Execution of the Circadian Negative Feedback Loop in Neurospora Requires the ATP-Dependent Chromatin-Remodeling Enzyme CLOCKSWITCH

Molecular Cell

Volumn 25, Issue 4, 2007, Pages 587-600

  Belden, William J ^a   Loros, Jennifer J ^a   Dunlap, Jay C ^a  

^a DARTMOUTH MEDICAL SCHOOL   (United States)

Author keywords

CELLCYCLE; DNA

Indexed keywords

ADENOSINE TRIPHOSPHATE; CLOCKSWITCH PROTEIN; DNA BINDING PROTEIN; GENE PRODUCT; HISTONE; NUCLEASE; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR CLOCK; TRANSCRIPTION FACTOR WC 1; TRANSCRIPTION FACTOR WC 2; UNCLASSIFIED DRUG;

ACETYLATION; ARTICLE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN IMMUNOPRECIPITATION; CHROMATIN STRUCTURE; CIRCADIAN RHYTHM; COMPLEX FORMATION; CONTROLLED STUDY; CSW 1 GENE; ENZYME ANALYSIS; FRQ GENE; FUNGAL GENE; FUNGAL GENETICS; GENE DELETION; GENE EXPRESSION REGULATION; GENE FUNCTION; GENOTYPE PHENOTYPE CORRELATION; NEGATIVE FEEDBACK; NEUROSPORA; NONHUMAN; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN DNA BINDING; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN MODIFICATION; SEQUENCE HOMOLOGY; TRANSCRIPTION REGULATION; TRANSCRIPTOMICS;

ACETYLATION; ADENOSINE TRIPHOSPHATE; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; CIRCADIAN RHYTHM; DNA, FUNGAL; FEEDBACK, BIOCHEMICAL; FUNGAL PROTEINS; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; HISTONES; MUTATION; NEUROSPORA CRASSA; PROMOTER REGIONS (GENETICS); PROTEIN BINDING; RNA, MESSENGER; SEQUENCE HOMOLOGY;

NEUROSPORA;

EID: 33847021355     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2007.01.010     Document Type: Article

References (55)

