메뉴 건너뛰기




Volumn 9, Issue 1, 2013, Pages

Structural Basis of a Histone H3 Lysine 4 Demethylase Required for Stem Elongation in Rice

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; CYTOKININ; FERROUS ION; GLYCINE; HISTONE DEMETHYLASE; HISTONE DEMETHYLASE JMJ703; HISTONE H3; LYSINE; N OXALYLGLYCINE; OXIDOREDUCTASE; UNCLASSIFIED DRUG;

EID: 84873502934     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1003239     Document Type: Article
Times cited : (77)

References (44)
  • 1
    • 77953644347 scopus 로고    scopus 로고
    • Reversal of histone methylation: biochemical and molecular mechanisms of histone demethylases
    • Mosammaparast N, Shi Y, (2010) Reversal of histone methylation: biochemical and molecular mechanisms of histone demethylases. Annu Rev Biochem 79: 155-179.
    • (2010) Annu Rev Biochem , vol.79 , pp. 155-179
    • Mosammaparast, N.1    Shi, Y.2
  • 2
    • 11144332565 scopus 로고    scopus 로고
    • Histone demethylation mediated by the nuclear amine oxidase homolog LSD1
    • Shi Y, Lan F, Matson C, Mulligan P, Whetstine JR, et al. (2004) Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119: 941-953.
    • (2004) Cell , vol.119 , pp. 941-953
    • Shi, Y.1    Lan, F.2    Matson, C.3    Mulligan, P.4    Whetstine, J.R.5
  • 4
    • 33747455678 scopus 로고    scopus 로고
    • JmjC-domain-containing proteins and histone demethylation
    • Klose RJ, Kallin EM, Zhang Y, (2006) JmjC-domain-containing proteins and histone demethylation. Nat Rev Genet 7: 715-727.
    • (2006) Nat Rev Genet , vol.7 , pp. 715-727
    • Klose, R.J.1    Kallin, E.M.2    Zhang, Y.3
  • 5
    • 33646138230 scopus 로고    scopus 로고
    • JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor
    • Yamane K, Toumazou C, Tsukada Y, Erdjument-Bromage H, Tempst P, et al. (2006) JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor. Cell 125: 483-495.
    • (2006) Cell , vol.125 , pp. 483-495
    • Yamane, K.1    Toumazou, C.2    Tsukada, Y.3    Erdjument-Bromage, H.4    Tempst, P.5
  • 6
    • 33646124469 scopus 로고    scopus 로고
    • Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases
    • Whetstine JR, Nottke A, Lan F, Huarte M, Smolikov S, et al. (2006) Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 125: 467-481.
    • (2006) Cell , vol.125 , pp. 467-481
    • Whetstine, J.R.1    Nottke, A.2    Lan, F.3    Huarte, M.4    Smolikov, S.5
  • 7
    • 35148867907 scopus 로고    scopus 로고
    • UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development
    • Agger K, Cloos PA, Christensen J, Pasini D, Rose S, et al. (2007) UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. Nature 449: 731-734.
    • (2007) Nature , vol.449 , pp. 731-734
    • Agger, K.1    Cloos, P.A.2    Christensen, J.3    Pasini, D.4    Rose, S.5
  • 8
    • 77954954200 scopus 로고    scopus 로고
    • PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression
    • Liu W, Tanasa B, Tyurina OV, Zhou TY, Gassmann R, et al. (2010) PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression. Nature 466: 508-512.
    • (2010) Nature , vol.466 , pp. 508-512
    • Liu, W.1    Tanasa, B.2    Tyurina, O.V.3    Zhou, T.Y.4    Gassmann, R.5
  • 9
    • 77954957901 scopus 로고    scopus 로고
    • Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development
    • Qi HH, Sarkissian M, Hu GQ, Wang Z, Bhattacharjee A, et al. (2010) Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development. Nature 466: 503-507.
