Extensive cis-Regulatory Variation Robust to Environmental Perturbation in Arabidopsis
Extensive cis-Regulatory Variation Robust to Environmental Perturbation in Arabidopsis
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DOI：
10.1105/tpc.114.130310
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发表时间：
2014-11-01
期刊：
影响因子：
11.6
通讯作者：
Loudet, Olivier
中科院分区：
文献类型：
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作者：
Cubillos, Francisco A.;Stegle, Oliver;Loudet, Olivier
顺式和反式作用因子影响基因表达和对环境条件的反应。然而，对于大多数植物系统，我们缺乏这些因素及其与环境变化的相互作用的综合地图。在这里，我们研究等位基因特异性表达（ASE）在F1杂交研究如何从两个拟南芥种质等位基因影响基因表达。为了研究环境的影响，我们使用干旱胁迫，并开发了一个方差分量模型来估计顺式和反式调节多态性，环境因素及其相互作用的综合遗传贡献。我们对11，003个基因的ASE进行了定量，鉴定出3318个基因在对照和胁迫条件下具有一致的ASE，表明顺式作用遗传效应对环境变化基本上是稳健的。此外，我们发现1618个基因与基因型×环境（GxE）的相互作用，主要是顺式× E相互作用的ASE的幅度变化。我们发现trans-x-E相互作用较少，但这些作用在不同条件下相对不那么稳健，显示出环境之间作用方向的更多变化;这证实了反式调节在对环境条件的反应中起着重要作用。我们的数据提供了一个详细的地图，顺式和反式调节和GxE相互作用的A。thaliana，为其他植物和环境的机制调查和研究奠定了基础。
cis- and trans-acting factors affect gene expression and responses to environmental conditions. However, for most plant systems, we lack a comprehensive map of these factors and their interaction with environmental variation. Here, we examined allele-specific expression (ASE) in an F1 hybrid to study how alleles from two Arabidopsis thaliana accessions affect gene expression. To investigate the effect of the environment, we used drought stress and developed a variance component model to estimate the combined genetic contributions of cis- and trans-regulatory polymorphisms, environmental factors, and their interactions. We quantified ASE for 11,003 genes, identifying 3318 genes with consistent ASE in control and stress conditions, demonstrating that cis- acting genetic effects are essentially robust to changes in the environment. Moreover, we found 1618 genes with genotype x environment (GxE) interactions, mostly cis x E interactions with magnitude changes in ASE. We found fewer trans x E interactions, but these effects were relatively less robust across conditions, showing more changes in the direction of the effect between environments; this confirms that trans-regulation plays an important role in the response to environmental conditions. Our data provide a detailed map of cis- and trans-regulation and GxE interactions in A. thaliana, laying the ground for mechanistic investigations and studies in other plants and environments.