Histone Lysine Demethylases and Their Functions in Plants

Plant Molecular Biology Reporter

Volumn 32, Issue 2, 2014, Pages 558-565

  Luo, Ming ^a   Hung, Fu Yu ^b   Yang, Songguang ^a   Liu, Xuncheng ^a   Wu, Keqiang ^b  

^a SOUTH CHINA INSTITUTE OF BOTANY   (China)

^b NATIONAL TAIWAN UNIVERSITY   (Taiwan)

Author keywords

Chromatin; Epigenetics; Histone demethylase; JmjC; Methylation

Indexed keywords

EUKARYOTA;

EID: 84894270452     PISSN: 07359640     EISSN: 15729818     Source Type: Journal    
DOI: 10.1007/s11105-013-0673-1     Document Type: Article

References (60)

1. Alabadí D, Oyama T, Yanovsky MJ, Harmon FG, Mas P, Kay SA (2001) Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock. Science 293: 880-883.
2. Anand R, Marmorstein R (2007) Structure and mechanism of lysine-specific demethylase enzymes. J Biol Chem 282: 35425-35429.
3. Berger SL (2007) The complex language of chromatin regulation during transcription. Nature 447: 407-412.
4. Binda C, Mattevi A, Edmondson DE (2002a) Structure-function relationships in flavoenzyme-dependent amine oxidations: a comparison of polyamine oxidase and monoamine oxidase. J Biol Chem 277: 23973-23976.
5. Binda C, Newton-Vinson P, Hubalek F, Edmondson DE, Mattevi A (2002b) Structure of human monoamine oxidase B, a drug target for the treatment of neurological disorders. Nat Struct Biol 9: 22-26.
6. Cao Y, Dai Y, Cui SJ, Ma LG (2008) Histone H2B monoubiquitination in the chromatin of FLOWERING LOCUS C regulates flowering time in Arabidopsis. Plant Cell 20: 2586-2602.
7. Chen Q, Chen X, Wang Q, Zhang F, Lou Z, Zhang Q, Zhou DX (2013) Structural basis of a histone H3 lysine 4 demethylase required for stem elongation in rice. PLoS Genet 9: e1003239.
8. Clouse SD (1996) Molecular genetic studies confirm the role of brassinosteroids in plant growth and development. Plant J 10: 1-8.
9. Cui X, Jin P, Gu L, Lu Z, Xue Y, Wei L, Qi J, Song X, Luo M, An G, Cao X (2013) Control of transposon activity by a histone H3K4 demethylase in rice. Proc Natl Acad Sci USA 110: 1953-1958.
10. Culhane JC, Cole PA (2007) LSD1 and the chemistry of histone demethylation. Curr Opin Chem Biol 11: 561-568.
11. Da G, Lenkart J, Zhao K, Shiekhattar R, Cairns BR, Marmorstein R (2006) Structure and function of the SWIRM domain, a conserved protein module found in chromatin regulatory complexes. Proc Natl Acad Sci USA 103: 2057-2062.
12. Dodsworth S (2009) A diverse and intricate signalling network regulates stem cell fate in the shoot apical meristem. Dev Biol 336: 1-9.
13. Du J, Zhong X, Bernatavichute YV, Stroud H, Feng S, Caro E, Vashisht AA, Terragni J, Chin HG, Tu A, Hetzel J, Wohlschlegel JA, Pradhan S, Patel DJ, Jacobsen SE (2012) Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants. Cell 151: 167-180.
14. Fan D, Dai Y, Wang X, Wang Z, He H, Yang H, Cao Y, Deng XW, Ma L (2012) IBM1, a JmjC domain-containing histone demethylase, is involved in the regulation of RNA-directed DNA methylation through the epigenetic control of RDR2 and DCL3 expression in Arabidopsis. Nucleic Acids Res 40: 8905-8916.
15. Feng S, Jacobsen SE (2011) Epigenetic modifications in plants: an evolutionary perspective. Curr Opin Plant Biol 14: 179-186.
16. Gu X, Le C, Wang Y, Li Z, Jiang D, Wang Y, He Y (2013) Arabidopsis FLC clade members form flowering-repressor complexes coordinating responses to endogenous and environmental cues. Nat Commun 4: 1947.
17. Harmer SL, Kay SA (2005) Positive and negative factors confer phase-specific circadian regulation of transcription in Arabidopsis. Plant Cell 17: 1926-1940.
