Cis-regulatory element based targeted gene finding: Genome-wide identification of abscisic acid- and abiotic stress-responsive genes in Arabidopsis thaliana

Bioinformatics

Volumn 21, Issue 14, 2005, Pages 3074-3081

  Zhang, Weixiong ^a,b   Ruan, Jianhua ^a   Ho, Tuan Hua David ^b   You, Youngsook ^b   Yu, Taotao ^a   Quatrano, Ralph S ^b  

^a WASHINGTON UNIVERSITY IN ST LOUIS   (United States)

^b WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABSCISIC ACID; PHYTOHORMONE; ARABIDOPSIS PROTEIN;

ACCURACY; ARABIDOPSIS; ARTICLE; CEREAL; COLD; DROUGHT; GENE TARGETING; GENETIC IDENTIFICATION; GENETIC TRANSCRIPTION; GENOME ANALYSIS; GENOMICS; NONHUMAN; PLANT GENETICS; PLANT STRESS; PREDICTION; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RICE; SALINITY; CHROMOSOME MAP; COMPARATIVE STUDY; DNA SEQUENCE; DRUG EFFECT; ENHANCER REGION; EVALUATION; GENE EXPRESSION PROFILING; GENETICS; GENOME; METHODOLOGY; OPEN READING FRAME; OXIDATIVE STRESS; PHYSIOLOGY; PROMOTER REGION; REGULATOR GENE; SEQUENCE ALIGNMENT; VALIDATION STUDY;

ARABIDOPSIS THALIANA;

ABSCISIC ACID; ARABIDOPSIS; ARABIDOPSIS PROTEINS; CHROMOSOME MAPPING; ENHANCER ELEMENTS (GENETICS); GENE EXPRESSION PROFILING; GENE TARGETING; GENES, REGULATOR; GENOME, PLANT; OPEN READING FRAMES; OXIDATIVE STRESS; PROMOTER REGIONS (GENETICS); SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 25144457599     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti490     Document Type: Article

References (37)

1. Bailey,T. and Elkan,C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In Proceedings of the 2nd ISMB Conference, Palo Alto, CA, pp. 28-36.
2. Brivanlou,A. and Darnell,J. (2002) Signal transduction and the control of gene expression. Science, 295, 813-818.
3. Busk,P. and Pages,M. (1997) Protein binding to the abscisic acid-responsive element is independent of viviparous1 in vivo. Plant Cell, 9, 2261-2270.
4. Busk,P. et al. (1997) Regulatory elements in vivo in the promoter of the abscisic acid responsive gene rab17 from maize. Plant J., 11, 1285-1295.
5. Carles,C. et al. (2002) Regulation of Arabidopsis thaliana Em genes: Role of ABI5. Plant J., 30, 373-383.
6. Choi,H.I. et al. (2000) ABFs, a family of ABA-responsive element binding factors. J. Biol. Chem., 275, 1723-1730.
7. Finkelstein,R. et al. (2002) Abscisic acid signaling in seeds and seedlings. Plant Cell, (suppl.), S15-S45.
8. Guiltinan,M. et al. (1990) A plant leucine zipper protein that recognizes an abscisic acid response elements. Science, 250, 267-271.
9. Harbison,C. et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature, 431, 99-104.
10. Hattori,T. et al. (1995) Regulation of the Osem gene by abscisic acid and the transcriptional activator VP1 : Analysis of cis acting promoter elements required for regulation by abscisic acid and VP1. Plant J., 7, 913-925.
11. Hattori,T. et al. (2002) Experimentally determined sequence requirement of ACGT-containing abscisic acid response element. Plant Cell Physiol., 43, 136-140.
12. Higo,K. et al. (1999) Plant cis-acting regulatory DNA elements (PLACE) database. Nucleic Acids Res., 27, 297-300.
13. Hobo,T. et al. (1999) ACGT-containing abscisic acid response element (ABRE) and coupling element 3 (CE3) are functionally equivalent. Plant J., 19, 679-689.
14. Hoth,S. et al. (2002) Genome-wide gene expression profiling in Arabidopsis thaliana reveals new targets of abscisic acid and largely impaired gene regulation in the abi1-1 mutant. J. Cell Sci., 115, 4891-4900.
15. Hughes,J. et al. (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol., 296, 1205-1214.
16. Kreps,J. et al. (2002) Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol., 130, 2129-2141.
17. Lander,E. et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
18. Lescot,M. et al. (2002) PlantCARE, a database of plant cis acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res., 30, 325-327.
19. Marcotte,W. et al. (1989) Abscisic acid-responsive sequence from the Em gene of wheat. Plant Cell, 1, 969-976.
20. Markstein,M. et al. (2002) Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc. Natl Acad. Sci. USA, 22, 763-768.
21. Matys,V. et al. (2003) TRANSFAC: Transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378.
22. Mundy,J. et al. (1990) Nuclear proteins bind conserved elements in the abscisic acid-responsive promoter of a rice rab gene. Proc. Natl Acad. Sci. USA, 87, 1406-1410.
23. Narusaka,Y. et al. (2003) Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses. Plant J. 34, 137-148.
24. Oeda,K. et al. (1991) A tobacco bZip transcription activator (TAF-1) binds to a G-box-like motif conserved in plant genes. EMBO J. 10, 1793-1802.
25. Ono,A. et al. (1996) The rab16b promoter of rice contains two distinct abscisic acid-responsive elements. Plant Physiol., 112 483-491.
26. Seki,M. et al. (2002a) Monitoring the expression pattern of around 7000 Arabidopsis genes under ABA treatments using a full-length cDNA microarray. Funct. Integr. Genomics, 2, 282-291.
27. Seki,M. et al. (2002b) Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J., 31, 279-292.
28. Shen,Q. and Ho,T. H. (1997) Promoter switches specific for abscisic acid (ABA)-induced gene expression in cereals. Physiol. Plantarum, 101, 653-664.
29. Shen,Q. et al. (1996) Modular nature of abscisic acid (ABA) response complexes: Composite promoter units that are necessary and sufficient for ABA induction of gene expression in barley. Plant Cell 8, 1107-1119.
30. Shinozaki,K. and Yamaguchi-Shinozaki,K. (2000) Molecular responses to dehydration and low temperature: Differences and cross-talk between two stress signaling pathways. Curr. Opin. Plant Biol., 3, 217-223.
31. Stormo,G. (2000) DNA binding sites: Representation and discovery. Bioinformatics, 16, 16-23.
32. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
33. Wenick,A. and Hobert,O. (2004) Genomic cis-regulatory architecture and trans-acting regulators of a single interneuron-specific gene battery in C.elegans. Dev. Cell, 6, 757-770.
34. Xu,D. et al. (1996) Expression of a late embryogenesis abundant protein gene, HVA1, from barley confers tolerance to water deficit and salt stress in transgeneic rice. Plant Physiol., 110, 249-257.
35. Yu,J. et al. (2002) A draft sequence of the rice genome (Oryza saliva L. ssp. indica). Science, 296, 79-91.
36. Zhang,M. (2002) Computational prediction of eukaryotic protein-coding genes. Nat. Rev. Genet., 3, 698-709.
37. Zhu,J.K. (2002) Salt and drought stress signal transduction in plants. Annu. Rev. Plant Biol., 53, 247-273.