Transcription factors in light and circadian clock signaling networks revealed by genomewide mapping of direct targets for neurospora white collar complex

Eukaryotic Cell

Volumn 9, Issue 10, 2010, Pages 1549-1556

  Smith, Kristina M ^a   Sancar, Gencer ^b   Dekhang, Rigzin ^c   Sullivan, Christopher M ^a   Li, Shaojie ^c,e   Tag, Andrew G ^c   Sancar, Cigdem ^b   Bredeweg, Erin L ^a   Priest, Henry D ^a   McCormick, Ryan F ^c   Thomas, Terry L ^c   Carrington, James C ^a   Stajich, Jason E ^d,f   Bell Pedersen, Deborah ^c   Brunner, Michael ^b   Freitag, Michael ^a  

^a OREGON STATE UNIVERSITY   (United States)

^b UNIVERSITY OF HEIDELBERG   (Germany)

^c TEXAS A AND M UNIVERSITY   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e INSTITUTE OF MICROBIOLOGY   (China)

^f UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL PROTEIN; TRANSCRIPTION FACTOR;

ARTICLE; CHROMATIN IMMUNOPRECIPITATION; CIRCADIAN RHYTHM; FUNGAL GENOME; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; HIGH THROUGHPUT NUCLEOTIDE SEQUENCING; LIGHT; METABOLISM; NEUROSPORA CRASSA; PHYSIOLOGY; POLYMERASE CHAIN REACTION; SIGNAL TRANSDUCTION;

CHROMATIN IMMUNOPRECIPITATION; CIRCADIAN CLOCKS; CIRCADIAN RHYTHM; FUNGAL PROTEINS; GENE EXPRESSION REGULATION, FUNGAL; GENE REGULATORY NETWORKS; GENOME, FUNGAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; LIGHT; NEUROSPORA CRASSA; POLYMERASE CHAIN REACTION; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS;

NEUROSPORA; NEUROSPORA CRASSA;

EID: 77956144334     PISSN: 15359778     EISSN: None     Source Type: Journal    
DOI: 10.1128/EC.00154-10     Document Type: Article

References (48)