    • (2010) Nature , vol.466 , pp. 503-507
    • Qi, H.H.1    Sarkissian, M.2    Hu, G.Q.3    Wang, Z.4    Bhattacharjee, A.5
  • 10
    • 84869096429 scopus 로고    scopus 로고
    • NOTCH1 Nuclear Interactome Reveals Key Regulators of Its Transcriptional Activity and Oncogenic Function
    • Yatim A, Benne C, Sobhian B, Laurent-Chabalier S, Deas O, et al. (2012) NOTCH1 Nuclear Interactome Reveals Key Regulators of Its Transcriptional Activity and Oncogenic Function. Mol Cell 48: 445-458.
    • (2012) Mol Cell , vol.48 , pp. 445-458
    • Yatim, A.1    Benne, C.2    Sobhian, B.3    Laurent-Chabalier, S.4    Deas, O.5
  • 11
    • 33847613217 scopus 로고    scopus 로고
    • Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC proteins
    • Seward DJ, Cubberley G, Kim S, Schonewald M, Zhang L, et al. (2007) Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC proteins. Nat Struct Mol Biol 14: 240-242.
    • (2007) Nat Struct Mol Biol , vol.14 , pp. 240-242
    • Seward, D.J.1    Cubberley, G.2    Kim, S.3    Schonewald, M.4    Zhang, L.5
  • 12
    • 35348938519 scopus 로고    scopus 로고
    • JMJD6 is a histone arginine demethylase
    • Chang B, Chen Y, Zhao Y, Bruick RK, (2007) JMJD6 is a histone arginine demethylase. Science 318: 444-447.
    • (2007) Science , vol.318 , pp. 444-447
    • Chang, B.1    Chen, Y.2    Zhao, Y.3    Bruick, R.K.4
  • 13
    • 0037097861 scopus 로고    scopus 로고
    • FIH-1 is an asparaginyl hydroxylase enzyme that regulates the transcriptional activity of hypoxia-inducible factor
    • Lando D, Peet DJ, Gorman JJ, Whelan DA, Whitelaw ML, et al. (2002) FIH-1 is an asparaginyl hydroxylase enzyme that regulates the transcriptional activity of hypoxia-inducible factor. Genes Dev 16: 1466-1471.
    • (2002) Genes Dev , vol.16 , pp. 1466-1471
    • Lando, D.1    Peet, D.J.2    Gorman, J.J.3    Whelan, D.A.4    Whitelaw, M.L.5
  • 14
    • 67650072604 scopus 로고    scopus 로고
    • Jmjd6 catalyses lysyl-hydroxylation of U2AF65, a protein associated with RNA splicing
    • Webby CJ, Wolf A, Gromak N, Dreger M, Kramer H, et al. (2009) Jmjd6 catalyses lysyl-hydroxylation of U2AF65, a protein associated with RNA splicing. Science 325: 90-93.
    • (2009) Science , vol.325 , pp. 90-93
    • Webby, C.J.1    Wolf, A.2    Gromak, N.3    Dreger, M.4    Kramer, H.5
  • 15
    • 79961209798 scopus 로고    scopus 로고
    • Epigenetic gene regulation by plant Jumonji group of histone demethylase
    • Chen X, Hu Y, Zhou DX, (2011) Epigenetic gene regulation by plant Jumonji group of histone demethylase. Biochim Biophys Acta 1809: 421-426.
    • (2011) Biochim Biophys Acta , vol.1809 , pp. 421-426
    • Chen, X.1    Hu, Y.2    Zhou, D.X.3
  • 16
    • 79959741225 scopus 로고    scopus 로고
    • Arabidopsis REF6 is a histone H3 lysine 27 demethylase
    • Lu F, Cui X, Zhang S, Jenuwein T, Cao X, (2011) Arabidopsis REF6 is a histone H3 lysine 27 demethylase. Nat Genet 43: 715-719.
