Arnold Cosmas D, Zabidi Muhammad A, Pagani Michaela, Rath Martina, Schernhuber Katharina, Kazmar Tomáš, Stark Alexander
Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
Nat Biotechnol. 2017 Feb;35(2):136-144. doi: 10.1038/nbt.3739. Epub 2016 Dec 26.
Gene expression is controlled by enhancers that activate transcription from the core promoters of their target genes. Although a key function of core promoters is to convert enhancer activities into gene transcription, whether and how strongly they activate transcription in response to enhancers has not been systematically assessed on a genome-wide level. Here we describe self-transcribing active core promoter sequencing (STAP-seq), a method to determine the responsiveness of genomic sequences to enhancers, and apply it to the Drosophila melanogaster genome. We cloned candidate fragments at the position of the core promoter (also called minimal promoter) in reporter plasmids with or without a strong enhancer, transfected the resulting library into cells, and quantified the transcripts that initiated from each candidate for each setup by deep sequencing. In the presence of a single strong enhancer, the enhancer responsiveness of different sequences differs by several orders of magnitude, and different levels of responsiveness are associated with genes of different functions. We also identify sequence features that predict enhancer responsiveness and discuss how different core promoters are employed for the regulation of gene expression.
基因表达受增强子调控，增强子可激活其靶基因核心启动子的转录。虽然核心启动子的一个关键功能是将增强子活性转化为基因转录，但它们是否以及在多大程度上响应增强子激活转录，尚未在全基因组水平上进行系统评估。在此，我们描述了自转录活性核心启动子测序（STAP-seq），这是一种确定基因组序列对增强子反应性的方法，并将其应用于黑腹果蝇基因组。我们将候选片段克隆到带有或不带有强增强子的报告质粒中核心启动子（也称为最小启动子）的位置，将所得文库转染到细胞中，并通过深度测序对每种设置下每个候选片段起始的转录本进行定量。在存在单个强增强子的情况下，不同序列的增强子反应性相差几个数量级，不同水平的反应性与不同功能的基因相关。我们还鉴定了预测增强子反应性的序列特征，并讨论了如何利用不同的核心启动子来调控基因表达。
