Chromatin remodeling and the circadian clock: Jumonji c domain-containing proteins

Plant Signaling and Behavior

Volumn 6, Issue 6, 2011, Pages 810-814

  Lu, Sheen X ^a   Tobin, Elaine M ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Arabidopsis; Chromatin remodeling; Circadian clock; Circadian rhythm; Histone demethylase; Jumonji c domain

Indexed keywords

HISTONE DEMETHYLASE; VEGETABLE PROTEIN;

ARABIDOPSIS; BIOLOGICAL MODEL; CHROMATIN ASSEMBLY AND DISASSEMBLY; CIRCADIAN RHYTHM; GENETICS; METABOLISM; PHYSIOLOGY; REVIEW;

ARABIDOPSIS; CHROMATIN ASSEMBLY AND DISASSEMBLY; CIRCADIAN CLOCKS; JUMONJI DOMAIN-CONTAINING HISTONE DEMETHYLASES; MODELS, BIOLOGICAL; PLANT PROTEINS;

ANIMALIA; ARABIDOPSIS; PROKARYOTA;

EID: 79958262049     PISSN: 15592316     EISSN: 15592324     Source Type: Journal    
DOI: 10.4161/psb.6.6.15171     Document Type: Review

References (60)

1. Ouyang Y, Andersson CR, Kondo T, Golden SS, Johnson CH. Resonating circadian clocks enhance fitness in cyanobacteria. Proc Natl Acad Sci USA 1998; 95:8660-4.
2. Green RM, Tingay S, Wang ZY, Tobin EM. Circadian rhythms confer a higher level of fitness to Arabidopsis plants. Plant Physiol 2002; 129:576-84.
3. Dodd AN, Salathia N, Hall A, Kevei E, Toth R, Nagy F, et al. Plant circadian clocks increase photosynthesis, growth, survival and competitive advantage. Science 2005; 309:630-3.
4. Moore RY. Circadian rhythms: basic neurobiology and clinical applications. Annu Rev Med 1997; 48:253-66.
5. Dunlap JC. Closely watched clocks: molecular analysis of circadian rhythms in Neurospora and Drosophila. Trends Genet 1990; 6:159-65.
6. Imaizumi T, Kay SA. Photoperiodic control of flowering: not only by coincidence. Trends Plant Sci 2006; 11:550-8.
7. Dowson-Day MJ, Millar AJ. Circadian dysfunction causes aberrant hypocotyl elongation patterns in Arabidopsis. Plant J 1999; 17:63-71.
8. Schaffer R, Ramsay N, Samach A, Corden S, Putterill J, Carre IA, et al. The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering. Cell 1998; 93:1219-29.
9. Wang ZY, Tobin EM. Constitutive expression of the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) gene disrupts circadian rhythms and suppresses its own expression. Cell 1998; 93:1207-17.
10. Knowles SM, Lu SX, Tobin EM. Testing Time: Can Ethanol-Induced Pulses of Proposed Oscillator Components Phase Shift Rhythms in Arabidopsis? J Biol Rhyth 2008; 23:463-71.
11. Locke JC, Southern MM, Kozma-Bognar L, Hibberd V, Brown PE, Turner MS, et al. Extension of a genetic network model by iterative experimentation and mathematical analysis. Mol Syst Biol 2005; 1:13.
12. Lu SX, Knowles SM, Andronis C, Ong MS, Tobin EM. CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL function synergistically in the circadian clock of Arabidopsis. Plant Physiol 2009; 150:834-43.
13. Strayer C, Oyama T, Schultz TF, Raman R, Somers DE, Más P, et al. Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homolog. Science 2000; 289:768-71.
14. Más P, Alabadi D, Yanovsky MJ, Oyama T, Kay SA. Dual role of TOC1 in the control of circadian and photomorphogenic responses in Arabidopsis. Plant Cell 2003; 15:223-36.
15. Somers DE, Webb AA, Pearson M, Kay SA. The shortperiod mutant, toc1-1, alters circadian clock regulation of multiple outputs throughout development in Arabidopsis thaliana. Development 1998; 125:485-94.
16. Alabadi D, Oyama T, Yanovsky MJ, Harmon FG, Más P, Kay SA. Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock. Science 2001; 293:880-3.
17. Perales M, Más P. A functional link between rhythmic changes in chromatin structure and the Arabidopsis biological clock. Plant Cell 2007; 19:2111-23.
18. Pruneda-Paz JL, Breton G, Para A, Kay SA. A functional genomics approach reveals CHE as a component of the Arabidopsis circadian clock. Science 2009; 323:1481-5.
