Yang Eric J Y, Maranas Cassandra J, Nemhauser Jennifer L
University of Washington, Department of Biology, Seattle, WA 98105-1800, USA.
bioRxiv. 2023 Jun 12:2023.06.12.544596. doi: 10.1101/2023.06.12.544596.
Promoters regulate both the amplitude and pattern of gene expression-key factors needed for optimization of many synthetic biology applications. Previous work in found that promoters that contain a TATA-box element tend to be expressed only under specific conditions or in particular tissues, while promoters which lack any known promoter elements, thus designated as Coreless, tend to be expressed more ubiquitously. To test whether this trend represents a conserved promoter design rule, we identified stably expressed genes across multiple angiosperm species using publicly available RNA-seq data. Comparisons between core promoter architectures and gene expression stability revealed differences in core promoter usage in monocots and eudicots. Furthermore, when tracing the evolution of a given promoter across species, we found that core promoter type was not a strong predictor of expression stability. Our analysis suggests that core promoter types are correlative rather than causative in promoter expression patterns and highlights the challenges in finding or building constitutive promoters that will work across diverse plant species.
启动子调控基因表达的幅度和模式，而基因表达的幅度和模式是许多合成生物学应用优化所需的关键因素。之前的研究发现，含有TATA框元件的启动子往往仅在特定条件下或特定组织中表达，而缺乏任何已知启动子元件的启动子（因此被称为无核心启动子）往往更广泛地表达。为了测试这种趋势是否代表一种保守的启动子设计规则，我们利用公开的RNA测序数据，在多个被子植物物种中鉴定出稳定表达的基因。核心启动子结构与基因表达稳定性之间的比较揭示了单子叶植物和双子叶植物在核心启动子使用上的差异。此外，当追踪给定启动子在物种间的进化时，我们发现核心启动子类型并不是表达稳定性的有力预测指标。我们的分析表明，核心启动子类型在启动子表达模式中是相关的而非因果关系，并突出了寻找或构建能在多种植物物种中起作用的组成型启动子所面临的挑战。