1. Aronson B.D., Johnson K.A., Loros J.J., and Dunlap J.C. Negative feedback defining a circadian clock: autoregulation of the clock gene frequency. Science 263 (1994) 1578-1584
2. Ausubel F.M., Brent R., Kingston R.E., Moore D.D., Seidman J.G., Smith J.A., and Struhl K. Current Protocols in Molecular Biology (1994), John Wiley & Sons, New York
3. Bell-Pedersen D., Cassone V.M., Earnest D.J., Golden S.S., Hardin P.E., Thomas T.L., and Zoran M.J. Circadian rhythms from multiple oscillators: lessons from diverse organisms. Nat. Rev. Genet. 6 (2005) 544-556
4. Boeger H., Griesenbeck J., Strattan J.S., and Kornberg R.D. Nucleosomes unfold completely at a transcriptionally active promoter. Mol. Cell 11 (2003) 1587-1598
5. Borkovich K.A., Alex L.A., Yarden O., Freitag M., Turner G.E., Read N.D., Seiler S., Bell-Pedersen D., Paietta J., Plesofsky N., et al. Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiol. Mol. Biol. Rev. 68 (2004) 1-108
6. Brunner M., and Schafmeier T. Transcriptional and post-transcriptional regulation of the circadian clock of cyanobacteria and Neurospora. Genes Dev. 20 (2006) 1061-1074
7. Cheng P., Yang Y., Heintzen C., and Liu Y. Coiled-coil domain-mediated FRQ-FRQ interaction is essential for its circadian clock function in Neurospora. EMBO J. 20 (2001) 101-108
8. Cheng P., Yang Y., and Liu Y. Interlocked feedback loops contribute to the robustness of the Neurospora circadian clock. Proc. Natl. Acad. Sci. USA 98 (2001) 7408-7413
9. Cheng P., He Q., Wang L., and Liu Y. Regulation of the Neurospora circadian clock by an RNA helicase. Genes Dev. 19 (2005) 234-241
10. Collins G.A., and Tansey W.P. The proteasome: a utility tool for transcription?. Curr. Opin. Genet. Dev. 16 (2006) 197-202
11. Colot H.V., Loros J.J., and Dunlap J.C. Temperature-modulated alternative splicing and promoter use in the Circadian clock gene frequency. Mol. Biol. Cell 16 (2005) 5563-5571
12. Colot H.V., Park G., Turner G.E., Ringelberg C., Crew C.M., Litvinkova L., Weiss R.L., Borkovich K.A., and Dunlap J.C. A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors. Proc. Natl. Acad. Sci. USA 103 (2006) 10352-10357
13. Crosthwaite S.K., Loros J.J., and Dunlap J.C. Light-induced resetting of a circadian clock is mediated by a rapid increase in frequency transcript. Cell 81 (1995) 1003-1012
14. Crosthwaite S.K., Dunlap J.C., and Loros J.J. Neurospora wc-1 and wc-2: transcription, photoresponses, and the origins of circadian rhythmicity. Science 276 (1997) 763-769
15. de la Serna I.L., Ohkawa Y., and Imbalzano A.N. Chromatin remodelling in mammalian differentiation: lessons from ATP-dependent remodellers. Nat. Rev. Genet. 7 (2006) 461-473
16. Denault D.L., Loros J.J., and Dunlap J.C. WC-2 mediates WC-1-FRQ interaction within the PAS protein-linked circadian feedback loop of Neurospora. EMBO J. 20 (2001) 109-117
17. Doi M., Hirayama J., and Sassone-Corsi P. Circadian regulator CLOCK is a histone acetyltransferase. Cell 125 (2006) 497-508
18. Dunlap J.C. Molecular bases for circadian clocks. Cell 96 (1999) 271-290
19. Dunlap J.C. Proteins in the Neurospora circadian clockworks. J. Biol. Chem. 281 (2006) 28489-28493
20. Dunlap J.C., and Loros J.J. Analysis of circadian rhythms in Neurospora: overview of assays and genetic and molecular biological manipulation. Methods Enzymol. 393 (2005) 3-22
21. Etchegaray J.P., Lee C., Wade P.A., and Reppert S.M. Rhythmic histone acetylation underlies transcription in the mammalian circadian clock. Nature 421 (2003) 177-182
22. Etchegaray J.P., Yang X., DeBruyne J.P., Peters A.H., Weaver D.R., Jenuwein T., and Reppert S.M. The polycomb group protein EZH2 is required for mammalian circadian clock function. J. Biol. Chem. 281 (2006) 21209-21215
23. Fischle W., Wang Y., and Allis C.D. Histone and chromatin cross-talk. Curr. Opin. Cell Biol. 15 (2003) 172-183
24. Fragoso G., John S., Roberts M.S., and Hager G.L. Nucleosome positioning on the MMTV LTR results from the frequency-biased occupancy of multiple frames. Genes Dev. 9 (1995) 1933-1947
25. Froehlich A.C., Liu Y., Loros J.J., and Dunlap J.C. White Collar-1, a circadian blue light photoreceptor, binding to the frequency promoter. Science 297 (2002) 815-819
26. Froehlich A.C., Loros J.J., and Dunlap J.C. Rhythmic binding of a WHITE COLLAR-containing complex to the frequency promoter is inhibited by FREQUENCY. Proc. Natl. Acad. Sci. USA 100 (2003) 5914-5919
27. Garceau N.Y., Liu Y., Loros J.J., and Dunlap J.C. Alternative initiation of translation and time-specific phosphorylation yield multiple forms of the essential clock protein FREQUENCY. Cell 89 (1997) 469-476
