Department of Biochemistry, Gene Center, Ludwig-Maximillians-Universität München, Feodor-Lynen-str 25, Munich, Germany.
Department of Biology II, Evolutionary Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
Mol Syst Biol. 2022 Feb;18(2):e9816. doi: 10.15252/msb.20209816.
The core promoter plays a central role in setting metazoan gene expression levels, but how exactly it "computes" expression remains poorly understood. To dissect its function, we carried out a comprehensive structure-function analysis in Drosophila. First, we performed a genome-wide bioinformatic analysis, providing an improved picture of the sequence motifs architecture. We then measured synthetic promoters' activities of ~3,000 mutational variants with and without an external stimulus (hormonal activation), at large scale and with high accuracy using robotics and a dual luciferase reporter assay. We observed a strong impact on activity of the different types of mutations, including knockout of individual sequence motifs and motif combinations, variations of motif strength, nucleosome positioning, and flanking sequences. A linear combination of the individual motif features largely accounts for the combinatorial effects on core promoter activity. These findings shed new light on the quantitative assessment of gene expression in metazoans.
核心启动子在设定后生动物基因表达水平方面起着核心作用，但它如何“计算”表达仍然知之甚少。为了剖析其功能，我们在果蝇中进行了全面的结构-功能分析。首先，我们进行了全基因组的生物信息学分析，提供了一个改进的序列基序结构图谱。然后，我们使用机器人和双荧光素酶报告基因检测，大规模、高精度地测量了约 3000 个带有和不带有外部刺激（激素激活）的突变型合成启动子的活性。我们观察到不同类型的突变对活性有强烈的影响，包括单个序列基序和基序组合的缺失、基序强度、核小体定位和侧翼序列的变化。单个基序特征的线性组合在很大程度上解释了核心启动子活性的组合效应。这些发现为后生动物基因表达的定量评估提供了新的线索。
