Identification of Promoter Motifs Involved in the Network of Phytochrome A-Regulated Gene Expression by Combined Analysis of Genomic Sequence and Microarray Data

Plant Physiology

Volumn 133, Issue 4, 2003, Pages 1605-1616

  Hudson, Matthew E ^a   Quail, Peter H ^b  

^a DIVERSA CORPORATION   (United States)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GENES; GENETIC ENGINEERING; PROTEINS;

TRANSCRIPTION FACTORS;

PLANTS (BOTANY);

ARABIDOPSIS; EMBRYOPHYTA;

EID: 0347859216     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.103.030437     Document Type: Article

References (40)

1. Arguello-Astorga GR, Herrera-Estrella LR (1996) Ancestral multipartite units in light-responsive plant promoters have structural features correlating with specific phototransduction pathways. Plant Physiol 112: 1151-1166
2. Arguello-Astorga GR, Herrera-Estrella LR (1998) Evolution of light-regulated plant promoters. Annu Rev Plant Physiol Plant Mol Biol 49: 525-555
3. Arias JA, Dixon RA, Lamb CJ (1993) Dissection of the functional architecture of a plant defense gene promoter using a homologous in vitro transcription initiation system. Plant Cell 5: 485-496
4. Brace WB, Deng XW, Quail PH (1991) A negatively acting DNA sequence element mediates phytochrome-directed repression of phyA gene transcription. EMBO J 10: 3015-3024
5. Chattopadhyay S, Ang L-H, Puente P, Deng X-W, Wei N (1998) Arabidopsis bZIP protein HY5 directly interacts with light-responsive promoters in mediating light control of gene expression. Plant Cell 10: 673-683
6. Corpet F (1988) Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res 16: 10881-10890
7. Darlington TK, Wager-Smith K, Ceriani MF, Staknis D, Gekakis N, Steeves TD, Weitz CJ, Takahashi JS, Kay SA (1998) Closing the circadian loop: CLOCK-induced transcription of its own inhibitors per and tim. Science 280: 1599-1603
8. Dehesh K, Franci C, Sharrock RA, Somers DE, Welsch JA, Quail PH (1994) The Arabidopsis phytochrome A gene has multiple transcription start sites and a promoter sequence motif homologous to the repressor element of monocot phytochrome A genes. Photochem Photobiol 59: 379-384
9. Futcher B (2002) Transcriptional regulatory networks and the yeast cell cycle. Curr Opin Cell Biol 14: 676-683
10. Gekakis N, Staknis D, Nguyen HB, Davis FC, Wilsbacher LD, King DP, Takahashi JS, Weitz CJ (1998) Role of the CLOCK protein in the mammalian circadian mechanism. Science 280: 1564-1569
11. Giuliano G, Pechersky E, Malik VS, Timko MP, Scolnik PA, Cashmore AR (1988) An evolutionarily conserved protein binding sequence upstream of a plant light-regulated gene. Proc Natl Acad Sci USA 85: 7089-7093
12. Grob U, Stuber K (1987) Discrimination of phytochrome dependent light inducible from non-light indudble plant genes: prediction of a common light-responsive element (LRE) in phytochrome dependent light inducible plant genes. Nucleic Acids Res 15: 9957-9973
13. Harmer SL, Hogenesch JB, Straume M, Chang HS, Han B, Zhu T, Wang X, Kreps JA, Kay SA (2000) Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290: 2110-2113
14. Hogenesch JB, Gu YZ, Jain S, Bradfield CA (1998) The basic-helix-loop- helix-PAS orphan MOP3 forms transcriptionally active complexes with circadian and hypoxia factors. Proc Natl Acad Sci USA 95: 5474-5479
15. Hulzink RJM, Weerdesteyn H, Croes AF, Gerats T, Antonius van Herpen MM, van Helden J (2003) In silico identification of putative regulatory sequence elements in the 5′-untranslated region of genes that are expressed during male gametogenesis. Plant Physiol 132: 75-83
16. Huq E, Quail PH (2002) PIF4, a phytochrome-interacting bHLH factor, functions as a negative regulator of phytochrome B signaling in Arabidopsis. EMBO J 21: 2441-2450
