Abstract
We used an 8987-EST collection to construct a cDNA microarray system with various genomics information (full-length cDNA, expression profile, high accuracy genome sequence, phenotype, genetic map, and physical map) in rice. This array was used as a probe to hybridize target RNAs prepared from normally grown callus of rice and from callus treated for 6 hr or 3 days with the hormones abscisic acid (ABA) or gibberellin (GA). We identified 509 clones, including many clones that had never been annotated as ABA- or GA-responsive. These genes included not only ABA- or GA-responsive genes but also genes responsive to other physiological conditions such as pathogen infection, heat shock, and metal ion stress. Comparison of ABA- and GA-responsive genes revealed antagonistic regulation for these genes by both hormones except for one defense-related gene, thionin. The gene for thionin was up-regulated by both hormone treatments for 3 days. The upstream regions of all the genes that were regulated by both hormones had cis-elements for ABA and GA response. We performed a clustering analysis of genes regulated by both hormones and various expression profiles that showed three notable clusters (seed tissues, low temperature and sugar starvation, and thionin-gene related). A comparison of the cis-elements for hormone response genes between rice and Arabidopsis thaliana, we identified cis-elements for dehydration-stress response or for expression of amylase gene as Arabidopsis gene-specific or rice gene-specific, respectively.
| Original language | English |
|---|---|
| Pages (from-to) | 249-261 |
| Number of pages | 13 |
| Journal | DNA Research |
| Volume | 10 |
| Issue number | 6 |
| DOIs | |
| Publication status | Published - Dec 1 2003 |
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All Science Journal Classification (ASJC) codes
- Molecular Biology
- Genetics
Cite this
Genomics Approach to Abscisic Acid- and Gibberellin-responsive Genes in Rice. / Yazaki, Junshi; Kishimoto, Naoki; Nagata, Yuko; Ishikawa, Masahiro; Fujii, Fumiko; Hashimoto, Akiko; Shimbo, Kanako; Shimatani, Zenpei; Kojima, Keiichi; Suzuki, Kouji; Yamamoto, Makoto; Honda, Sachiko; Endo, Ayano; Yoshida, Yumiko; Sato, Yuki; Takeuchi, Keiko; Toyoshima, Kazuko; Miyamoto, Chikako; Wu, Jianzhong; Sasaki, Takuji; Sakata, Katsumi; Yamamoto, Kimiko; Iba, Koh; Oda, Takahiro; Otomo, Yasuhiro; Murakami, Kazuo; Matsubara, Kenichi; Kawai, Jun; Carninci, Piero; Hayashizaki, Yoshihide; Kikuchi, Shoshi.
In: DNA Research, Vol. 10, No. 6, 01.12.2003, p. 249-261.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Genomics Approach to Abscisic Acid- and Gibberellin-responsive Genes in Rice
AU - Yazaki, Junshi
AU - Kishimoto, Naoki
AU - Nagata, Yuko
AU - Ishikawa, Masahiro
AU - Fujii, Fumiko
AU - Hashimoto, Akiko
AU - Shimbo, Kanako
AU - Shimatani, Zenpei
AU - Kojima, Keiichi
AU - Suzuki, Kouji
AU - Yamamoto, Makoto
AU - Honda, Sachiko
AU - Endo, Ayano
AU - Yoshida, Yumiko
AU - Sato, Yuki
AU - Takeuchi, Keiko
AU - Toyoshima, Kazuko
AU - Miyamoto, Chikako
AU - Wu, Jianzhong
AU - Sasaki, Takuji
AU - Sakata, Katsumi
AU - Yamamoto, Kimiko
AU - Iba, Koh
AU - Oda, Takahiro
AU - Otomo, Yasuhiro
AU - Murakami, Kazuo
AU - Matsubara, Kenichi
AU - Kawai, Jun
AU - Carninci, Piero
AU - Hayashizaki, Yoshihide
AU - Kikuchi, Shoshi
PY - 2003/12/1
Y1 - 2003/12/1
N2 - We used an 8987-EST collection to construct a cDNA microarray system with various genomics information (full-length cDNA, expression profile, high accuracy genome sequence, phenotype, genetic map, and physical map) in rice. This array was used as a probe to hybridize target RNAs prepared from normally grown callus of rice and from callus treated for 6 hr or 3 days with the hormones abscisic acid (ABA) or gibberellin (GA). We identified 509 clones, including many clones that had never been annotated as ABA- or GA-responsive. These genes included not only ABA- or GA-responsive genes but also genes responsive to other physiological conditions such as pathogen infection, heat shock, and metal ion stress. Comparison of ABA- and GA-responsive genes revealed antagonistic regulation for these genes by both hormones except for one defense-related gene, thionin. The gene for thionin was up-regulated by both hormone treatments for 3 days. The upstream regions of all the genes that were regulated by both hormones had cis-elements for ABA and GA response. We performed a clustering analysis of genes regulated by both hormones and various expression profiles that showed three notable clusters (seed tissues, low temperature and sugar starvation, and thionin-gene related). A comparison of the cis-elements for hormone response genes between rice and Arabidopsis thaliana, we identified cis-elements for dehydration-stress response or for expression of amylase gene as Arabidopsis gene-specific or rice gene-specific, respectively.
AB - We used an 8987-EST collection to construct a cDNA microarray system with various genomics information (full-length cDNA, expression profile, high accuracy genome sequence, phenotype, genetic map, and physical map) in rice. This array was used as a probe to hybridize target RNAs prepared from normally grown callus of rice and from callus treated for 6 hr or 3 days with the hormones abscisic acid (ABA) or gibberellin (GA). We identified 509 clones, including many clones that had never been annotated as ABA- or GA-responsive. These genes included not only ABA- or GA-responsive genes but also genes responsive to other physiological conditions such as pathogen infection, heat shock, and metal ion stress. Comparison of ABA- and GA-responsive genes revealed antagonistic regulation for these genes by both hormones except for one defense-related gene, thionin. The gene for thionin was up-regulated by both hormone treatments for 3 days. The upstream regions of all the genes that were regulated by both hormones had cis-elements for ABA and GA response. We performed a clustering analysis of genes regulated by both hormones and various expression profiles that showed three notable clusters (seed tissues, low temperature and sugar starvation, and thionin-gene related). A comparison of the cis-elements for hormone response genes between rice and Arabidopsis thaliana, we identified cis-elements for dehydration-stress response or for expression of amylase gene as Arabidopsis gene-specific or rice gene-specific, respectively.
UR - http://www.scopus.com/inward/record.url?scp=10744228998&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=10744228998&partnerID=8YFLogxK
U2 - 10.1093/dnares/10.6.249
DO - 10.1093/dnares/10.6.249
M3 - Article
C2 - 15029956
AN - SCOPUS:10744228998
VL - 10
SP - 249
EP - 261
JO - DNA Research
JF - DNA Research
SN - 1340-2838
IS - 6
ER -