18. He Y, Amasino RM (2005) Role of chromatin modification in flowering-time control. Trends Plant Sci 10: 30-35.
19. Helliwell CA, Wood CC, Robertson M, James Peacock W, Dennis ES (2006) The Arabidopsis FLC protein interacts directly in vivo with SOC1 and FT chromatin and is part of a high-molecular-weight protein complex. Plant J 46: 183-192.
20. Jeong JH, Song HR, Ko JH, Jeong YM, Kwon YE, Seol JH, Amasino RM, Noh B, Noh YS (2009) Repression of FLOWERING LOCUS T chromatin by functionally redundant histone H3 lysine 4 demethylases in Arabidopsis. PLoS One 4: e8033.
21. Jiang D, Yang W, He Y, Amasino RM (2007) Arabidopsis relatives of the human lysine-specific Demethylase1 repress the expression of FWA and FLOWERING LOCUS C and thus promote the floral transition. Plant Cell 19: 2975-2987.
22. Johnson LM, Bostick M, Zhang X, Kraft E, Henderson I, Callis J, Jacobsen SE (2007) The SRA methyl-cytosine-binding domain links DNA and histone methylation. Curr Biol 17: 379-384.
23. Jones MA, Covington MF, DiTacchio L, Vollmers C, Panda S, Harmer SL (2010) Jumonji domain protein JMJD5 functions in both the plant and human circadian systems. Proc Natl Acad Sci USA 107: 21623-21628.
24. Ko JH, Mitina I, Tamada Y, Hyun Y, Choi Y, Amasino RM, Noh B, Noh YS (2010) Growth habit determination by the balance of histone methylation activities in Arabidopsis. EMBO J 29: 3208-3215.
25. Krishna P (2003) Brassinosteroid-mediated stress responses. J Plant Growth Regul 22: 289-297.
26. Lan F, Nottke AC, Shi Y (2008) Mechanisms involved in the regulation of histone lysine demethylases. Curr Opin Cell Biol 20: 316-325.
27. Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev 11: 204-220.
28. Li J, Chory J (1999) Brassinosteroid actions in plants. J Exp Bot 50: 275-282.
29. Li W, Liu H, Cheng ZJ, Su YH, Han HN, Zhang Y, Zhang XS (2011) DNA methylation and histone modifications regulate de novo shoot regeneration in Arabidopsis by modulating WUSCHEL expression and auxin signaling. PLoS Genet 7: e1002243.
30. Lindroth AM, Shultis D, Jasencakova Z, Fuchs J, Johnson L, Schubert D, Patnaik D, Pradhan S, Goodrich J, Schubert I (2004) Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J 23: 4146-4155.
31. Liu F, Quesada V, Crevillen P, Baurle I, Swiezewski S, Dean C (2007) The Arabidopsis RNA-binding protein FCA requires a lysine-specific demethylase 1 homolog to downregulate FLC. Mol Cell 28: 398-407.
32. 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.
33. 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.
34. Lu F, Li G, Cui X, Liu C, Wang XJ, Cao X (2008) Comparative analysis of JmjC domain-containing proteins reveals the potential histone demethylases in Arabidopsis and rice. J Integr Plant Biol 50: 886-896.
35. Malagnac F, Bartee L, Bender J (2002) An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation. EMBO J 21: 6842-6852.
36. Martin C, Zhang Y (2005) The diverse functions of histone lysine methylation. Nat Rev Mol Cell Biol 6: 838-849.
37. Michaels SD, Amasino RM (1999) FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell 11: 949-956.
38. Mizoguchi T, Wheatley K, Hanzawa Y, Wright L, Mizoguchi M, Song HR, Carre IA, Coupland G (2002) LHY and CCA1 are partially redundant genes required to maintain circadian rhythms in Arabidopsis. Dev Cell 2: 629-641.
39. Noh B, Lee SH, Kim HJ, Yi G, Shin EA, Lee M, Jung KJ, Doyle MR, Amasino RM, Noh YS (2004) Divergent roles of a pair of homologous jumonji/zinc-finger-class transcription factor proteins in the regulation of Arabidopsis flowering time. Plant Cell 16: 2601-2613.
