2005
DOI: 10.1104/pp.104.058412
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Quantitative Statistical Analysis of cis-Regulatory Sequences in ABA/VP1- and CBF/DREB1-Regulated Genes of Arabidopsis

Abstract: We have developed a simple quantitative computational approach for objective analysis of cis-regulatory sequences in promoters of coregulated genes. The program, designated MotifFinder, identifies oligo sequences that are overrepresented in promoters of coregulated genes. We used this approach to analyze promoter sequences of Viviparous1 (VP1)/abscisic acid (ABA)-regulated genes and cold-regulated genes, respectively, of Arabidopsis (Arabidopsis thaliana). We detected significantly enriched sequences in up-reg… Show more

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Cited by 71 publications
(66 citation statements)
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References 104 publications
(160 reference statements)
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“…ABA responsive genes predicted here are not exhaustive, but represent considerable number of genes with a similar cis-regulatory element. The variability in ABRE and other over-presented motifs organization might be a reason for multiple signal integration points in combinatorial cis-trans interaction and versatile gene action under varied conditions (Suzuki et al 2005). In our study, genes predicted by using only ABRE (CGMCACGTGB) cis-element showed 80% prediction accuracy among the randomly selected 45 genes of top 402 genes.…”
Section: Discussionmentioning
confidence: 99%
“…ABA responsive genes predicted here are not exhaustive, but represent considerable number of genes with a similar cis-regulatory element. The variability in ABRE and other over-presented motifs organization might be a reason for multiple signal integration points in combinatorial cis-trans interaction and versatile gene action under varied conditions (Suzuki et al 2005). In our study, genes predicted by using only ABRE (CGMCACGTGB) cis-element showed 80% prediction accuracy among the randomly selected 45 genes of top 402 genes.…”
Section: Discussionmentioning
confidence: 99%
“…Analysis of the sequences in the promoter region of Rio Blanco identified six cis-acting abscisic acid (ABA) responsive elements (ABREs) that were reported to be involved in ABA responsiveness, two RY elements involved in seed-specific regulation, one motif IIB, and an ABA responsive element (Baumlein et al 1992;Suzuki et al 2005) (Figure S5). Two SNPs, both transversions, between Rio Blanco and NW97S186, were detected in two ABREs at positions 2314 and 2222.…”
Section: Mis-splicing In Taphs1 Causes Phs Susceptibilitymentioning
confidence: 99%
“…Importantly, motif definitions were determined stringently, meaning that differences in flanking nucleotides were considered as different motifs, as can be seen for PIF5. Flanking nucleotides have been shown to add important specificity in motif recognition and are therefore not collapsed into a single degenerate consensus binding site (Williams et al, 1992;Catron et al, 1993;Suzuki et al, 2005). Motifs were ranked by occurrence, with the most frequent motif denoted as the primary motif.…”
Section: Hypotheses To Explain the Diversity Of Motifs In Bound Regionsmentioning
confidence: 99%