002) A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus. Science 296:343-346.
    • (2002) Science , vol.296 , pp. 343-346
    • Vrebalov, J.1
  • 26
    • 33746513103 scopus 로고    scopus 로고
    • A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening
    • 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.
    • (2006) Nat Genet , vol.38 , pp. 948-952
    • Manning, K.1
  • 27
    • 34248213602 scopus 로고    scopus 로고
    • Fruit ripening mutants yield insights into ripening control
    • Giovannoni JJ (2007) Fruit ripening mutants yield insights into ripening control. Curr Opin Plant Biol 10:283-289.
    • (2007) Curr Opin Plant Biol , vol.10 , pp. 283-289
    • Giovannoni, J.J.1
  • 28
    • 84873587727 scopus 로고    scopus 로고
    • Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening
    • Zhong S, et al. (2013) Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat Biotechnol 31: 154-159.
    • (2013) Nat Biotechnol , vol.31 , pp. 154-159
    • Zhong, S.1
  • 29
    • 84993965450 scopus 로고    scopus 로고
    • Chilling-induced tomato flavor loss is associated with altered volatile synthesis and transient changes in DNA methylation
    • 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.
    • (2016) Proc Natl Acad Sci USA , vol.113 , pp. 12580-12585
    • Zhang, B.1
  • 30
    • 84940536894 scopus 로고    scopus 로고
    • A DEMETER-like DNA demethylase governs tomato fruit ripening
    • Liu R, et al. (2015) A DEMETER-like DNA demethylase governs tomato fruit ripening. Proc Natl Acad Sci USA 112:10804-10809.
    • (2015) Proc Natl Acad Sci USA , vol.112 , pp. 10804-10809
    • Liu, R.1
  • 31
    • 84921656781 scopus 로고    scopus 로고
    • Genome-wide identification of cytosine-5 DNA methyltransferases and demethylases in Solanum lycopersicum
    • Cao D, et al. (2014) Genome-wide identification of cytosine-5 DNA methyltransferases and demethylases in Solanum lycopersicum. Gene 550:230-237.
    • (2014) Gene , vol.550 , pp. 230-237
    • Cao, D.1
  • 32
    • 84891932593 scopus 로고    scopus 로고
    • Application of the CRISPR-Cas system for efficient genome engineering in plants
    • Mao Y, et al. (2013) Application of the CRISPR-Cas system for efficient genome engineering in plants. Mol Plant 6:2008-2011.
    • (2013) Mol Plant , vol.6 , pp. 2008-2011
    • Mao, Y.1
  • 33
    • 80455140281 scopus 로고    scopus 로고
    • The tomato MADS-box transcription factor RIPENING INHIBITOR interacts with promoters involved in numerous ripening processes in a COLORLESS NONRIPENING-dependent manner
    • Martel C, Vrebalov J, Tafelmeyer P, Giovannoni JJ (2011) 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) Plant Physiol , vol.157 , pp. 1568-1579
    • Martel, C.1    Vrebalov, J.2    Tafelmeyer, P.3    Giovannoni, J.J.4
  • 34
    • 84905453371 scopus 로고    scopus 로고
    • Increasing tomato fruit quality by enhancing fruit chloroplast function: A double-edged sword
    • Cocaliadis MF, Fernández-Munõz R, Pons C, Orzaez D, Granell A (2014) Increasing tomato fruit quality by enhancing fruit chloroplast function: A double-edged sword J Exp Bot 65:4589-4598.
    • (2014) J Exp Bot , vol.65 , pp. 4589-4598
    • Cocaliadis, M.F.1    Fernández-Munõz, R.2    Pons, C.3    Orzaez, D.4    Granell, A.5
  • 35
    • 84875514782 scopus 로고    scopus 로고
    • A large-scale identification of direct targets of the tomato MADS box transcription factor RIPENING INHIBITOR reveals the regulation of fruit ripening
    • Fujisawa M, Nakano T, Shima Y, Ito Y (2013) A large-scale identification of direct targets of the tomato MADS box transcription factor RIPENING INHIBITOR reveals the regulation of fruit ripening. Plant Cell 25:371-386.