17. Fairchild CD, Schumaker MA, Quail PH (2000) HFR1 encodes an atypical bHLH protein that acts in phytochrome A signal transduction. Genes Dev 14: 2377-2391
18. Inaba T, Nagano Y, Reid JB, Sasaki Y (2000) DE1: a 12 bp cis-regulatory element sufficient to confer dark-inducible and light down-regulated expression to a minimal promoter in pea. J Biol Chem 275: 19723-19727
19. Inaba T, Nagano Y, Sakakibara T, Sasaki Y (1999) Identification of a cis-regulatory element involved in phytochrome down-regulated expression of the pea small GTPase gene pra2. Plant Physiol 120: 491-500
20. Jensen LJ, Knudsen S (2000) Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation. Bioinformatics 16: 326-333
21. Lohmer S, Maddaloni M, Motto M, Di Fonzo N, Hartings H, Salamini F, Thompson RD (1991) The maize regulatory locus Opaque-2 encodes a DNA-binding protein which activates the transcription of the b-32 gene. EMBO J 10: 617-624
22. Martinez-Garcia JF, Huq E, Quail PH (2000) Direct targeting of light signals to a promoter element-bound transcription factor. Science 288: 859-863
23. Menkens AE, Schindler U, Cashmore AR (1995) The G-box: a ubiquitous regulatory DNA element in plants bound by the GBF family of bZIP proteins. Trends Biochem Sci 20: 506-510
24. Michael TP, McClung CR (2003) Enhancer trapping reveals widespread circadian clock transcriptional control in Arabidopsis. Plant Physiol 132: 629-639
25. Ni M, Tepperman JM, Quail PH (1999) Binding of phytochrome B to its nuclear signalling partner PIF3 is reversibly induced by light. Nature 400: 781-784
26. Ohler U, Niemann H (2001) Identification and analysis of eukaryotic promoters: recent computational approaches. Trends Genet 17: 56-60
27. Oyama T, Shimura Y, Okada K (1997) The Arabidopsis HY5 gene encodes a bZIP protein that regulates stimulus-induced development of root and hypocotyl. Genes Dev 11: 2983-2995
28. Putterill J, Robson F, Lee K, Simon R, Coupland G (1995) The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc finger transcription factors. Cell 80: 847-857
29. Roth FP, Hughes JD, Estep PW, Church GM (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol 16: 939-945
30. Sakai H, Honma T, Aoyama T, Sato S, Kato T, Tabata S, Oka A (2001) ARR1, a transcription factor for genes immediately responsive to cytokinins. Science 294: 1519-1521
31. Salinas J, Oeda K, Chua NH (1992) Two G-box-related sequences confer different expression patterns in transgenic tobacco. Plant Cell 4: 1485-1493
32. Smith H (2000) Phytochromes and light signal perception by plants: an emerging synthesis. Nature 407: 585-591
33. Stockinger EJ, Gilmour SJ, Thomashow MF (1997) Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit. Proc Natl Acad Sci USA 94: 1035-1040
34. Tepperman JM, Zhu T, Chang HS, Wang X, Quail PH (2001) Multiple transcription-factor genes are early targets of phytochrome A signaling. Proc Natl Acad Sci USA 98: 9437-9442
35. Terzaghi WB, Cashmore AR (1995) Light-regulated transcription. Annu Rev Plant Physiol Plant Mol Biol 46: 445-474
36. Thijs G, Marchal K, Lescot M, Rombauts S, De Moor B, Rouze P, Moreau Y (2002) A gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. J Comput Biol 9: 447-464
37. Toledo-Oritz G, Huq E, Quail PH (2003) The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell 15: 1749-1770
38. van Helden J, Andre B, Collado-Vides J (1998) Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J Mol Biol 281: 827-842
39. Vanet A, Marsan L, Labigne A, Sagot MF (2000) Inferring regulatory elements from a whole genome. An analysis of Helicobacter pylori sigma(80) family of promoter signals. J Mol Biol 297: 335-353
40. Zhu T, Wang X (2000) Large-scale profiling of the Arabidopsis transcriptome. Plant Physiol 124: 1472-1476