Plant Physiology 133:1605-1616 (2003)
© 2003 American Society of Plant Biologists
Identification of Promoter Motifs Involved in the Network of Phytochrome A-Regulated Gene Expression by Combined Analysis of Genomic Sequence and Microarray Data1,[w]
Matthew E. Hudson2 and
Peter H. Quail*
Department of Plant and Microbial Biology, University of California, Berkeley, California 94720; and University of California, Berkeley/United States Department of Agriculture Plant Gene Expression Center, 800 Buchanan Street, Albany, California 94710
Several hundred Arabidopsis genes, transcriptionally regulated by phytochrome A (phyA), were previously identified using an oligonucleotide microarray. We have now identified, in silico, conserved sequence motifs in the promoters of these genes by comparing the promoter sequences to those of all the genes present on the microarray from which they were sampled. This was done using a Perl script (called Sift) that identifies over-represented motifs using an enumerative approach. The utility of Sift was verified by analysis of circadian-regulated promoters known to contain a biologically significant motif. Several elements were then identified in phyA-responsive promoters by their over-representation. Five previously undescribed motifs were detected in the promoters of phyA-induced genes. Four novel motifs were found in phyA-repressed promoters, plus a motif that strongly resembles the DE1 element. The G-box, CACGTG, was a prominent hit in both induced and repressed phyA-responsive promoters. Intriguingly, two distinct flanking consensus sequences were observed adjacent to the G-box core sequence: one predominating in phyA-induced promoters, the other in phyA-repressed promoters. Such different conserved flanking nucleotides around the core motif in these two sets of promoters may indicate that different members of the same family of DNA-binding proteins mediate phyA induction and repression. An increased abundance of G-box sequences was observed in the most rapidly phyA-responsive genes and in the promoters of phyA-regulated transcription factors, indicating that G-box-binding transcription factors are upstream components in a transcriptional cascade that mediates phyA-regulated development.
Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.103.030437.
1 This work was supported by the National Institutes of Health (grant no. GM47475), by the U.S. Department of Agriculture-Agricultural Research Service Current Research Information Service (grant no. 5335–2100–017–00D), and by Torrey Mesa Research Institute (San Diego).
[w] The online version of this article contains Web-only data.
2 Present address: Diversa Corporation, 4955 Directors Place, San Diego, CA 92121.
* Corresponding author; e-mail quail{at}nature.berkeley.edu; fax 510–559–5678.
Received July 17, 2003;
returned for revision August 21, 2003;
accepted September 13, 2003.
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