19. Hazen SP, Schultz TF, Pruneda-Paz JL, Borevitz JO, Ecker JR, Kay SA. LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms. Proc Natl Acad Sci USA 2005; 102:10387-92.
20. Onai K, Ishiura M. PHYTOCLOCK 1 encoding a novel GARP protein essential for the Arabidopsis circadian clock. Genes Cells 2005; 10:963-72.
21. Doyle MR, Davis SJ, Bastow RM, McWatters HG, Kozma-Bognar L, Nagy F, et al. The ELF4 gene controls circadian rhythms and flowering time in Arabidopsis thaliana. Nature 2002; 419:74-7.
22. Kikis EA, Khanna R, Quail PH. ELF4 is a phytochrome- regulated component of a negative-feedback loop involving the central oscillator components CCA1 and LHY. Plant J 2005; 44:300-13.
23. Covington MF, Panda S, Liu XL, Strayer CA, Wagner DR, Kay SA. ELF3 modulates resetting of the circadian clock in Arabidopsis. Plant Cell 2001; 13:1305-15.
24. Liu XL, Covington MF, Fankhauser C, Chory J, Wagner DR. ELF3 encodes a circadian clock-regulated nuclear protein that functions in an Arabidopsis PHYB signal transduction pathway. Plant Cell 2001; 13:1293-304.
25. Nakamichi N, Kiba T, Henriques R, Mizuno T, Chua NH, Sakakibara H. PSEUDO-RESPONSE REGULATORS 9, 7 and 5 are transcriptional repressors in the Arabidopsis circadian clock. Plant Cell 2010; 22:594-605.
26. Farre EM, Harmer SL, Harmon FG, Yanovsky MJ, Kay SA. Overlapping and distinct roles of PRR7 and PRR9 in the Arabidopsis circadian clock. Curr Biol 2005; 15:47-54.
27. Locke JC, Southern MM, Kozma-Bognar L, Hibberd V, Brown PE, Turner MS, et al. Extension of a genetic network model by iterative experimentation and mathematical analysis. Mol Syst Biol 2005; 1:13.
28. McClung CR. Plant circadian rhythms. Plant Cell 2006; 18:792-803.
29. Duffield GE, Best JD, Meurers BH, Bittner A, Loros JJ, Dunlap JC. Circadian programs of transcriptional activation, signaling and protein turnover revealed by microarray analysis of mammalian cells. Curr Biol 2002; 12:551-7.
30. Edwards KD, Anderson PE, Hall A, Salathia NS, Locke JC, Lynn JR, et al. FLOWERING LOCUS C mediates natural variation in the high-temperature response of the Arabidopsis circadian clock. Plant Cell 2006; 18:639-50.
31. Michael TP, Mockler TC, Breton G, McEntee C, Byer A, Trout JD, et al. Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules. PLoS Genet 2008; 4:e14.
32. Jenuwein T, Allis CD. Translating the histone code. Science 2001; 293:1074-80.
33. Kouzarides T. Chromatin modifications and their function. Cell 2007; 128:693-705.
34. Belden WJ, Loros JJ, Dunlap JC. Execution of the circadian negative feedback loop in Neurospora requires the ATP-dependent chromatin-remodeling enzyme CLOCKSWITCH. Mol Cell 2007; 25:587-600.
35. Etchegaray JP, Lee C, Wade PA, Reppert SM. Rhythmic histone acetylation underlies transcription in the mammalian circadian clock. Nature 2003; 421:177-82.
36. Doi M, Hirayama J, Sassone-Corsi P. Circadian regulator CLOCK is a histone acetyltransferase. Cell 2006; 125:497-508.
37. Etchegaray JP, Yang X, DeBruyne JP, Peters AH, Weaver DR, Jenuwein T, et al. The polycomb group protein EZH2 is required for mammalian circadian clock function. J Biol Chem 2006; 281:21209-15.
38. Brown SA, Ripperger J, Kadener S, Fleury-Olela F, Vilbois F, Rosbash M, et al. PERIOD1-associated proteins modulate the negative limb of the mammalian circadian oscillator. Science 2005; 308:693-6.
39. Ni Z, Kim ED, Ha M, Lackey E, Liu J, Zhang Y, et al. Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature 2009; 457:327-31.
40. Jones MA, Covington MF, Ditacchio L, Vollmers C, Panda S, Harmer SL. Jumonji domain protein JMJD5 functions in both the plant and human circadian systems. Proc Natl Acad Sci USA 2010; 107:21623-8.