1. Ballario, P., P. Vittorioso, A. Magrelli, C. Talora, A. Cabibbo, and G. Macino. 1996. WHITE COLLAR-1, a central regulator of blue light responses in Neurospora, is a zinc finger protein. EMBO J. 15:1650-1657.
2. Belden, W. J., J. J. Loros, and J. C. Dunlap. 2007. Execution of the circadian negative feedback loop in Neurospora requires the ATP-dependent chromatin-remodeling enzyme CLOCKSWITCH. Mol. Cell 25:587-600.
3. Campbell, M. A., B. J. Haas, J. P. Hamilton, S. M. Mount, and C. R. Buell. 2006. Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics 7:327.
4. Carlson, J. M., A. Chakravarty, C. E. DeZiel, and R. H. Gross. 2007. SCOPE: a web server for practical de novo motif discovery. Nucleic Acids Res. 35:W259-W264.
5. Cermakian, N., and P. Sassone-Corsi. 2002. Environmental stimulus perception and control of circadian clocks. Curr. Opin. Neurobiol. 12:359-365.
6. Chen, C. H., C. S. Ringelberg, R. H. Gross, J. C. Dunlap, and J. J. Loros. 2009. Genome-wide analysis of light-inducible responses reveals hierarchical light signalling in Neurospora. EMBO J. 28:1029-1042.
7. Cheng, M. Y., C. M. Bullock, C. Li, A. G. Lee, J. C. Bermak, J. Belluzzi, D. R. Weaver, F. M. Leslie, and Q. Y. Zhou. 2002. Prokineticin 2 transmits the behavioural circadian rhythm of the suprachiasmatic nucleus. Nature 417:405-410.
8. Cheng, P., Q. He, L. Wang, and Y. Liu. 2005. Regulation of the Neurospora circadian clock by an RNA helicase. Genes Dev. 19:234-241.
9. Cheng, P., Y. Yang, K. H. Gardner, and Y. Liu. 2002. PAS domain-mediated WC-1/WC-2 interaction is essential for maintaining the steady-state level of WC-1 and the function of both proteins in circadian clock and light responses of Neurospora. Mol. Cell. Biol. 22:517-524.
10. Collett, M. A., J. C. Dunlap, and J. J. Loros. 2001. Circadian clock-specific roles for the light response protein WHITE COLLAR-2. Mol. Cell. Biol. 21:2619-2628.
11. Colot, H. V., G. Park, G. E. Turner, C. Ringelberg, C. M. Crew, L. Litvinkova, R. L. Weiss, K. A. Borkovich, and J. C. Dunlap. 2006. A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors. Proc. Natl. Acad. Sci. U. S. A. 103:10352-10357.
12. Correa, A., Z. A. Lewis, A. V. Greene, I. J. March, R. H. Gomer, and D. Bell-Pedersen. 2003. Multiple oscillators regulate circadian gene expression in Neurospora. Proc. Natl. Acad. Sci. U. S. A. 100:13597-13602.
13. Crosthwaite, S. K., J. J. Loros, and J. C. Dunlap. 1995. Light-induced resetting of a circadian clock is mediated by a rapid increase in frequency transcript. Cell 81:1003-1012.
14. Davis, R. H. 2000. Neurospora: contributions of a model organism. Oxford University Press, Oxford, United Kingdom.
15. Dong, W., X. Tang, Y. Yu, R. Nilsen, R. Kim, J. Griffith, J. Arnold, and H. B. Schüttler. 2008. Systems biology of the clock in Neurospora crassa. PLoS One 3:e3105.
16. Dunlap, J. C., J. J. Loros, H. V. Colot, A. Mehra, W. J. Belden, M. Shi, C. I. Hong, L. F. Larrondo, C. L. Baker, C. H. Chen, C. Schwerdtfeger, P. D. Collopy, J. J. Gamsby, and R. Lambreghts. 2007. A circadian clock in Neurospora: how genes and proteins cooperate to produce a sustained, entrainable, and compensated biological oscillator with a period of about a day. Cold Spring Harbor Symp. Quant. Biol. 72:57-68.
17. Fahlgren, N., C. M. Sullivan, K. D. Kasschau, E. J. Chapman, J. S. Cumbie, T. A. Montgomery, S. D. Gilbert, M. Dasenko, S. A. Givan, and J. C. Carrington. 2009. Computational and analytical framework for small RNA profiling by high-throughput sequencing. RNA 15:992-1002.
18. Froehlich, A. C., Y. Liu, J. J. Loros, and J. C. Dunlap. 2002. WHITE COLLAR-1, a circadian blue light photoreceptor, binding to the frequency promoter. Science 297:815-819.
19. Froehlich, A. C., J. J. Loros, and J. C. Dunlap. 2003. Rhythmic binding of a WHITE COLLAR-containing complex to the frequency promoter is inhibited by FREQUENCY. Proc. Natl. Acad. Sci. U. S. A. 100:5914-5919.
20. Galagan, J. E., S. E. Calvo, K. A. Borkovich, E. U. Selker, N. D. Read, D. Jaffe, W. FitzHugh, L. J. Ma, S. Smirnov, S. Purcell, B. Rehman, T. Elkins, R. Engels, S. Wang, C. B. Nielsen, J. Butler, M. Endrizzi, D. Qui, P. Ianakiev, D. Bell-Pedersen, M. A. Nelson, M. Werner-Washburne, C. P. Selitrennikoff, J. A. Kinsey, E. L. Braun, A. Zelter, U. Schulte, G. O. Kothe, G. Jedd, W. Mewes, C. Staben, E. Marcotte, D. Greenberg, A. Roy, K. Foley, J. Naylor, N. Stange-Thomann, R. Barrett, S. Gnerre, M. Kamal, M. Kamvysselis, E. Mauceli, C. Bielke, S. Rudd, D. Frishman, S. Krystofova, C. Rasmussen, R. L. Metzenberg, D. D. Perkins, S. Kroken, C. Cogoni, G. Macino, D. Catcheside, W. Li, R. J. Pratt, S. A. Osmani, C. P. DeSouza, L. Glass, M. J. Orbach, J. A. Berglund, R. Voelker, O. Yarden, M. Plamann, S. Seiler, J. Dunlap, A. Radford, R. Aramayo, D. O. Natvig, L. A. Alex, G. Mannhaupt, D. J. Ebbole, M. Freitag, I. Paulsen, M. S. Sachs, E. S. Lander, C. Nusbaum, and B. Birren. 2003. The genome sequence of the filamentous fungus Neurospora crassa. Nature 422:859-868.
21. Garceau, N. Y., Y. Liu, J. J. Loros, and J. C. Dunlap. 1997. Alternative initiation of translation and time-specific phosphorylation yield multiple forms of the essential clock protein FREQUENCY. Cell 89:469-476.
