Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice.
Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice.
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DOI：
10.1186/1471-2164-8-260
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发表时间：
2007-08-01
期刊：
影响因子：
4.4
通讯作者：
Mueller-Roeber B
中科院分区：
文献类型：
--
作者：
Gómez-Porras JL;Riaño-Pachón DM;Dreyer I;Mayer JE;Mueller-Roeber B
在植物中，复杂的调节机制是生理和发育过程的核心。植物激素脱落酸（阿坝）参与调节各种此类过程，包括气孔关闭，种子和芽休眠，以及对寒冷，干旱和盐胁迫的生理反应。潜在的组织或植物范围的控制电路通常包括组合基因调控机制和网络，我们只是在新分子工具的帮助下才开始解开。越来越多的基因组序列和基因表达数据的可用性，使我们能够剖析阿坝调控机制，在个别基因表达水平。在本文中，我们使用了一种基于计算机的方法，针对全基因组的预测和识别的特定功能的ABA响应元件。特别是，我们分析了全基因组的发生和位置安排的两个众所周知的ABA响应顺式调控元件（克雷斯），ABRE和CE 3，在塔勒水芹（拟南芥）和水稻（水稻）。我们的研究结果表明，拟南芥和水稻使用ABA响应元件ABRE和CE 3不同。早期关于各种单子叶植物的报道已经将CE 3确定为与ABRE相关的耦合元件（CE）。令人惊讶的是，我们发现，虽然ABRE是同样丰富的两个物种，CE 3是几乎没有在拟南芥。ABRE-ABRE对在两个基因组中都很常见，这表明它们可以在拟南芥和水稻中形成功能性ABA响应复合物（ABRCs）。此外，我们还检测到水稻基因启动子中ABRE和CE 3基序的不同组合、取向模式和DNA链偏好。我们的计算分析揭示了不同的招聘模式ABA响应克雷斯的上游序列的拟南芥和水稻。在拟南芥中CE 3的明显缺失表明另一个CE与ABRE配对以建立能够与转录因子相互作用的功能性ABRC。需要进一步研究，以测试观察到的差异是否可以外推到一般的单子叶植物和双子叶植物，并了解它们如何有助于激素反应的微调。我们的研究结果现在可以用来指导未来的实验，旨在进一步剖析ABA依赖的调控网络。
In plants, complex regulatory mechanisms are at the core of physiological and developmental processes. The phytohormone abscisic acid (ABA) is involved in the regulation of various such processes, including stomatal closure, seed and bud dormancy, and physiological responses to cold, drought and salinity stress. The underlying tissue or plant-wide control circuits often include combinatorial gene regulatory mechanisms and networks that we are only beginning to unravel with the help of new molecular tools. The increasing availability of genomic sequences and gene expression data enables us to dissect ABA regulatory mechanisms at the individual gene expression level. In this paper we used an in-silico-based approach directed towards genome-wide prediction and identification of specific features of ABA-responsive elements. In particular we analysed the genome-wide occurrence and positional arrangements of two well-described ABA-responsive cis-regulatory elements (CREs), ABRE and CE3, in thale cress (Arabidopsis thaliana) and rice (Oryza sativa). Our results show that Arabidopsis and rice use the ABA-responsive elements ABRE and CE3 distinctively. Earlier reports for various monocots have identified CE3 as a coupling element (CE) associated with ABRE. Surprisingly, we found that while ABRE is equally abundant in both species, CE3 is practically absent in Arabidopsis. ABRE-ABRE pairs are common in both genomes, suggesting that these can form functional ABA-responsive complexes (ABRCs) in Arabidopsis and rice. Furthermore, we detected distinct combinations, orientation patterns and DNA strand preferences of ABRE and CE3 motifs in rice gene promoters. Our computational analyses revealed distinct recruitment patterns of ABA-responsive CREs in upstream sequences of Arabidopsis and rice. The apparent absence of CE3s in Arabidopsis suggests that another CE pairs with ABRE to establish a functional ABRC capable of interacting with transcription factors. Further studies will be needed to test whether the observed differences are extrapolatable to monocots and dicots in general, and to understand how they contribute to the fine-tuning of the hormonal response. The outcome of our investigation can now be used to direct future experimentation designed to further dissect the ABA-dependent regulatory networks.
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