ArticleNature biotechnology2017
Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution.
Article in Nature biotechnology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed.
- Intrinsic promoter responsiveness dictates sensitivity to transcriptional activation by enhancers.bioRxiv : the preprint server for biology · 2026Article
- Visualizing genetic information flow in space and time.Science China. Life sciences · 2025Review
- Applications of high-throughput reporter assays to gene regulation studies.Current opinion in structural biology · 2025Review
- Chromatin interaction-based annotation of regulatory elements reveals dynamic promoter-enhancer interactions in lymphocyte development.iScience · 2025Article
- Update on the genetics of allergic diseases.The Journal of allergy and clinical immunology · 2025Review
- Technology to the rescue: how to uncover the role of transposable elements in preimplantation development.Biochemical Society transactions · 2024Review
- Sequence basis of transcription initiation in the human genome.Science (New York, N.Y.) · 2024Article
- From Genotype to Phenotype: How Enhancers Control Gene Expression and Cell Identity in Hematopoiesis.HemaSphere · 2023Review
- Review
- Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation.Nucleic acids research · 2023Article
- POSTRE: a tool to predict the pathological effects of human structural variants.Nucleic acids research · 2023Article
- Functionally distinct promoter classes initiate transcription via different mechanisms reflected in focused versus dispersed initiation patterns.The EMBO journal · 2023Article
- Leveraging massively parallel reporter assays for evolutionary questions.Genome biology · 2023Review
- Systematic identification and characterization of repressive domains in Drosophila transcription factors.The EMBO journal · 2023Article
- Identification and characterization of enhancer elements controlling cell type-specific and signalling dependent chromatin programming during hematopoietic development.Stem cell investigation · 2023Review
- Article
- Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes.Cell · 2022Article
- CTCF shapes chromatin structure and gene expression in health and disease.EMBO reports · 2022Review
- Altering enhancer-promoter linear distance impacts promoter competition in cis and in trans.Genetics · 2022Article
- Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome.Molecular cell · 2022Article
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7 authors.
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Abstract
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.