22. Görl, M., M. Merrow, B. Huttner, J. Johnson, T. Roenneberg, and M. Brunner. 2001. A PEST-like element in FREQUENCY determines the length of the circadian period in Neurospora crassa. EMBO J. 20:7074-7084.
23. He, Q., J. Cha, H. C. Lee, Y. Yang, and Y. Liu. 2006. CKI and CKII mediate the FREQUENCY-dependent phosphorylation of the WHITE COLLAR COMPLEX to close the Neurospora circadian negative feedback loop. Genes Dev. 20:2552-2565.
24. He, Q., and Y. Liu. 2005. Molecular mechanism of light responses in Neurospora: from light-induced transcription to photoadaptation. Genes Dev. 19:2888-2899.
25. Johnson, D. S., A. Mortazavi, R. M. Myers, and B. Wold. 2007. Genomewide mapping of in vivo protein-DNA interactions. Science 316:1497-1502.
26. Johnson, L., X. Cao, and S. Jacobsen. 2002. Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation. Curr. Biol. 12:1360-1367.
27. Káldi, K., B. H. Gonzalez, and M. Brunner. 2006. Transcriptional regulation of the Neurospora circadian clock gene wc-1 affects the phase of circadian output. EMBO Rep. 7:199-204.
28. Lauter, F. R., V. E. Russo, and C. Yanofsky. 1992. Developmental and light regulation of eas, the structural gene for the rodlet protein of Neurospora. Genes Dev. 6:2373-2381.
29. Lewis, Z. A., A. Correa, C. Schwerdtfeger, K. L. Link, X. Xie, R. H. Gomer, T. Thomas, D. J. Ebbole, and D. Bell-Pedersen. 2002. Overexpression of WHITE COLLAR-1 (WC-1) activates circadian clock-associated genes, but is not sufficient to induce most light-regulated gene expression in Neurospora crassa. Mol. Microbiol. 45:917-931.
30. Li, R., Y. Li, K. Kristiansen, and J. Wang. 2008. SOAP: short oligonucleotide alignment program. Bioinformatics 24:713-714.
31. Linden, H., and G. Macino. 1997. WHITE COLLAR-2, a partner in bluelight signal transduction, controlling expression of light-regulated genes in Neurospora crassa. EMBO J. 16:98-109.
32. Liu, Y., J. Loros, and J. C. Dunlap. 2000. Phosphorylation of the Neurospora clock protein FREQUENCY determines its degradation rate and strongly influences the period length of the circadian clock. Proc. Natl. Acad. Sci. U. S. A. 97:234-239.
33. Luo, C., J. J. Loros, and J. C. Dunlap. 1998. Nuclear localization is required for function of the essential clock protein FRQ. EMBO J. 17:1228-1235.
34. Mikkelsen, T. S., M. Ku, D. B. Jaffe, B. Issac, E. Lieberman, G. Giannoukos, P. Alvarez, W. Brockman, T. K. Kim, R. P. Koche, W. Lee, E. Mendenhall, A. O'Donovan, A. Presser, C. Russ, X. Xie, A. Meissner, M. Wernig, R. Jaenisch, C. Nusbaum, E. S. Lander, and B. E. Bernstein. 2007. Genomewide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448:553-560.
35. Ni, M., and J. H. Yu. 2007. A novel regulator couples sporogenesis and trehalose biogenesis in Aspergillus nidulans. PLoS One 2:e970.
36. Olmedo, M., C. Ruger-Herreros, and L. M. Corrochano. 2010. Regulation by blue light of the fluffy gene encoding a major regulator of conidiation in Neurospora crassa. Genetics 184:651-658.
37. Pavesi, G., P. Mereghetti, G. Mauri, and G. Pesole. 2004. Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. Nucleic Acids Res. 32:W199-W203.
38. Pomraning, K. R., K. M. Smith, and M. Freitag. 2009. Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods 47:142-150.
39. Sargent, M. L., W. R. Briggs, and D. O. Woodward. 1966. Circadian nature of a rhythm expressed by an invertaseless strain of Neurospora crassa. Plant Physiol. 41:1343-1349.
40. Schafmeier, T., A. Diernfellner, A. Schafer, O. Dintsis, A. Neiss, and M. Brunner. 2008. Circadian activity and abundance rhythms of the Neurospora clock transcription factor WCC associated with rapid nucleo-cytoplasmic shuttling. Genes Dev. 22:3397-3402.
41. Schafmeier, T., A. Haase, K. Kaldi, J. Scholz, M. Fuchs, and M. Brunner. 2005. Transcriptional feedback of Neurospora circadian clock gene by phosphorylation-dependent inactivation of its transcription factor. Cell 122:235-246.
42. Stein, L. D., C. Mungall, S. Shu, M. Caudy, M. Mangone, A. Day, E. Nickerson, J. E. Stajich, T. W. Harris, A. Arva, and S. Lewis. 2002. The generic genome browser: a building block for a model organism system database. Genome Res. 12:1599-1610.
43. Taghert, P. H., and O. T. Shafer. 2006. Mechanisms of clock output in the Drosophila circadian pacemaker system. J. Biol. Rhythms 21:445-457.
44. Talora, C., L. Franchi, H. Linden, P. Ballario, and G. Macino. 1999. Role of a WHITE COLLAR-1-WHITE COLLAR-2 complex in blue-light signal transduction. EMBO J. 18:4961-4968.
45. Tamaru, H., X. Zhang, D. McMillen, P. B. Singh, J. Nakayama, S. I. Grewal, C. D. Allis, X. Cheng, and E. U. Selker. 2003. Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa. Nat. Genet. 34:75-79.
46. Thompson, S., N. J. Croft, A. Sotiriou, H. D. Piggins, and S. K. Crosthwaite. 2008. Neurospora crassa heat shock factor-1 is an essential gene; a second heat shock factor-like gene, hsf-2, is required for asexual spore formation. Eukaryot. Cell 7:1573-1581.
47. Vitalini, M. W., R. M. de Paula, W. D. Park, and D. Bell-Pedersen. 2006. The rhythms of life: circadian output pathways in Neurospora. J. Biol. Rhythms 21:432-444.
48. Zhou, L. W., H. Haas, and G. A. Marzluf. 1998. Isolation and characterization of a new gene, sre, which encodes a GATA-type regulatory protein that controls iron transport in Neurospora crassa. Mol. Gen. Genet. 259:532-540.