28. Grimaldi B., Coiro P., Filetici P., Berge E., Dobosy J.R., Freitag M., Selker E.U., and Ballario P. The Neurospora crassa White Collar-1 dependent blue light response requires acetylation of histone H3 lysine 14 by NGF-1. Mol. Biol. Cell 17 (2006) 4576-4583
29. He Q., and Liu Y. Molecular mechanism of light responses in Neurospora: from light-induced transcription to photoadaptation. Genes Dev. 19 (2005) 2888-2899
30. He Q., Cheng P., Yang Y., Wang L., Gardner K.H., and Liu Y. White collar-1, a DNA binding transcription factor and a light sensor. Science 297 (2002) 840-843
31. He Q., Cha J., He Q., Lee H.C., Yang Y., and Liu Y. CKI and CKII mediate the FREQUENCY-dependent phosphorylation of the WHITE COLLAR complex to close the Neurospora circadian negative feedback loop. Genes Dev. 20 (2006) 2552-2565
32. Heintzen C., Loros J.J., and Dunlap J.C. The PAS protein VIVID defines a clock-associated feedback loop that represses light input, modulates gating, and regulates clock resetting. Cell 104 (2001) 453-464
33. Hirayama J., and Sassone-Corsi P. Structural and functional features of transcription factors controlling the circadian clock. Curr. Opin. Genet. Dev. 15 (2005) 548-556
34. Komarnitsky P., Cho E.J., and Buratowski S. Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev. 14 (2000) 2452-2460
35. Kuras L., and Struhl K. Binding of TBP to promoters in vivo is stimulated by activators and requires Pol II holoenzyme. Nature 399 (1999) 609-613
36. Lee K., Loros J.J., and Dunlap J.C. Interconnected feedback loops in the Neurospora circadian system. Science 289 (2000) 107-110
37. Lee C., Etchegaray J.P., Cagampang F.R., Loudon A.S., and Reppert S.M. Posttranslational mechanisms regulate the mammalian circadian clock. Cell 107 (2001) 855-867
38. Liu Y., and Bell-Pedersen D. Circadian rhythms in Neurospora crassa and other filamentous fungi. Eukaryot. Cell 5 (2006) 1184-1193
39. Luo C., Loros J.J., and Dunlap J.C. Nuclear localization is required for function of the essential clock protein FRQ. EMBO J. 17 (1998) 1228-1235
40. Mellor J. The dynamics of chromatin remodeling at promoters. Mol. Cell 19 (2005) 147-157
41. Mellor J. Dynamic nucleosomes and gene transcription. Trends Genet. 22 (2006) 320-329
42. Metivier R., Penot G., Hubner M.R., Reid G., Brand H., Kos M., and Gannon F. Estrogen receptor-alpha directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 115 (2003) 751-763
43. Mizuguchi G., Shen X., Landry J., Wu W.H., Sen S., and Wu C. ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science 303 (2004) 343-348
44. Narlikar G.J., Fan H.Y., and Kingston R.E. Cooperation between complexes that regulate chromatin structure and transcription. Cell 108 (2002) 475-487
45. 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. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122 (2005) 517-527
46. Raisner R.M., Hartley P.D., Meneghini M.D., Bao M.Z., Liu C.L., Schreiber S.L., Rando O.J., and Madhani H.D. Histone variant H2A.Z marks the 5′ ends of both active and inactive genes in euchromatin. Cell 123 (2005) 233-248
47. Reinke H., and Horz W. Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. Mol. Cell 11 (2003) 1599-1607
48. Reppert S.M., and Weaver D.R. Coordination of circadian timing in mammals. Nature 418 (2002) 935-941
49. Ripperger J.A., and Schibler U. Rhythmic CLOCK-BMAL1 binding to multiple E-box motifs drives circadian Dbp transcription and chromatin transitions. Nat. Genet. 38 (2006) 369-374
50. Roh T.Y., Ngau W.C., Cui K., Landsman D., and Zhao K. High-resolution genome-wide mapping of histone modifications. Nat. Biotechnol. 22 (2004) 1013-1016
51. Schafmeier T., Haase A., Kaldi K., Scholz J., Fuchs M., and Brunner M. Transcriptional feedback of Neurospora circadian clock gene by phosphorylation-dependent inactivation of its transcription factor. Cell 122 (2005) 235-246
52. Schafmeier T., Kaldi K., Diernfellner A., Mohr C., and Brunner M. Phosphorylation-dependent maturation of Neurospora circadian clock protein from a nuclear repressor toward a cytoplasmic activator. Genes Dev. 20 (2006) 297-306
53. Strahl B.D., and Allis C.D. The language of covalent histone modifications. Nature 403 (2000) 41-45
54. Talora C., Franchi L., Linden H., Ballario P., and Macino G. Role of a White collar-1-White collar-2 complex in blue-light signal transduction. EMBO J. 18 (1999) 4961-4968
55. Zhang H., Roberts D.N., and Cairns B.R. Genome-wide dynamics of Htz1, a histone H2A variant that poises repressed/basal promoters for activation through histone loss. Cell 123 (2005) 219-231