Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development.
Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development.
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DOI：
10.1186/gb-2008-9-8-r130
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发表时间：
2008
期刊：
影响因子：
12.3
通讯作者：
Harmer, Stacey L.
中科院分区：
文献类型：
--
作者：
Covington, Michael F.;Maloof, Julin N.;Straume, Marty;Kay, Steve A.;Harmer, Stacey L.
在拟南芥表达的基因中，约有三分之一的转录丰度受昼夜节律控制。作为不活动的生物，植物必须迅速适应不断变化的环境条件，包括那些由日常光/暗循环引起的环境条件。预测和准备这种可预测的变化的一个重要机制是生物钟。几乎所有生物体都有昼夜节律振荡器，当它们与地球自转同步时，就提供了竞争优势。为了了解生物钟如何使植物受益，有必要确定由时钟控制的途径和过程。我们整合了对拟南芥进行的多个昼夜节律微阵列实验的信息，以便更好地估计植物转录组中受昼夜节律调控的部分。通过对时钟控制基因启动子的分析，我们确定了与阶段特异转录积累相关的生物钟调控元件。我们还发现了几条生理通路，丰富了转录丰度的时钟调节变化，表明它们可能受到生物钟的调节。我们的分析表明，大约三分之一的拟南芥基因的转录丰度是受昼夜节律调节的。我们发现了四个启动子元件，它们富含在具有四个离散阶段的基因的启动子中，这可能有助于这些基因转录丰度的时间特异性变化。在所有经典的植物激素和多种逆境反应途径中，时钟调节基因的表达都过高，这表明所有这些途径都受到生物钟的影响。进一步探索生物钟和这些途径之间的联系将有助于更好地理解生物钟是如何影响植物生长并提高适应性的。
Transcript abundance of roughly a third of expressed Arabidopsis thaliana genes is circadian-regulated. As nonmotile organisms, plants must rapidly adapt to ever-changing environmental conditions, including those caused by daily light/dark cycles. One important mechanism for anticipating and preparing for such predictable changes is the circadian clock. Nearly all organisms have circadian oscillators that, when they are in phase with the Earth's rotation, provide a competitive advantage. In order to understand how circadian clocks benefit plants, it is necessary to identify the pathways and processes that are clock controlled. We have integrated information from multiple circadian microarray experiments performed on Arabidopsis thaliana in order to better estimate the fraction of the plant transcriptome that is circadian regulated. Analyzing the promoters of clock-controlled genes, we identified circadian clock regulatory elements correlated with phase-specific transcript accumulation. We have also identified several physiological pathways enriched for clock-regulated changes in transcript abundance, suggesting they may be modulated by the circadian clock. Our analysis suggests that transcript abundance of roughly one-third of expressed A. thaliana genes is circadian regulated. We found four promoter elements, enriched in the promoters of genes with four discrete phases, which may contribute to the time-of-day specific changes in the transcript abundance of these genes. Clock-regulated genes are over-represented among all of the classical plant hormone and multiple stress response pathways, suggesting that all of these pathways are influenced by the circadian clock. Further exploration of the links between the clock and these pathways will lead to a better understanding of how the circadian clock affects plant growth and leads to improved fitness.
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