Interpretation of knockout experiments: the congenic footprint
Interpretation of knockout experiments: the congenic footprint
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DOI：
10.1111/j.1601-183x.2007.00304.x
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发表时间：
2007-04-01
影响因子：
2.5
通讯作者：
Koks, S.
中科院分区：
文献类型：
--
作者：
Schalkwyk, L. C.;Fernandes, C.;Koks, S.
在基因靶向实验中，遗传背景的重要性现在被广泛认识到，并且敲除等位基因通常被回交到标准近交背景上。这产生了一个同源株与胚胎干（ES）细胞来源的染色体的实质性部分仍然侧翼敲除等位基因，敲除研究中经常被忽视的现象。在胆囊收缩素2（Cckbr）敲除小鼠与C57 BL/6回交，我们已经发现了一个明确的'同源足迹'的表达差异，在至少10个基因的40 Mb序列侧翼的Cckbr基因座，其中每一个是潜在的负责方面的'敲除'表型。表达差异绝大多数在敲除低方向，这可能指向背景依赖性的一般现象。这一发现强调了在使用基因敲除将表型效应归因于基因时需要谨慎。当基因的功能未知或表型出乎意料时，尤其如此，这是大规模敲除和表型筛选程序的一个特别关注点。然而，遗传背景的影响不应被简单地视为一种潜在的混淆，而是一个独特的机会，研究系统对特定（遗传）扰动的更广泛的反应。
In gene targeting experiments, the importance of genetic background is now widely appreciated, and knockout alleles are routinely backcrossed onto a standard inbred background. This produces a congenic strain with a substantial segment of embryonic stem (ES)-cell-derived chromosome still flanking the knockout allele, a phenomenon often neglected in knockout studies. In cholecystokynin 2 (Cckbr) knockout mice backcrossed with C57BL/6, we have found a clear 'congenic footprint' of expression differences in at least 10 genes across 40 Mb sequence flanking the Cckbr locus, each of which is potentially responsible for aspects of the 'knockout' phenotype. The expression differences are overwhelmingly in the knockout-low direction, which may point to a general phenomenon of background dependence. This finding emphasizes the need for caution in using gene knockouts to attribute phenotypic effects to genes. This is especially the case when the gene is of unknown function or the phenotype is unexpected, and is a particular concern for large-scale knockout and phenotypic screening programmes. However, the impact of genetic background should not be simply viewed as a potential confound, but as a unique opportunity to study the broader responses of a system to a specific (genetic) perturbation.