Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation

Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature.

生物体通过运用转录调控因子来应对变化。然而，在面临罕见环境时，转录调控因子及其启动子的进化可能过于缓慢。本研究旨在探讨基因复制和扩增的内禀不稳定性是否为经典基因调控提供了一种通用的替代方案。通过实时监测大肠杆菌中的基因拷贝数突变，我们发现基因复制和扩增能够通过快速产生拷贝数，从而表达水平的多态性，使生物体适应环境波动。这种‘扩增介导的基因表达调控’在时间尺度上与经典基因调控相似，并能应对快速的环境变化。数学建模表明，在转录因子方案难以进化或维持的随机环境中，扩增同样可以调节基因表达。基因扩增的短暂性引发了一种通用的种群级机制，该机制依赖于遗传异质性，能够迅速调节任何基因的表达，而不留下任何基因组特征。