A genomic bias for genotype-environment interactions in C. elegans.
A genomic bias for genotype-environment interactions in C. elegans.
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DOI：
10.1038/msb.2012.19
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发表时间：
2012-06-05
影响因子：
9.9
通讯作者：
Yanai, Itai
中科院分区：
文献类型：
--
作者：
Grishkevich, Vladislav;Ben-Elazar, Shay;Hashimshony, Tamar;Schott, Daniel H.;Hunter, Craig P.;Yanai, Itai
生物体的表型由其基因和环境决定。这两者之间的相互作用源于环境对不同基因类型的基因表达的不同影响；然而，识别这些差异的基因组特性还没有被很好地理解。在这里，我们分析了在五种生长条件(环境)下培养的五个线虫菌株(基因型)的转录本，发现高度调控的基因，如基因间长度、基序浓度和表达水平，特别偏向于基因与环境的相互作用。对这些菌株进行测序后，我们发现，正如预期的那样，不同基因类型之间表达差异的基因具有丰富的启动子单核苷酸多态(SNPs)。然而，具有基因型-环境互作的基因在其启动子SNPs方面与背景没有显著差异。总而言之，这些结果表明，由于上游调控因子的变化，特定基因的高度调控性质使它们更容易表现出基因型与环境的相互作用。这一观察结果可能会让我们更深入地了解甚至在近亲物种中也存在着非凡的基因表达多样性的起源。
The phenotype of an organism is determined by its genotype and environment. An interaction between these two arises from the differential effect of the environment on gene expression in distinct genotypes; however, the genomic properties identifying these are not well understood. Here we analyze the transcriptomes of five C. elegans strains (genotype) cultivated in five growth conditions (environment), and find that highly regulated genes, as distinguished by intergenic lengths, motif concentration, and expression levels, are particularly biased toward genotype–environment interactions. Sequencing these strains, we find that genes with expression variation across genotypes are enriched for promoter single-nucleotide polymorphisms (SNPs), as expected. However, genes with genotype–environment interactions do not significantly differ from background in terms of their promoter SNPs. Collectively, these results indicate that the highly regulated nature of particular genes predispose them for exhibiting genotype–environment interaction as a consequence of changes to upstream regulators. This observation may provide a deeper understanding into the origin of the extraordinary gene expression diversity present in even closely related species.
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影响因子：
9.8
作者：
Smith EN;Kruglyak L
通讯作者：
Kruglyak L
影响因子：
56.9
作者：
Garsin, DA;Villanueva, JM;Ausubel, FM
通讯作者：
Ausubel, FM
影响因子：
12.3
作者：
Shen-Orr, Shai S.;Pilpel, Yitzhak;Hunter, Craig P.
通讯作者：
Hunter, Craig P.
DOI：
10.1073/pnas.1113718108
发表时间：
2011-10-04
影响因子：
11.1
作者：
Tirosh, Itay;Wong, Koon Ho;Struhl, Kevin
通讯作者：
Struhl, Kevin
影响因子：
3.3
作者：
Yanai, I;Graur, D;Ophir, R
通讯作者：
Ophir, R