title: Comprehensive comparison of auxin-regulated and brassinosteroid-regulated genes in Arabidopsis.
abstract: Although numerous physiological studies have addressed the interactions between brassinosteroids and auxins, little is known about the underlying molecular mechanisms. Using an Affymetrix GeneChip representing approximately 8,300 Arabidopsis genes, we studied comprehensive transcript profiles over 24 h in response to indole-3-acetic acid (IAA) and brassinolide (BL). We identified 409 genes as BL inducible, 276 genes as IAA inducible, and 637 genes in total. These two hormones regulated only 48 genes in common, suggesting that most of the actions of each hormone are mediated by gene expression that is unique to each. IAA-up-regulated genes were enriched in genes regulated in common. They were induced quickly by IAA and more slowly by BL, suggesting divergent physiological roles. Many were early auxin-inducible genes and their homologs, namely SAUR, GH3, and IAA. The comprehensive comparison also identified IAA- and BL-specific genes, which should help to elucidate the specific actions of each hormone. The identified genes were classified using hierarchical clustering based on the similarity of their responses to the two hormones. Gene classification also allowed us to analyze the frequency of cis-elements. The TGTCTC element, a core element of the previously reported auxin response element, was not enriched in genes specifically regulated by IAA but was enriched in the 5'-flanking region of genes up-regulated by both IAA and BL. Such gene classification should be useful for predicting the functions of unknown genes, to understand the roles of these two hormones, and the promoter analysis should provide insight into the interaction of transcriptional regulation by the two hormones.
authors.affiliation: Plant Science Center, RIKEN, Suehirocho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Hideki
authors.initials: H
authors.lastname: Goda
authors.forename: Shinichiro
authors.initials: S
authors.lastname: Sawa
authors.forename: Tadao
authors.initials: T
authors.lastname: Asami
authors.forename: Shozo
authors.initials: S
authors.lastname: Fujioka
authors.forename: Yukihisa
authors.initials: Y
authors.lastname: Shimada
authors.forename: Shigeo
authors.initials: S
authors.lastname: Yoshida
mesh_terms: D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development; D029681:Arabidopsis Proteins / Q000187:drug effects / Q000235:genetics / Q000378:metabolism; D060406:Brassinosteroids; D002473:Cell Wall / Q000235:genetics / Q000378:metabolism / Q000502:physiology; D002777:Cholestanols / Q000494:pharmacology*; D018507:Gene Expression Regulation, Developmental / Q000187:drug effects; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D007210:Indoleacetic Acids / Q000494:pharmacology*; D005810:Multigene Family; D010802:Phylogeny; D010937:Plant Growth Regulators / Q000494:pharmacology*; D015398:Signal Transduction / Q000187:drug effects / Q000235:genetics* / Q000502:physiology; D013260:Steroids, Heterocyclic / Q000494:pharmacology*; D015533:Transcriptional Activation / Q000187:drug effects
chemical_list: D029681:Arabidopsis Proteins; D060406:Brassinosteroids; D002777:Cholestanols; D007210:Indoleacetic Acids; D010937:Plant Growth Regulators; C086789:SAUR-AC1 protein, Arabidopsis; D013260:Steroids, Heterocyclic; C030737:indoleacetic acid; C023623:brassinolide