Rhythmic oscillation of histone acetylation and methylation at the arabidopsis central clock loci

Molecules and Cells

Volumn 34, Issue 3, 2012, Pages 279-287

  Song, Hae Ryong ^a,b   Noh, Yoo Sun ^a,c  

^a Seoul National University   (South Korea)

^b National Institute of Environmental Research   (South Korea)

^c Seoul National University   (South Korea)

Author keywords

Arabidopsis; Chromatin; Circadian clock; Circadian rhythm; Histone modification

Indexed keywords

ARABIDOPSIS PROTEIN; CIRCADIAN CLOCK ASSOCIATED 1; HISTONE H3; LATE ELONGATED HYPOCOTYL; LYSINE; TIMING OF CAB EXPRESSION 1; UNCLASSIFIED DRUG;

ARABIDOPSIS; ARTICLE; CIRCADIAN RHYTHM; GENE ACTIVITY; GENE EXPRESSION; GENE LOCUS; HISTONE ACETYLATION; HISTONE METHYLATION; HISTONE MODIFICATION; NONHUMAN; PROTEIN EXPRESSION;

ACETYLATION; ARABIDOPSIS; ARABIDOPSIS PROTEINS; CIRCADIAN CLOCKS; CIRCADIAN RHYTHM; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION, PLANT; HISTONES; LYSINE; METHYLATION; TRANSCRIPTION FACTORS;

ARABIDOPSIS;

EID: 84870317601     PISSN: 10168478     EISSN: 02191032     Source Type: Journal    
DOI: 10.1007/s10059-012-0103-5     Document Type: Article

References (53)