    • (2011) Nat Genet , vol.43 , pp. 715-719
    • Lu, F.1    Cui, X.2    Zhang, S.3    Jenuwein, T.4    Cao, X.5
  • 17
    • 51649112913 scopus 로고    scopus 로고
    • Rice jmjC domain-containing gene JMJ706 encodes H3K9 demethylase required for floral organ development
    • Sun Q, Zhou DX, (2008) Rice jmjC domain-containing gene JMJ706 encodes H3K9 demethylase required for floral organ development. Proc Natl Acad Sci U S A 105: 13679-13684.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 13679-13684
    • Sun, Q.1    Zhou, D.X.2
  • 18
    • 48249088454 scopus 로고    scopus 로고
    • Comparative analysis of JmjC domain-containing proteins reveals the potential histone demethylases in Arabidopsis and rice
    • Lu F, Li G, Cui X, Liu C, Wang XJ, et al. (2008) Comparative analysis of JmjC domain-containing proteins reveals the potential histone demethylases in Arabidopsis and rice. J Integr Plant Biol 50: 886-896.
    • (2008) J Integr Plant Biol , vol.50 , pp. 886-896
    • Lu, F.1    Li, G.2    Cui, X.3    Liu, C.4    Wang, X.J.5
  • 19
    • 78649664485 scopus 로고    scopus 로고
    • Structural insights into histone lysine demethylation
    • Hou H, Yu H, (2010) Structural insights into histone lysine demethylation. Curr Opin Struct Biol 20: 739-748.
    • (2010) Curr Opin Struct Biol , vol.20 , pp. 739-748
    • Hou, H.1    Yu, H.2
  • 20
    • 78651305163 scopus 로고    scopus 로고
    • Crystal structure of the catalytic core of Saccharomyces cerevesiae histone demethylase Rph1: insights into the substrate specificity and catalytic mechanism
    • Chang Y, Wu J, Tong XJ, Zhou JQ, Ding J, (2010) Crystal structure of the catalytic core of Saccharomyces cerevesiae histone demethylase Rph1: insights into the substrate specificity and catalytic mechanism. Biochem J 433: 295-302.
    • (2010) Biochem J , vol.433 , pp. 295-302
    • Chang, Y.1    Wu, J.2    Tong, X.J.3    Zhou, J.Q.4    Ding, J.5
  • 21
    • 80455140217 scopus 로고    scopus 로고
    • Structural basis for histone H3 Lys 27 demethylation by UTX/KDM6A
    • Sengoku T, Yokoyama S, (2011) Structural basis for histone H3 Lys 27 demethylation by UTX/KDM6A. Genes Dev 25: 2266-2277.
    • (2011) Genes Dev , vol.25 , pp. 2266-2277
    • Sengoku, T.1    Yokoyama, S.2
  • 22
    • 33646505724 scopus 로고    scopus 로고
    • Structural insights into histone demethylation by JMJD2 family members
    • Chen Z, Zang J, Whetstine J, Hong X, Davrazou F, et al. (2006) Structural insights into histone demethylation by JMJD2 family members. Cell 125: 691-702.
    • (2006) Cell , vol.125 , pp. 691-702
    • Chen, Z.1    Zang, J.2    Whetstine, J.3    Hong, X.4    Davrazou, F.5
  • 23
    • 0014432781 scopus 로고
    • Solvent content of protein crystals
    • Matthews BW, (1968) Solvent content of protein crystals. J Mol Biol 33: 491-497.
    • (1968) J Mol Biol , vol.33 , pp. 491-497
    • Matthews, B.W.1
  • 24
    • 0035150397 scopus 로고    scopus 로고
    • JmjC: cupin metalloenzyme-like domains in jumonji, hairless and phospholipase A2beta
    • Clissold PM, Ponting CP, (2001) JmjC: cupin metalloenzyme-like domains in jumonji, hairless and phospholipase A2beta. Trends Biochem Sci 26: 7-9.
    • (2001) Trends Biochem Sci , vol.26 , pp. 7-9
    • Clissold, P.M.1    Ponting, C.P.2
  • 25
    • 34547471432 scopus 로고    scopus 로고
    • Structural basis of the recognition of a methylated histone tail by JMJD2A
    • Chen Z, Zang J, Kappler J, Hong X, Crawford F, et al. (2007) Structural basis of the recognition of a methylated histone tail by JMJD2A. Proc Natl Acad Sci U S A 104: 10818-10823.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 10818-10823
    • Chen, Z.1    Zang, J.2    Kappler, J.3    Hong, X.4    Crawford, F.5
  • 27
    • 77949269527 scopus 로고    scopus 로고
    • JMJ14 is an H3K4 demethylase regulating flowering time in Arabidopsis
    • Lu F, Cui X, Zhang S, Liu C, Cao X, (2010) JMJ14 is an H3K4 demethylase regulating flowering time in Arabidopsis. Cell Res 20: 387-390.
