Karagiannis Jim
Department of Biology, The University of Western Ontario, London, Ontario, Canada.
PLoS Genet. 2025 Jun 10;21(6):e1011730. doi: 10.1371/journal.pgen.1011730. eCollection 2025 Jun.
Genetic buffering plays a pivotal role in orchestrating the relationship between genotype and phenotype in outbred populations. While high-throughput screens have identified many instances of genetic buffering - through the detection of "synthetic lethality" or "synthetic sickness" - a formal and general method for its quantitative analysis across systems is lacking. In this report, an axiomatic mathematical framework that can be used to classify, quantify, and compare buffering relationships between genes is described. Importantly, this methodology employs a ratio scale as its basis, thereby permitting the definition of a novel neutrality model for gene interaction - the "parallel" model - which complements the commonly used "product" model. Evidence supporting the parallel model is provided through the statistical analysis of previously published yeast gene interaction data. This analysis reveals the consistent underestimation of double mutant fitness in strains carrying non-interacting query-array pairings (as predicted by the existence of "parallel" relationships between genes). Moreover, a model incorporating parallel neutrality in the determination of expected double mutant fitness largely corrects the underestimation. Finally, it is shown that simple extensions of this newly developed framework permit the unambiguous definition and classification of gene interactions in a formal, general, and mathematical way. Consequently, the concept of genetic buffering as first conceived by Leland Hartwell becomes a specific case within a comprehensive model of gene interaction.
遗传缓冲在调控远交群体中基因型与表型之间的关系方面发挥着关键作用。虽然高通量筛选已通过检测“合成致死”或“合成病变”发现了许多遗传缓冲的实例,但缺乏一种用于跨系统对其进行定量分析的正式通用方法。在本报告中,描述了一种公理化数学框架,可用于对基因之间的缓冲关系进行分类、量化和比较。重要的是,该方法以比率量表为基础,从而允许定义一种新的基因相互作用中性模型——“平行”模型,它补充了常用的“乘积”模型。通过对先前发表的酵母基因相互作用数据进行统计分析,提供了支持平行模型的证据。该分析揭示了在携带非相互作用查询阵列配对的菌株中双突变体适应性一直被低估(正如基因之间“平行”关系的存在所预测的那样)。此外,一个在确定预期双突变体适应性时纳入平行中性的模型在很大程度上纠正了这种低估。最后,结果表明,这个新开发框架的简单扩展允许以正式、通用和数学的方式明确界定和分类基因相互作用。因此,由利兰·哈特韦尔最初提出的遗传缓冲概念成为基因相互作用综合模型中的一个具体例子。