Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis.
Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis.
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DOI：
10.1152/physiolgenomics.00201.2003
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发表时间：
2004-04
影响因子：
4.6
通讯作者：
J. Yazaki;Zenpei Shimatani;Akiko H. Hashimoto;Y. Nagata;F. Fujii;Keiichi Kojima;Kohji Suzuki;T. Taya;M. Tonouchi;C. Nelson;A. Nakagawa;Y. Otomo;K. Murakami;K. Matsubara;J. Kawai;Piero Carninci;Y. Hayashizaki;S. Kikuchi
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文献类型：
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作者：
J. Yazaki;Zenpei Shimatani;Akiko H. Hashimoto;Y. Nagata;F. Fujii;Keiichi Kojima;Kohji Suzuki;T. Taya;M. Tonouchi;C. Nelson;A. Nakagawa;Y. Otomo;K. Murakami;K. Matsubara;J. Kawai;Piero Carninci;Y. Hayashizaki;S. Kikuchi
我们收集了32，127个水稻全长互补DNA克隆并进行了全序列测定。SSP. n.粳稻“日本晴。这些克隆与基因组DNA的映射显示水稻基因组中约有20，500个转录单位（TU）。对于每个TU，我们使用一种算法选择60聚体，该算法考虑了一些DNA条件，如碱基组成和序列复杂性。利用原位合成技术，我们构建了寡核苷酸阵列与这些TU的玻璃载玻片上。我们的目标是从正常生长的水稻愈伤组织和用脱落酸（阿坝）或赤霉素（GA）处理的愈伤组织中制备的RNA。我们鉴定了200个ABA响应基因和301个GA响应基因，其中许多基因以前从未在其他表达分析中被注释为阿坝或GA响应基因。这些基因的比较揭示了几乎所有的拮抗调节激素;这些以前被注释为负责蛋白质储存和防御病原体。比较对一种激素反应的基因和对两种激素反应的拮抗基因的顺式元件，发现拮抗基因中含有与阿坝和GA反应相关的顺式元件。只对一种激素反应的基因富含支持阿坝和GA反应的顺式元件。在寻找突变体的表型，其中一个反转录转座子插入这些基因的响应，我们确定了表型相关的种子形成或植物高度，包括不育，胎生，和矮化。在水稻和拟南芥之间的激素反应基因的顺式元件的比较，我们确定的顺式元件的脱水胁迫响应拟南芥特异性和水稻特异性的蛋白质存储。
We collected and completely sequenced 32,127 full-length complementary DNA clones from Oryza sativa L. ssp. japonica cv. "Nipponbare." Mapping of these clones to genomic DNA revealed approximately 20,500 transcriptional units (TUs) in the rice genome. For each TU, we selected 60-mers using an algorithm that took into account some DNA conditions such as base composition and sequence complexity. Using in situ synthesis technology, we constructed oligonucleotide arrays with these TUs on glass slides. We targeted RNAs prepared from normally grown rice callus and from callus treated with abscisic acid (ABA) or gibberellin (GA). We identified 200 ABA-responsive and 301 GA-responsive genes, many of which had never before been annotated as ABA or GA responsive in other expression analysis. Comparison of these genes revealed antagonistic regulation of almost all by both hormones; these had previously been annotated as being responsible for protein storage and defense against pathogens. Comparison of the cis-elements of genes responsive to one or antagonistic to both hormones revealed that the antagonistic genes had cis-elements related to ABA and GA responses. The genes responsive to only one hormone were rich in cis-elements that supported ABA and GA responses. In a search for the phenotypes of mutants in which a retrotransposon was inserted in these hormone-responsive genes, we identified phenotypes related to seed formation or plant height, including sterility, vivipary, and dwarfism. In comparison of cis-elements for hormone response genes between rice and Arabidopsis thaliana, we identified cis-elements for dehydration-stress response as Arabidopsis specific and for protein storage as rice specific.