    • (2013) Plant Cell , vol.25 , pp. 371-386
    • Fujisawa, M.1    Nakano, T.2    Shima, Y.3    Ito, Y.4
  • 36
    • 84876072593 scopus 로고    scopus 로고
    • A potential role for CHH DNA methylation in cotton fiber growth patterns
    • Jin X, et al. (2013) A potential role for CHH DNA methylation in cotton fiber growth patterns. PLoS One 8:e60547.
    • (2013) PLoS One , vol.8 , pp. e60547
    • Jin, X.1
  • 37
    • 84925379649 scopus 로고    scopus 로고
    • Regulatory link between DNA methylation and active demethylation in Arabidopsis
    • Lei M, et al. (2015) Regulatory link between DNA methylation and active demethylation in Arabidopsis. Proc Natl Acad Sci USA 112:3553-3557.
    • (2015) Proc Natl Acad Sci USA , vol.112 , pp. 3553-3557
    • Lei, M.1
  • 38
    • 85007574973 scopus 로고    scopus 로고
    • DNA methylation signatures of the plant chromomethyltransferases
    • Gouil Q, Baulcombe DC (2016) DNA methylation signatures of the plant chromomethyltransferases. PLoS Genet 12:e1006526.
    • (2016) PLoS Genet , vol.12 , pp. e1006526
    • Gouil, Q.1    Baulcombe, D.C.2
  • 39
    • 78649810751 scopus 로고    scopus 로고
    • Local DNA hypomethylation activates genes in rice endosperm
    • Zemach A, et al. (2010) Local DNA hypomethylation activates genes in rice endosperm. Proc Natl Acad Sci USA 107:18729-18734.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 18729-18734
    • Zemach, A.1
  • 40
    • 33645713175 scopus 로고    scopus 로고
    • A highly efficient transformation protocol for Micro-Tom, a model cultivar for tomato functional genomics
    • Sun H-J, Uchii S, Watanabe S, Ezura H (2006) A highly efficient transformation protocol for Micro-Tom, a model cultivar for tomato functional genomics. Plant Cell Physiol 47:426-431.
    • (2006) Plant Cell Physiol , vol.47 , pp. 426-431
    • Sun, H.-J.1    Uchii, S.2    Watanabe, S.3    Ezura, H.4
  • 41
    • 84863995390 scopus 로고    scopus 로고
    • BRAT-BW: Efficient and accurate mapping of bisulfite-treated reads
    • Harris EY, Ponts N, Le Roch KG, Lonardi S (2012) BRAT-BW: Efficient and accurate mapping of bisulfite-treated reads. Bioinformatics 28:1795-1796.
    • (2012) Bioinformatics , vol.28 , pp. 1795-1796
    • Harris, E.Y.1    Ponts, N.2    Le Roch, K.G.3    Lonardi, S.4
  • 42
    • 84863693752 scopus 로고    scopus 로고
    • The tomato genome sequence provides insights into fleshy fruit evolution
    • Tomato Genome Consortium
    • Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635-641.
    • (2012) Nature , vol.485 , pp. 635-641
  • 43
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim D, et al. (2013) TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:R36.
    • (2013) Genome Biol , vol.14 , pp. R36
    • Kim, D.1
  • 44
    • 84897397058 scopus 로고    scopus 로고
    • FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features
    • Liao Y, Smyth GK, Shi W (2014) featureCounts: An efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923-930.
    • (2014) Bioinformatics , vol.30 , pp. 923-930
    • Liao, Y.1    Smyth, G.K.2    Shi, W.3
  • 45
    • 75249087100 scopus 로고    scopus 로고
    • EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
    • Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140.
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 46
    • 0037314097 scopus 로고    scopus 로고
    • Matrix2png: A utility for visualizing matrix data
    • Pavlidis P, Noble WS (2003) Matrix2png: A utility for visualizing matrix data. Bioinformatics 19:295-296.
    • (2003) Bioinformatics , vol.19 , pp. 295-296
    • Pavlidis, P.1    Noble, W.S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.