    • (2010) Cell Res , vol.20 , pp. 387-390
    • Lu, F.1    Cui, X.2    Zhang, S.3    Liu, C.4    Cao, X.5
  • 28
    • 67650091251 scopus 로고    scopus 로고
    • Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana
    • Zhang X, Bernatavichute YV, Cokus S, Pellegrini M, Jacobsen SE, (2009) Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol 10: R62.
    • (2009) Genome Biol , vol.10
    • Zhang, X.1    Bernatavichute, Y.V.2    Cokus, S.3    Pellegrini, M.4    Jacobsen, S.E.5
  • 29
    • 77950346035 scopus 로고    scopus 로고
    • Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids
    • He G, Zhu X, Elling AA, Chen L, Wang X, et al. (2010) Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell 22: 17-33.
    • (2010) Plant Cell , vol.22 , pp. 17-33
    • He, G.1    Zhu, X.2    Elling, A.A.3    Chen, L.4    Wang, X.5
  • 30
    • 77952352352 scopus 로고    scopus 로고
    • JMJ14, a JmjC domain protein, is required for RNA silencing and cell-to-cell movement of an RNA silencing signal in Arabidopsis
    • Searle IR, Pontes O, Melnyk CW, Smith LM, Baulcombe DC, (2010) JMJ14, a JmjC domain protein, is required for RNA silencing and cell-to-cell movement of an RNA silencing signal in Arabidopsis. Genes Dev 24: 986-991.
    • (2010) Genes Dev , vol.24 , pp. 986-991
    • Searle, I.R.1    Pontes, O.2    Melnyk, C.W.3    Smith, L.M.4    Baulcombe, D.C.5
  • 31
    • 77952174701 scopus 로고    scopus 로고
    • A plant-specific histone H3 lysine 4 demethylase represses the floral transition in Arabidopsis
    • Yang W, Jiang D, Jiang J, He Y, (2010) A plant-specific histone H3 lysine 4 demethylase represses the floral transition in Arabidopsis. Plant J 62: 663-673.
    • (2010) Plant J , vol.62 , pp. 663-673
    • Yang, W.1    Jiang, D.2    Jiang, J.3    He, Y.4
  • 32
    • 71049163028 scopus 로고    scopus 로고
    • Repression of FLOWERING LOCUS T chromatin by functionally redundant histone H3 lysine 4 demethylases in Arabidopsis
    • doi:10.1371/journal.pone.0008033
    • Jeong JH, Song HR, Ko JH, Jeong YM, Kwon YE, et al. (2009) Repression of FLOWERING LOCUS T chromatin by functionally redundant histone H3 lysine 4 demethylases in Arabidopsis. PLoS ONE 4: e8033 doi:10.1371/journal.pone.0008033.
    • (2009) PLoS ONE , vol.4
    • Jeong, J.H.1    Song, H.R.2    Ko, J.H.3    Jeong, Y.M.4    Kwon, Y.E.5
  • 33
    • 78649485519 scopus 로고    scopus 로고
    • Involvement of a Jumonji-C domain-containing histone demethylase in DRM2-mediated maintenance of DNA methylation
    • Deleris A, Greenberg MV, Ausin I, Law RW, Moissiard G, et al. (2010) Involvement of a Jumonji-C domain-containing histone demethylase in DRM2-mediated maintenance of DNA methylation. EMBO Rep 11: 950-955.
    • (2010) EMBO Rep , vol.11 , pp. 950-955
    • Deleris, A.1    Greenberg, M.V.2    Ausin, I.3    Law, R.W.4    Moissiard, G.5
  • 34
    • 75649129700 scopus 로고    scopus 로고
    • Dynamic landscapes of four histone modifications during deetiolation in Arabidopsis
    • Charron JB, He H, Elling AA, Deng XW, (2009) Dynamic landscapes of four histone modifications during deetiolation in Arabidopsis. Plant Cell 21: 3732-3748.
