Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans.
Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans.
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DOI：
10.1186/s12864-017-3899-8
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发表时间：
2017-06-29
期刊：
影响因子：
4.4
通讯作者：
Kammenga JE
中科院分区：
文献类型：
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作者：
Snoek BL;Sterken MG;Bevers RPJ;Volkers RJM;Van't Hof A;Brenchley R;Riksen JAG;Cossins A;Kammenga JE
隐性遗传变异（CGV）是一种可以通过干扰正常条件而被解锁的隐性遗传变异。CGV可以通过改变基因表达来驱动新的复杂表型的出现。虽然我们对CGV的理论认识在过去十年中已经彻底增加，但对CGV背后的多态基因表达调控的见解却很少。本文研究了秀丽隐杆线虫CGV在快速温度变化下的转录结构。我们分析了重组近交系群体在热应激和恢复反应过程中基因表达的调控变异（并绘制了eQTL）。我们测量了三种温度处理下的基因表达：i)控制，ii)热应激，以及iii)热应激后的恢复。与对照组相比，暴露于热应激影响了3305个基因的转录，而恢复动物的942个基因受到影响。这些受影响的基因主要与代谢和繁殖有关。恢复动物的基因表达模式与对照组和热应激处理相似。我们利用重组自交系群体的遗传变异定位了eQTL，在热胁迫处理中检测到2626个基因，在对照中检测到1797个基因，在恢复中检测到1880个基因。顺式- eqtl在不同处理间高度共享。相当一部分trans-eQTL（40-57%）映射到19个治疗特异性反带。与顺式eqtl相比，反式eqtl具有高度的环境特异性，因此具有隐秘性。大约67%的反式eqtl仅在一次处理中诱导，其中热胁迫表现出最独特的反式eqtl。这些结果表明，在相对较短的时间跨度（2 h）内，应激反应可以诱发三种不同环境条件下的CGV的高度动态模式，并且CGV主要由响应相关的反调控eQTL决定。本文的在线版本（doi:10.1186/s12864-017-3899-8）包含补充材料，可供授权用户使用。
Cryptic genetic variation (CGV) is the hidden genetic variation that can be unlocked by perturbing normal conditions. CGV can drive the emergence of novel complex phenotypes through changes in gene expression. Although our theoretical understanding of CGV has thoroughly increased over the past decade, insight into polymorphic gene expression regulation underlying CGV is scarce. Here we investigated the transcriptional architecture of CGV in response to rapid temperature changes in the nematode Caenorhabditis elegans. We analyzed regulatory variation in gene expression (and mapped eQTL) across the course of a heat stress and recovery response in a recombinant inbred population. We measured gene expression over three temperature treatments: i) control, ii) heat stress, and iii) recovery from heat stress. Compared to control, exposure to heat stress affected the transcription of 3305 genes, whereas 942 were affected in recovering animals. These affected genes were mainly involved in metabolism and reproduction. The gene expression pattern in recovering animals resembled both the control and the heat-stress treatment. We mapped eQTL using the genetic variation of the recombinant inbred population and detected 2626 genes with an eQTL in the heat-stress treatment, 1797 in the control, and 1880 in the recovery. The cis-eQTL were highly shared across treatments. A considerable fraction of the trans-eQTL (40–57%) mapped to 19 treatment specific trans-bands. In contrast to cis-eQTL, trans-eQTL were highly environment specific and thus cryptic. Approximately 67% of the trans-eQTL were only induced in a single treatment, with heat-stress showing the most unique trans-eQTL. These results illustrate the highly dynamic pattern of CGV across three different environmental conditions that can be evoked by a stress response over a relatively short time-span (2 h) and that CGV is mainly determined by response related trans regulatory eQTL. The online version of this article (doi:10.1186/s12864-017-3899-8) contains supplementary material, which is available to authorized users.