40. Pfluger J, Wagner D (2007) Histone modifications and dynamic regulation of genome accessibility in plants. Curr Opin Plant Biol 10: 645-652.
41. Reyes JC (2006) Chromatin modifiers that control plant development. Curr Opin Plant Biol 9: 21-27.
42. Rudolph T, Yonezawa M, Lein S, Heidrich K, Kubicek S, Schäfer C, Phalke S, Walther M, Schmidt A, Jenuwein T (2007) Heterochromatin formation in Drosophila is initiated through active removal of H3K4 methylation by the LSD1 homolog SU (VAR) 3-3. Mol Cell 26: 103-115.
43. Saze H, Shiraishi A, Miura A, Kakutani T (2008) Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana. Science 319: 462-465.
44. 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. Gene Dev 24: 986-991.
45. Shen WH, Xu L (2009) Chromatin remodeling in stem cell maintenance in Arabidopsis thaliana. Mol Plant 2: 600-609.
46. Shi Y, Lan F, Matson C, Mulligan P, Whetstine JR, Cole PA, Casero RA (2004) Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119: 941-953.
47. Stavropoulos P, Blobel G, Hoelz A (2006) Crystal structure and mechanism of human lysine-specific demethylase-1. Nat Struct Mol Biol 13: 626-632.
48. Su YH, Zhao XY, Liu YB, Zhang CL, O'Neill SD, Zhang XS (2009) Auxin-induced WUS expression is essential for embryonic stem cell renewal during somatic embryogenesis in Arabidopsis. Plant J 59: 448-460.
49. Sun Q, Zhou DX (2008) Rice jmjC domain-containing gene JMJ706 encodes H3K9 demethylase required for floral organ development. Proc Natl Acad Sci USA 105: 13679-13684.
50. Sung S, Amasino RM (2004) Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature 427: 159-164.
51. Takeuchi T, Yamazaki Y, Katoh-Fukui Y, Tsuchiya R, Kondo S, Motoyama J, Higashinakagawa T (1995) Gene trap capture of a novel mouse gene, jumonji, required for neural tube formation. Gene Dev 9: 1211-1222.
52. Xu L, Ménard R, Berr A, Fuchs J, Cognat V, Meyer D, Shen WH (2009) The E2 ubiquitin-conjugating enzymes, AtUBC1 and AtUBC2, play redundant roles and are involved in activation of FLC expression and repression of flowering in Arabidopsis thaliana. Plant J 57: 279-288.
53. Yang H, Mo H, Fan D, Cao Y, Cui S, Ma L (2012a) Overexpression of a histone H3K4 demethylase, JMJ15, accelerates flowering time in Arabidopsis. Plant Cell Rep 31: 1297-1308.
54. Yang H, Han Z, Cao Y, Fan D, Li H, Mo H, Feng Y, Liu L, Wang Z, Yue Y, Cui S, Chen S, Chai J, Ma L (2012b) A companion cell-dominant and developmentally regulated H3K4 demethylase controls flowering time in Arabidopsis via the repression of FLC expression. PLoS Genet 8: e1002664.
55. Yang M, Gocke CB, Luo X, Borek D, Tomchick DR, Machius M, Otwinowski Z, Yu H (2006) Structural basis for CoREST-dependent demethylation of nucleosomes by the human LSD1 histone demethylase. Mol Cell 23: 377-387.
56. 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.
57. Yu CW, Liu X, Luo M, Chen C, Lin X, Tian G, Lu Q, Cui Y, Wu K (2011) HISTONE DEACETYLASE6 interacts with FLOWERING LOCUS D and regulates flowering in Arabidopsis. Plant Physiol 156: 173-184.
58. Yu X, Li L, Guo M, Chory J, Yin Y (2008) Modulation of brassinosteroid-regulated gene expression by Jumonji domain-containing proteins ELF6 and REF6 in Arabidopsis. Proc Natl Acad Sci USA 105: 7618-7623.
59. Zhou D-X, Hu Y (2010) Regulatory function of histone modifications in controlling rice gene expression and plant growth. Rice 3: 103-111.
60. Zhou X, Ma H (2008) Evolutionary history of histone demethylase families: distinct evolutionary patterns suggest functional divergence. BMC Evol Biol 8: 294.