Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules.
Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules.
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DOI：
10.1371/journal.pgen.0040014
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发表时间：
2008-02
期刊：
影响因子：
4.5
通讯作者：
Chory J
中科院分区：
文献类型：
--
作者：
Michael TP;Mockler TC;Breton G;McEntee C;Byer A;Trout JD;Hazen SP;Shen R;Priest HD;Sullivan CM;Givan SA;Yanovsky M;Hong F;Kay SA;Chory J
转录的正确的每日定相赋予几乎所有生物体（包括高等植物）适应性优势。在这项研究中，我们描述了一个假设驱动的网络发现管道，识别基因组规模数据中的生物相关模式。为了证明其实用性，我们分析了一个全面的矩阵的时间进程询问不同的热循环，光循环和昼夜节律条件下生长的拟南芥植物的核转录组。我们发现，89%的拟南芥转录物在至少一种条件下循环，并且大多数基因在一天中的特定时间具有峰值表达，这取决于环境。仅热循环就可以驱动至少一半的转录物，这些转录物对于同步内部过程（如细胞周期和蛋白质合成）至关重要。我们确定了至少三个控制阶段特异性表达的不同转录模块，包括一个新的午夜特异性模块，PBX/TBX/SBX。我们验证了网络发现管道，以及午夜特定的模块，通过证明PBX元素足以驱动昼夜和昼夜条件依赖的表达。此外，我们表明，这三个转录模块是保守的拟南芥，白杨，水稻。这些结果证实了热循环，光循环和昼夜节律钟对日常转录程序之间的复杂相互作用，并提供了一个全面的观点保守的基因组目标的转录网络的关键成功的适应。随着地球的旋转，环境条件在明亮的温暖白天和黑暗的凉爽夜晚之间振荡。植物通过将生理过程安排在白天或夜晚的特定时间来适应这些变化。光和温度信号以及生物钟调节这种适应性反应。为了确定这些因素中的每一个对基因调节的贡献，我们分析了询问光、温度和昼夜节律条件的微阵列时间过程实验。我们发现几乎所有的拟南芥基因都在至少一种条件下循环。从信号传导的角度来看，这表明光、温度和生物钟在调节许多生理通路中起着重要作用。为了阐明转录调控对这一过程的贡献，我们挖掘了循环基因的启动子，以确定与一天中特定时间的表达相关的DNA元件。这证实了几个DNA基序，如G盒和晚上元件在光和昼夜节律钟调控基因表达中的重要性，但也促进了与新的午夜调控模块相关的新元素的发现。在水稻和白杨中的orthopathy启动子元件的鉴定揭示了一个保守的转录调控网络，使全球适应不断变化的日常环境。
Correct daily phasing of transcription confers an adaptive advantage to almost all organisms, including higher plants. In this study, we describe a hypothesis-driven network discovery pipeline that identifies biologically relevant patterns in genome-scale data. To demonstrate its utility, we analyzed a comprehensive matrix of time courses interrogating the nuclear transcriptome of Arabidopsis thaliana plants grown under different thermocycles, photocycles, and circadian conditions. We show that 89% of Arabidopsis transcripts cycle in at least one condition and that most genes have peak expression at a particular time of day, which shifts depending on the environment. Thermocycles alone can drive at least half of all transcripts critical for synchronizing internal processes such as cell cycle and protein synthesis. We identified at least three distinct transcription modules controlling phase-specific expression, including a new midnight specific module, PBX/TBX/SBX. We validated the network discovery pipeline, as well as the midnight specific module, by demonstrating that the PBX element was sufficient to drive diurnal and circadian condition-dependent expression. Moreover, we show that the three transcription modules are conserved across Arabidopsis, poplar, and rice. These results confirm the complex interplay between thermocycles, photocycles, and the circadian clock on the daily transcription program, and provide a comprehensive view of the conserved genomic targets for a transcriptional network key to successful adaptation. As the earth rotates, environmental conditions oscillate between illuminated warm days and dark cool nights. Plants have adapted to these changes by timing physiological processes to specific times of the day or night. Light and temperature signaling and the circadian clock regulate this adaptive response. To determine the contributions of each of these factors on gene regulation, we analyzed microarray time course experiments interrogating light, temperature, and circadian conditions. We discovered that almost all Arabidopsis genes cycle in at least one condition. From a signaling perspective, this suggests that light, temperature, and circadian clock play an important role in modulating many physiological pathways. To clarify the contribution of transcriptional regulation on this process, we mined the promoters of cycling genes to identify DNA elements associated with expression at specific times of day. This confirmed the importance of several DNA motifs such as the G-box and the evening element in the regulation of gene expression by light and the circadian clock, but also facilitated the discovery of new elements linked to a novel midnight regulatory module. Identification of orthologous promoter elements in rice and poplar revealed a conserved transcriptional regulatory network that allows global adaptation to the ever-changing daily environment.
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影响因子：
56.9
作者：
Harmer, SL;Hogenesch, LB;Kay, SA
通讯作者：
Kay, SA
影响因子：
10.5
作者：
Diernfellner, ACR;Schafmeier, T;Brunner, M
通讯作者：
Brunner, M
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
9.8
作者：
Lahiri K;Vallone D;Gondi SB;Santoriello C;Dickmeis T;Foulkes NS
通讯作者：
Foulkes NS
影响因子：
3.3
作者：
Colot, HV;Loros, JJ;Dunlap, JC
通讯作者：
Dunlap, JC