    • (2009) Plant Cell , vol.21 , pp. 3732-3748
    • Charron, J.B.1    He, H.2    Elling, A.A.3    Deng, X.W.4
  • 35
    • 33747866294 scopus 로고    scopus 로고
    • Dynamic and reversible changes in histone H3-Lys4 methylation and H3 acetylation occurring at submergence-inducible genes in rice
    • Tsuji H, Saika H, Tsutsumi N, Hirai A, Nakazono M, (2006) Dynamic and reversible changes in histone H3-Lys4 methylation and H3 acetylation occurring at submergence-inducible genes in rice. Plant Cell Physiol 47: 995-1003.
    • (2006) Plant Cell Physiol , vol.47 , pp. 995-1003
    • Tsuji, H.1    Saika, H.2    Tsutsumi, N.3    Hirai, A.4    Nakazono, M.5
  • 36
    • 54149108452 scopus 로고    scopus 로고
    • Alterations of lysine modifications on the histone H3 N-tail under drought stress conditions in Arabidopsis thaliana
    • Kim JM, To TK, Ishida J, Morosawa T, Kawashima M, et al. (2008) Alterations of lysine modifications on the histone H3 N-tail under drought stress conditions in Arabidopsis thaliana. Plant Cell Physiol 49: 1580-1588.
    • (2008) Plant Cell Physiol , vol.49 , pp. 1580-1588
    • Kim, J.M.1    To, T.K.2    Ishida, J.3    Morosawa, T.4    Kawashima, M.5
  • 37
    • 34447133035 scopus 로고    scopus 로고
    • Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity
    • Ng SS, Kavanagh KL, McDonough MA, Butler D, Pilka ES, et al. (2007) Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity. Nature 448: 87-91.
    • (2007) Nature , vol.448 , pp. 87-91
    • Ng, S.S.1    Kavanagh, K.L.2    McDonough, M.A.3    Butler, D.4    Pilka, E.S.5
  • 38
    • 34447126368 scopus 로고    scopus 로고
    • Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice
    • Huang L, Sun Q, Qin F, Li C, Zhao Y, et al. (2007) Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice. Plant Physiol 144: 1508-1519.
    • (2007) Plant Physiol , vol.144 , pp. 1508-1519
    • Huang, L.1    Sun, Q.2    Qin, F.3    Li, C.4    Zhao, Y.5
  • 39
    • 0037342553 scopus 로고    scopus 로고
    • An enhanced transient expression system in plants based on suppression of gene silencing by the p19 protein of tomato bushy stunt virus
    • Voinnet O, Rivas S, Mestre P, Baulcombe D, (2003) An enhanced transient expression system in plants based on suppression of gene silencing by the p19 protein of tomato bushy stunt virus. Plant J 33: 949-956.
    • (2003) Plant J , vol.33 , pp. 949-956
    • Voinnet, O.1    Rivas, S.2    Mestre, P.3    Baulcombe, D.4
  • 40
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • In: Carter Jr CW, Sweet RM, editors, Academic Press
    • Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. In: Carter Jr CW, Sweet RM, editors. Macromolecular Crystallography, part A: Academic Press. pp. 307-326.
    • (1997) Macromolecular Crystallography , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 42
    • 13244281317 scopus 로고    scopus 로고
    • Coot: model-building tools for molecular graphics
    • Emsley P, Cowtan K, (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60: 2126-2132.
    • (2004) Acta Crystallogr D Biol Crystallogr , vol.60 , pp. 2126-2132
    • Emsley, P.1    Cowtan, K.2
  • 44
    • 0000243829 scopus 로고
    • PROCHECK: a program to check the stereochemical quality of protein structures
    • Laskowski R, MacArthur M, Moss D, Thornton J, (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 26: 283-291.
    • (1993) J Appl Cryst , vol.26 , pp. 283-291
    • Laskowski, R.1    MacArthur, M.2    Moss, D.3    Thornton, J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.