Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation
Open accessAbstract
Gene transcription in animals involves the assembly of RNA polymerase II at core promoters and its cell-type-specific activation by enhancers that can be located more distally. However, how ubiquitous expression of housekeeping genes is achieved has been less clear. In particular, it is unknown whether ubiquitously active enhancers exist and how developmental and housekeeping gene regulation is separated. An attractive hypothesis is that different core promoters might exhibit an intrinsic specificity to certain enhancers. This is conceivable, as various core promoter sequence elements are differentially distributed between genes of different functions, including elements that are predominantly found at either developmentally regulated or at housekeeping genes. Here we show that thousands of enhancers in Drosophila melanogaster S2 and ovarian somatic cells (OSCs) exhibit a marked specificity to one of two core promoters--one derived from a ubiquitously expressed ribosomal protein gene and another from a developmentally regulated transcription factor--and confirm the existence of these two classes for five additional core promoters from genes with diverse functions. Housekeeping enhancers are active across the two cell types, while developmental enhancers exhibit strong cell-type specificity. Both enhancer classes differ in their genomic distribution, the functions of neighbouring genes, and the core promoter elements of these neighbouring genes. In addition, we identify two transcription factors--Dref and Trl--that bind and activate housekeeping versus developmental enhancers, respectively. Our results provide evidence for a sequence-encoded enhancer-core-promoter specificity that separates developmental and housekeeping gene regulatory programs for thousands of enhancers and their target genes across the entire genome.
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Most conventional MPRAs utilize a single promoter for the reporter, which may not be sensitive to all enhancers.
“Of note, most conventional MPRAs utilize a single promoter for the reporter, that may not be sensitive to all enhancers79.”
From Towards a comprehensive catalogue of validated and target-linked human enhancers (2020) · cites this paper as [79]
The Extended Data Figure 3 caption shows that many enhancers were active with one core promoter but not the other, supporting the concern that a reporter using one promoter may miss enhancers. The passages do not establish that most conventional MPRAs use a single promoter. (LLM, conf=0.83)
Experimental — accuracy not yet measuredMost MPRAs only test for enhancer activity using a single promoter, or at best a handful, which could contribute to a high false negative rate.
“The fact that most MPRAs only test for enhancer activity using a single promoter, or at best a handful79, could contribute to a high false negative rate.”
From Towards a comprehensive catalogue of validated and target-linked human enhancers (2020) · cites this paper as [79]
The study tested enhancer activity with two core promoters, and its results show that many enhancers were much more active with one than the other (Abstract; page not provided). It therefore supports the relevance of testing more than one promoter, but does not establish the cited claim that most MPRAs use only one or a handful of promoters. The possible false-negative consequence is framed as the citing authors’ inference. (LLM, conf=0.82)
Experimental — accuracy not yet measuredMany epromoters control house-keeping genes in cis as promoters, but may regulate lineage-specific or inducible genes distally as enhancers.
“Notably, while many such elements control house-keeping genes in cis (as promoters), they may regulate lineage-specific or inducible genes distally (as enhancers) [240, 247].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [247]
The Results passage on genomic distributions (labelled Abstract in our copy; no page supplied) reports that many housekeeping-core-promoter enhancers overlap or lie near transcription start sites and can act as enhancers from a distal position in reporter assays. Extended Data Figure 5 also discusses their promoter-like appearance. The paper does not show that those same elements distally regulate lineage-specific or inducible genes; it instead describes developmental and housekeeping enhancers as largely distinct classes. (LLM, conf=0.87)
Experimental — accuracy not yet measuredEnhancers regulating housekeeping genes may act via distinct sets of TFs and cofactors than enhancers regulating developmentally specific genes.
“Enhancers regulating housekeeping genes may act via a distinct sets of TFs and cofactors than enhancers regulating developmentally specific genes79,120.”
From Towards a comprehensive catalogue of validated and target-linked human enhancers (2020) · cites this paper as [79]
This preference was consistent with the tissue-invariant or tissue-specific activity of the enhancers themselves.
“Notably, this preference was consistent with the tissue-invariant or tissue-specific activity of the enhancers themselves [247].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [247]
A massively parallel reporter assay in Drosophila cells revealed distinct groups of enhancers that preferred one of two types of core promoter, derived from either a housekeeping or a developmental gene and enriched for different TF binding motifs.
“a massively parallel reporter assay in Drosophila cells revealed distinct groups of enhancers that preferred one of two types of core promoter, derived from either a housekeeping or a developmental gene and enriched for different TF binding motifs [247].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [247]
Biochemical annotations fail to specify which gene(s) a putative enhancer regulates, let alone the degree of activation conferred.
“Third, biochemical annotations fail to specify which gene(s) a putative enhancer regulates, let alone the degree of activation conferred78,79.”
From Towards a comprehensive catalogue of validated and target-linked human enhancers (2020) · cites this paper as [79]
The Methods section on enhancer-to-gene assignment (page unavailable) describes proximity-based assignment strategies, and the reported STARR-seq results measure promoter-specific activation. Neither passage assesses whether biochemical annotations can identify an enhancer’s target genes or quantify its activation. Searches for biochemical annotations, target-gene prediction, and quantitative activity found no passage making that comparison. (LLM, conf=0.69)
Experimental — accuracy not yet measured
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- Authors
- Zabidi, M. A., Arnold, C. D., Schernhuber, K., Pagani, M., Rath, M., Frank, O., & Stark, A.
- Affiliations
- Research Institute of Molecular Pathology (AT)
- Corresponding author
- Stark, Alexander
- Venue
- Nature
- Published
- 2014-12-15
- Volume
- 518
- Issue
- 7540
- Pages
- 556-559
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC6795551
- OpenAlex
- W2029492292
- Cited by
- 471
- References
- 6
- Citations by year
- 2026: 24 · 2025: 37 · 2024: 37 · 2023: 44 · 2022: 43 · 2021: 47 · 2020: 43 · 2019: 46 · 2018: 36 · 2017: 40 · 2016: 41 · 2015: 33
- FWCI
- 15.59
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- housekeeping genes, developmental gene regulation, Drosophila melanogaster, enhancer-promoter interactions, RNA polymerase II, cell type-specific enhancers, DREF, transcription factor binding, ribosomal protein genes, ovarian somatic cells, S2 cells, gene regulatory programs
- MeSH terms
- Animals, Base Sequence, Cell Line, DNA-Binding Proteins, Drosophila melanogaster, Enhancer Elements, Genetic, Models, Genetic, Organ Specificity, Promoter Regions, Genetic, Substrate Specificity, Transcription Factors, Transcriptional Activation, Gene Expression Regulation, Developmental, Genes, Essential, Drosophila Proteins, Genome, Insect
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