41. Lu SX, Knowles SM, Webb CJ, Celaya RB, Cha C, Siu JP, et al. The JmjC domain-containing protein JMJ30 regulates period length in the Arabidopsis circadian clock. Plant Physiol 2011; 155:906-15.
42. Mosammaparast N, Shi Y. Reversal of histone methylation: biochemical and molecular mechanisms of histone demethylases. Annu Rev Biochem 2010; 79:155-79.
43. Tsukada Y, Fang J, Erdjument-Bromage H, Warren ME, Borchers CH, Tempst P, et al. Histone demethylation by a family of JmjC domain-containing proteins. Nature 2006; 439:811-6.
44. Loh YH, Zhang W, Chen X, George J, Ng HH. Jmjd1a and Jmjd2c histone H3 Lys 9 demethylases regulate self-renewal in embryonic stem cells. Genes Dev 2007; 21:2545-57.
45. Lan F, Bayliss PE, Rinn JL, Whetstine JR, Wang JK, Chen S, et al. A histone H3 lysine 27 demethylase regulates animal posterior development. Nature 2007; 449:689-94.
46. Hsia DA, Tepper CG, Pochampalli MR, Hsia EY, Izumiya C, Huerta SB, et al. KDM8, a H3K36me2 histone demethylase that acts in the cyclin A1 coding region to regulate cancer cell proliferation. Proc Natl Acad Sci USA 2010; 107:9671-6.
47. Suzuki T, Minehata K, Akagi K, Jenkins NA, Copeland NG. Tumor suppressor gene identification using retroviral insertional mutagenesis in Blm-deficient mice. EMBO J 2006; 25:3422-31.
48. Iwase S, Lan F, Bayliss P, de la Torre-Ubieta L, Huarte M, Qi HH, et al. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell 2007; 128:1077-88.
49. Jepsen K, Solum D, Zhou T, McEvilly RJ, Kim HJ, Glass CK, et al. SMRT-mediated repression of an H3K27 demethylase in progression from neural stem cell to neuron. Nature 2007; 450:415-9.
50. Tateishi K, Okada Y, Kallin EM, Zhang Y. Role of Jhdm2a in regulating metabolic gene expression and obesity resistance. Nature 2009; 458:757-61.
51. Hong EH, Jeong YM, Ryu JY, Amasino RM, Noh B, Noh YS. Temporal and spatial expression patterns of nine Arabidopsis genes encoding Jumonji C-domain proteins. Mol Cells 2009; 27:481-90.
52. Lu F, Li G, Cui X, Liu C, Wang XJ, Cao X. Comparative analysis of JmjC domain-containing proteins reveals the potential histone demethylases in Arabidopsis and rice. J Integr Plant Biol 2008; 50:886-96.
53. Pagnussat GC, Yu HJ, Ngo QA, Rajani S, Mayalagu S, Johnson CS, et al. Genetic and molecular identification of genes required for female gametophyte development and function in Arabidopsis. Development 2005; 132:603-14.
54. Saze H, Shiraishi A, Miura A, Kakutani T. Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana. Science 2008; 319:462-5.
55. Yu X, Li L, Guo M, Chory J, Yin Y. Modulation of brassinosteroid-regulated gene expression by Jumonji domaincontaining proteins ELF6 and REF6 in Arabidopsis. Proc Natl Acad Sci USA 2008; 105:7618-23.
56. Searle IR, Pontes O, Melnyk CW, Smith LM, Baulcombe DC. JMJ14, a JmjC domain protein, is required for RNA silencing and cell-to-cell movement of an RNA silencing signal in Arabidopsis. Genes Dev 2010; 24:986-91.
57. Deleris A, Greenberg MV, Ausin I, Law RW, Moissiard G, Schubert D, et al. Involvement of a Jumonji-C domain-containing histone demethylase in DRM2-mediated maintenance of DNA methylation. EMBO Rep 2010; 11:950-5.
58. Noh B, Lee SH, Kim HJ, Yi G, Shin EA, Lee M, et al. Divergent roles of a pair of homologous jumonji/ zinc-finger-class transcription factor proteins in the regulation of Arabidopsis flowering time. Plant Cell 2004; 16:2601-13.
59. Yang W, Jiang D, Jiang J, He Y. A plant-specific histone H3 lysine 4 demethylase represses the floral transition in Arabidopsis. Plant J 2010; 62:663-73.
60. Lu F, Cui X, Zhang S, Liu C, Cao X. JMJ14 is an H3K4 demethylase regulating flowering time in Arabidopsis. Cell Res 2010; 20:387-90.