School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr NW, EBB Building, Atlanta, GA 30332, USA.
G3 (Bethesda). 2023 Aug 9;13(8). doi: 10.1093/g3journal/jkad112.
Though natural systems harbor genetic and phenotypic variation, research in model organisms is often restricted to a reference strain. Focusing on a reference strain yields a great depth of knowledge but potentially at the cost of breadth of understanding. Furthermore, tools developed in the reference context may introduce bias when applied to other strains, posing challenges to defining the scope of variation within model systems. Here, we evaluate how genetic differences among 5 wild Caenorhabditis elegans strains affect gene expression and its quantification, in general and after induction of the RNA interference (RNAi) response. Across strains, 34% of genes were differentially expressed in the control condition, including 411 genes that were not expressed at all in at least 1 strain; 49 of these were unexpressed in reference strain N2. Reference genome mapping bias caused limited concern: despite hyperdiverse hotspots throughout the genome, 92% of variably expressed genes were robust to mapping issues. The transcriptional response to RNAi was highly strain- and target-gene-specific and did not correlate with RNAi efficiency, as the 2 RNAi-insensitive strains showed more differentially expressed genes following RNAi treatment than the RNAi-sensitive reference strain. We conclude that gene expression, generally and in response to RNAi, differs across C. elegans strains such that the choice of strain may meaningfully influence scientific inferences. Finally, we introduce a resource for querying gene expression variation in this dataset at https://wildworm.biosci.gatech.edu/rnai/.
尽管自然系统中存在遗传和表型变异，但在模式生物的研究中，通常仅限于参考菌株。关注参考菌株可以获得更深入的知识，但可能会以理解的广度为代价。此外，在参考背景下开发的工具在应用于其他菌株时可能会引入偏差，从而对定义模型系统内变异的范围提出挑战。在这里，我们评估了 5 种野生秀丽隐杆线虫菌株之间的遗传差异如何影响基因表达及其定量，一般情况下以及在 RNA 干扰 (RNAi) 反应诱导后。在所有菌株中，有 34%的基因在对照条件下表达差异，其中包括至少在 1 个菌株中完全不表达的 411 个基因；这些基因中有 49 个在参考菌株 N2 中不表达。参考基因组映射偏差引起的问题有限：尽管整个基因组中存在高度多样化的热点，但 92%的表达差异基因对映射问题具有鲁棒性。RNAi 对基因表达的转录反应具有高度的菌株和靶基因特异性，并且与 RNAi 效率不相关，因为 2 个 RNAi 不敏感的菌株在 RNAi 处理后表现出更多的差异表达基因，而 RNAi 敏感的参考菌株则没有。我们得出结论，基因表达，一般和对 RNAi 的反应，在秀丽隐杆线虫菌株之间存在差异，因此菌株的选择可能会对科学推断产生有意义的影响。最后，我们在 https://wildworm.biosci.gatech.edu/rnai/ 上引入了一个查询该数据集基因表达变异的资源。
