Deep indel mutagenesis reveals the impact of insertions and deletions on protein stability and function

Amino acid insertions and deletions (indels) are an abundant class of genetic variants. However, compared to substitutions, the effects of indels are not well understood and poorly predicted. Here we address this shortcoming by performing deep indel mutagenesis (DIM) of structurally diverse proteins. Indel tolerance is strikingly different to substitution tolerance and varies extensively both between different proteins and within different regions of the same protein. Although state of the art variant effect predictors perform poorly on indels, we show that both experimentally-measured and computationally-predicted substitution scores can be repurposed as good indel variant effect predictors by incorporating information on protein secondary structures. Quantifying the effects of indels on protein-protein interactions reveals that insertions can be an important class of gain-of-function variants. Our results provide an overview of the impact of indels on proteins and a method to predict their effects genome-wide. DNA-seq of PCR amplicon

氨基酸插入与缺失（indels，全称为insertions and deletions）是一类分布广泛的遗传变异类型。然而，与碱基替换相比，学界对indels的效应尚未形成充分认知，其效应预测精度也相对较差。为此，我们通过对结构多样性丰富的蛋白质开展深度indel诱变（deep indel mutagenesis，简称DIM）研究，弥补了这一研究短板。indel耐受特性与替换耐受特性存在显著差异，且在不同蛋白质之间以及同一蛋白质的不同区域内均存在广泛差异。尽管当前顶尖的变异效应预测工具在indels预测任务中表现不佳，但我们证明，通过引入蛋白质二级结构信息，可将实验测得与计算预测得到的替换得分重新用作优质的indel变异效应预测工具。通过量化indels对蛋白质-蛋白质相互作用的影响，研究发现插入变异可作为一类重要的功能获得性（gain-of-function）变异类型。本研究全面概述了indels对蛋白质的影响，并提供了一种可在全基因组范围内预测其效应的方法。PCR扩增子的DNA测序