Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure.
Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure.
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DOI：
10.1098/rsob.150042
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发表时间：
2015-10
期刊：
影响因子：
5.8
通讯作者：
Millar AJ
中科院分区：
文献类型：
--
作者：
Flis A;Fernández AP;Zielinski T;Mengin V;Sulpice R;Stratford K;Hume A;Pokhilko A;Southern MM;Seaton DD;McWatters HG;Stitt M;Halliday KJ;Millar AJ
我们对生物钟机制中复杂的转录反馈循环的理解依赖于来自不同来源的定量时间序列数据。我们测量了在有或没有外源蔗糖的情况下生长的拟南芥幼苗，或者在土壤生长的植物以及野生型和突变体背景下的时钟基因RNA谱。 RNA 谱在整个实验条件下都非常稳健，因此当前的数学模型可能广泛适用于叶组织。除了提供参考数据外，意想不到的行为还包括PRR9和ELF4的共表达，以及GI对PRR5的调节。绝对 RNA 定量显示，与其他时钟基因相比，PRR9 转录本水平较低（峰值约为 50 个拷贝 cell−1），而 LHY RNA 水平（超过 1500 个拷贝 cell−1）比其近亲 CCA1 高出三倍。这些数据是从 BioDare 传播的，BioDare 是一个集中时间序列数据的在线存储库，预计将有利于机械建模。一个数据子集成功地限制了复杂模型中的时钟基因表达，使用并行计算机上的公开软件，无需专家调整或编程。我们概述了数据聚合在理解时钟等高度互连的动态网络方面的经验和数学论证，以及观察到的对使这种方法广泛可用所需资源的设计限制。
Our understanding of the complex, transcriptional feedback loops in the circadian clock mechanism has depended upon quantitative, timeseries data from disparate sources. We measure clock gene RNA profiles in Arabidopsis thaliana seedlings, grown with or without exogenous sucrose, or in soil-grown plants and in wild-type and mutant backgrounds. The RNA profiles were strikingly robust across the experimental conditions, so current mathematical models are likely to be broadly applicable in leaf tissue. In addition to providing reference data, unexpected behaviours included co-expression of PRR9 and ELF4, and regulation of PRR5 by GI. Absolute RNA quantification revealed low levels of PRR9 transcripts (peak approx. 50 copies cell−1) compared with other clock genes, and threefold higher levels of LHY RNA (more than 1500 copies cell−1) than of its close relative CCA1. The data are disseminated from BioDare, an online repository for focused timeseries data, which is expected to benefit mechanistic modelling. One data subset successfully constrained clock gene expression in a complex model, using publicly available software on parallel computers, without expert tuning or programming. We outline the empirical and mathematical justification for data aggregation in understanding highly interconnected, dynamic networks such as the clock, and the observed design constraints on the resources required to make this approach widely accessible.