1. Alabadí, D., Oyama, T., Yanovsky, M.J., Harmon, F.G., Más, P., and Kay, S.A. (2001). Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock. Science 293, 880-883.
2. Belden, W.J., Loros, J.J., and Dunlap, J.C. (2007). Execution of the circadian negative feedback loop in Neurospora requires the ATP-dependent chromatin-remodeling enzyme CLOCKSWITCH. Mol. Cell 25, 587-600.
3. Brown, S.A., Ripperger, J., Kadener, S., Fleury-Olela, F., Vilbois, F., Rosbash, M., and Schibler, U. (2005). PERIOD1-associated proteins modulate the negative limb of the mammalian circadian oscillator. Science 308, 693-696.
4. Cedar, H., and Bergman, Y. (2009). Linking DNA methylation and histone modification: Patterns and paradigms. Nat. Rev. Genet. 10, 295-304.
5. Charron, J.B., He, H., Elling, A.A., and Deng, X.W. (2009). Dynamic landscapes of four histone modifications during deetiolation in Arabidopsis. Plant Cell 21, 3732-3748.
6. Chen, Z.J., and Tian, L. (2007). Roles of dynamic and reversible histone acetylation in plant development and polyploidy. Biochim. Biophys. Acta 1769, 295-307.
7. Cho, J.-N., Ryu, J.-Y., Jeong, Y.-M., Park, J., Song, J.-J., Amasino, R.M., Noh, B., and Noh, Y.-S. (2012). Control of seed germination by light-induced histone arginine demethylation activity. Dev. Cell 22, 736-748.
8. Clapier, C.R., and Cairns, B.R. (2009). The biology of chromatin remodeling complexes. Annu. Rev. Biochem. 78, 273-304.
9. Covington, M.F., Maloof, J.N., Straume, M., Kay, S.A., and Harmer, S.L. (2008). Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development. Genome Biol. 9, R130.
10. Crosio, C., Cermakian, N., Allis, C.D., and Sassone-Corsi, P. (2000). Light induces chromatin modification in cells of the mammalian circadian clock. Nat. Neurosci. 3, 1241-1247.
11. Dodd, A.N., Salathia, N., Hall, A., Kevei, E., Toth, R., Nagy, F., Hibberd, J.M., Millar, A.J., and Webb, A.A. (2005). Plant circadian clocks increase photosynthesis, growth, survival and competitive advantage. Science 309, 630-633.
12. Doi, M., Hirayama, J., and Sassone-Corsi, P. (2006). Circadian regulator CLOCK is a histone acetyltransferase. Cell 125, 497-508.
13. Dowson-Day, M.J., and Millar, A.J. (1999). Circadian dysfunction causes aberrant hypocotyl elongation patterns in Arabidopsis. Plant J. 17, 63-71.
14. Dunlap, J.C. (1990). Closely watched clocks: Molecular analysis of circadian rhythms in Neurospora and Drosophila. Trends Genet. 6, 159-165.
15. Etchegaray, J.P., Lee, C., Wade, P.A., and Reppert, S.M. (2003). Rhythmic histone acetylation underlies transcription in the mammalian circadian clock. Nature 421, 177-182.
16. Etchegaray, J.P., Yang, X., DeBruyne, J.P., Peters, A.H., Weaver, D.R., Jenuwein, T., and Reppert, S.M. (2006). The polycomb group protein EZH2 is required for mammalian circadian clock function. J. Biol. Chem. 281, 21209-21215.
17. Han, S.K., Song, J.D., Noh, Y.S., and Noh, B. (2007). Role of plant CBP/p300-like genes in the regulation of flowering time. Plant J. 49, 103-114.
18. Harmer, S.L. (2009). The circadian system in higher plants. Annu. Rev. Plant Biol. 60, 357-377.
19. Harmer, S.L., Hogenesch, J.B., Straume, M., Chang, H.-S., Han, B., Zhu, T., Wang, X., Kreps, J.A., and Kay, S.A. (2000). Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290, 2110-2113.
20. Hirayama, J., Sahar, S., Grimaldi, B., Tamaru, T., Takamatsu, K., Nakahata, Y., and Sassone-Corsi, P. (2007). CLOCK-mediated acetylation of BMAL1 controls circadian function. Nature 450, 1086-1090.
21. Hollender, C., and Liu, Z. (2008). Histone deacetylase genes in Arabidopsis development. Integr. Plant Biol. 50, 875-885.
22. Imaizumi, T., and Kay, S.A. (2006). Photoperiodic control of flowering: Not only by coincidence. Trends Plant Sci. 11, 550-558.
23. Kim, T., and Buratowski, S. (2009). Dimethylation of H3K4 by Set1 recruits the Set3 histone deacetylase complex to 5′ transcribed regions. Cell 137, 259-272.
24. Kim, S.Y., Lee, J., Eshed-Williams, L., Zilberman, D., and Sung, Z.R. (2012). EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genet. 3, e1002512.
25. Kouzarides, T. (2007). Chromatin modifications and their function. Cell 128, 693-705.
26. Landry, J., Sutton, A., Hesman, T., Min, J., Xu, R.M., Johnston, M., and Sternglanz, R. (2003). Set2-catalyzed methylation of histone H3 represses basal expression of GAL4 in Saccharomyces cerevisiae. Mol. Cell. Biol. 23, 5972-5978.
27. Latham, J.A., and Dent, S.Y.R. (2007). Cross-regulation of histone modifications. Nat. Struct. Mol. Biol. 14, 1017-1024.
28. Lee, J.S., Smith, E., and Shilatifard, A. (2010). The language of histone crosstalk. Cell 142, 682-685.
