Journal
NATURE BIOTECHNOLOGY
Volume 35, Issue 2, Pages 136-144Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/nbt.3739
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Funding
- European Research Council (ERC) under the European Union's Horizon research and innovation programme [647320]
- Austrian Science Fund (FWF) [F4303-B09]
- Boehringer Ingelheim GmbH
- Austrian Research Promotion Agency (FFG)
- European Research Council (ERC) [647320] Funding Source: European Research Council (ERC)
- Austrian Science Fund (FWF) [W1207] Funding Source: Austrian Science Fund (FWF)
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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 melanogastergenome. 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.
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