Skip to main content
ARS Home » Pacific West Area » Albany, California » Plant Gene Expression Center » Research » Publications at this Location » Publication #161022
Title: IDENTIFICATION OF PROMOTER MOTIFS INVOLVED IN THE NETWORK OF PHYTOCHROME A-REGULATED GENE EXPRESSION BY COMBINED ANALYSIS OF GENOMIC SEQUENCE AND MICROARRAY DATA

Author
item HUDSON, MATTHEW - UCB-ARS PLNT GENE EXP CTR
item QUAIL, PETER - UCB-ARS PLNT GENE EXP CTR

Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/13/2003
Publication Date: 12/1/2003
Citation: HUDSON, M.E., QUAIL, P.H. 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. 2003. 133:1605-1616.

Interpretive Summary: This work describes the development and use of a computer program for identifying short DNA segments involved in regulating the switching of genes on and off. Using this program, we identified such DNA segments involved in controling light-regulated genes in plants.

Technical Abstract: 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.