Genome-wide analysis of endogenous abscisic acid-mediated transcription in dry and imbibed seeds of Arabidopsis using tiling arrays
Genome-wide analysis of endogenous abscisic acid-mediated transcription in dry and imbibed seeds of Arabidopsis using tiling arrays
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DOI：
10.1111/j.1365-313x.2010.04135.x
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发表时间：
2010-04-01
期刊：
影响因子：
7.2
通讯作者：
Seki, Motoaki
中科院分区：
文献类型：
--
作者：
Okamoto, Masanori;Tatematsu, Kiyoshi;Seki, Motoaki
植物激素脱落酸（阿坝）在种子休眠的诱导和维持中起重要作用.虽然外源阿坝的应用抑制萌发，外源阿坝对ABA介导的基因转录的影响不同于内源阿坝。为了了解内源性阿坝如何调节种子中的转录组，我们使用全基因组Affyphidine平铺阵列在两个阿坝代谢突变体中进行了全面的表达分析-ABA缺陷突变体（aba 2）和阿坝过度积累突变体（cyp 707 a1 a2 a3三重突变体）。系统聚类和主成分分析表明，内源阿坝水平的差异并不影响干种子中储存的mRNA的全球表达。然而，种子吸胀后的转录组相关的内源阿坝水平在这两种类型的突变体。在吸胀种子中表达的内源ABA调控基因包括编码关键阿坝信号因子和赤霉素相关成分的基因。此外，ABA上调基因的队列部分类似于休眠基因，而ABA下调基因与后熟调节基因部分重叠。生物信息学分析显示，6105个新基因[非Aradopsis基因组倡议（AGI）转录单位（TU）]从未注释的区域表达。有趣的是，大约97%的非AGI TU可能编码假设的非蛋白质编码RNA，包括大量的反义RNA。在干种子和吸胀种子中，非AGI TU的全局表达谱与AGI基因的表达谱相似。对于非AGI TU和AGI编码基因，我们确定了那些在胚和胚乳组织中受到不同调控的基因。我们的研究结果表明，拟南芥种子中的转录比以前认为的更复杂和动态。
P>The phytohormone abscisic acid (ABA) plays important roles in the induction and maintenance of seed dormancy. Although application of exogenous ABA inhibits germination, the effects of exogenous ABA on ABA-mediated gene transcription differ from those of endogenous ABA. To understand how endogenous ABA regulates the transcriptomes in seeds, we performed comprehensive expression analyses using whole-genome Affymetrix tiling arrays in two ABA metabolism mutants - an ABA-deficient mutant (aba2) and an ABA over-accumulation mutant (cyp707a1a2a3 triple mutant). Hierarchical clustering and principal components analyses showed that differences in endogenous ABA levels do not influence global expression of stored mRNA in dry seeds. However, the transcriptome after seed imbibition was related to endogenous ABA levels in both types of mutant. Endogenous ABA-regulated genes expressed in imbibed seeds included those encoding key ABA signaling factors and gibberellin-related components. In addition, cohorts of ABA-upregulated genes partially resembled those of dormant genes, whereas ABA-downregulated genes were partially overlapped with after-ripening-regulated genes. Bioinformatic analyses revealed that 6105 novel genes [non-Aradopsis Genome Initiative (AGI) transcriptional units (TUs)] were expressed from unannotated regions. Interestingly, approximately 97% of non-AGI TUs possibly encoded hypothetical non-protein-coding RNAs, including a large number of antisense RNAs. In dry and imbibed seeds, global expression profiles of non-AGI TUs were similar to those of AGI genes. For both non-AGI TUs and AGI code genes, we identified those that were regulated differently in embryo and endosperm tissues. Our results suggest that transcription in Arabidopsis seeds is more complex and dynamic than previously thought.