29. Li, B., Carey, M., and Workman, J.L. (2007). The role of chromatin during transcription. Cell 128, 707-719.
30. Locke, J.C., Kozma-Bognar, L., Gould, P.D., Feher, B., Kevei, E., Nagy, F., Turner, M.S., Hall, A., and Millar, A.J. (2006). Experimental validation of a predicted feedback loop in the multioscillator clock of Arabidopsis thaliana. Mol. Syst. Biol. 2, 59
31. Lorincz, M.C., Dickerson, D.R., Schmitt, M., and Groudine, M. (2004). Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nat. Struct. Mol. Biol. 11, 1068-1075.
32. Masri, S., and Sassone-Corsi, P. (2010). Plasticity and specificity of the circadian epigenome. Nat. Neurosci. 13, 1324-1329.
33. McClung, C.R., and Gutiérrez, R.A. (2010). Network news: Prime time for systems biology of the plant circadian clock. Curr. Opin. Genet. Dev. 20, 588-598.
34. Moore, R.Y. (1997). Circadian rhythms: Basic neurobiology and clinical applications. Annu. Rev. Med. 48, 253-266.
35. Naruse, Y., Oh-hashi, K., Iijima, N., Naruse, M., Yoshioka, H., and Tanaka, M. (2004). Circadian and light-induced transcription of clock gene Per1 depends on histone acetylation and deacetylation. Mol. Cell. Biol. 24, 6278-6287.
36. Niwa, Y., Ito, S., Nakamichi, N., Mizoguchi, T., Niinuma, K., Yamashino, T., and Mizuno, T. (2007). Genetic linkages of the circadian clock-associated genes, TOC1, CCA1 and LHY, in the photoperiodic control of flowering time in Arabidopsis thaliana. Plant Cell Physiol. 48, 925-937.
37. Okitsu, C.Y., and Hsieh, C.-L. (2007). DNA methylation dictates histone H3K4 methylation. Mol. Cell. Biol. 27, 2746-2757.
38. Perales, M., and Más, P. (2007). A functional link between rhythmic changes in chromatin structure and the Arabidopsis biological clock. Plant Cell 19, 2111-2123.
39. Pokholok, D.K., Harbison, C.T., Levine, S., Cole, M., Hannett, N.M., Lee, T.I., Bell, G.W., Walker, K., Rolfe, P.A., Herbolsheimer, E., et al. (2005). Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122, 517-527.
40. Pruneda-Paz, J.L., Breton, G., Para, A., and Kay, S.A. (2009). A functional genomics approach reveals CHE as a component of the Arabidopsis circadian clock. Science 323, 1481-1485.
41. Ripperger, J.A., and Schibler, U. (2006). Rhythmic CLOCK-BMAL1 binding to multiple E-box motifs drives circadian Dbp transcription and chromatin transitions. Nat. Genet. 38, 369-374.
42. Sasaki, T., Kobayashi, A., Saze, H., and Kakutani, T. (2012). RNAiindependent de novo DNA methylation revealed in Arabidopsis mutants of chromatin remodeling gene DDM1. Plant J. 70, 750-758.
43. Schaffer, R., Ramsay, N., Samach, A., Corden, S., Putterill, J., Carré, I.A., and Coupland, G. (1998). The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering. Cell 93, 1219-1229.
44. Song, H.-R., and Noh, Y.-S. (2007). Plants measure the time. J. Plant Biol. 50, 257-265.
45. Strahl, B.D., Grant, P.A., Briggs, S.D., Sun, Z.W., Bone, J.R., Caldwell, J.A., Mollah, S., Cook, R.G., Shabanowitz, J., Hunt, D.F., et al. (2002). Set2 is a nucleosomal histone H3-selective methyltransferase that mediates transcriptional repression. Mol. Cell. Biol. 22, 1298-1306.
46. Tan, M., Luo, H., Lee, S., Jin, F., Yang, J.S., Montellier, E., Buchou, T., Cheng, Z., Rousseaux, S., Rajagopal, N., et al. (2011). Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 146, 1016-1028.
47. To, T.K., Kim, J.M., Matsui, A., Kurihara, Y., Morosawa, T., Ishida, J., Tanaka, M., Endo, T., Kakutani, T., Toyoda, T., et al. (2011). Arabidopsis HDA6 regulates locus-directed heterochromatin silencing in cooperation with MET1. PLoS Genet. 4, e1002055.
48. Vermeulen, M., Mulder, K.W., Denissov, S., Pijnappel, W.W., van Schaik, F.M., Varier, R.A., Baltissen, M.P., Stunnenberg, H.G., Mann, M., and Timmers, H.T. (2007). Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell 131, 58-69.
49. Wang, Z.-Y., and Tobin, E.M. (1998). Constitutive expression of the CIRCADIAN CLOCK ASSOCIATED (CCA1) gene disrupts circadian rhythms and suppresses its own expression. Cell 93, 1207-1217.
50. Wenden, B., Kozma-Bognar, L., Edwards, K.D., Hall, A.J., Locke, J.C., and Millar, A.J. (2011). Light inputs shape the Arabidopsis circadian system. Plant J. 66, 480-491.
51. Yamashino, T., Ito, S., Niwa, Y., Kunihiro, A., Nakamichi, N., and Mizuno, T. (2008). Involvement of Arabidopsis clock-associated pseudo-response regulators in diurnal oscillations of gene expression in the presence of environmental time cues. Plant Cell Physiol. 49, 1839-1850.
52. Yerushalmi, S., Yakir, E., and Green, R.M. (2011). Circadian clocks and adaptation in Arabidopsis. Mol. Ecol. 20, 1155-1165.
53. Zhang, E.E., and Kay, S.A. (2010). Clocks not winding down: Unraveling circadian networks. Nat. Rev. Mol. Cell Biol. 11, 764-776.