The DOI matches its Crossref record; 214 of the 218 references it cites were found in a registry or an index.
Long-range enhancer–promoter contacts in gene expression control
Abstract
Spatiotemporal gene expression programmes are orchestrated by transcriptional enhancers, which are key regulatory DNA elements that engage in physical contacts with their target-gene promoters, often bridging considerable genomic distances. Recent progress in genomics, genome editing and microscopy methodologies have enabled the genome-wide mapping of enhancer-promoter contacts and their functional dissection. In this Review, we discuss novel concepts on how enhancer-promoter interactions are established and maintained, how the 3D architecture of mammalian genomes both facilitates and constrains enhancer-promoter contacts, and the role they play in gene expression control during normal development and disease.
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In the citing paper
“It is clear from both genome-wide profiling and perturbation studies that, of the multitudes of enhancers in a locus, not all of them provide input to every promoter [430, 431].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [431]
In the citing paper
“Promoter-interacting regions identified using these approaches typically show enrichment for enhancer-associated chromatin marks and disease-associated variants, and in a number of cases their target genes have been validated directly (reviewed in [431]).”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [431]
In the citing paper
“During the “search” of a target promoter (regardless of the “searching mechanism”), enhancers meet other genes that, however, are not activated by this enhancer [21,128,129].”
From Enhancer Function in the 3D Genome (2023) · cites this paper as [128]
In the citing paper
“Chromatin loops enable interactions between enhancers and promoters enabling fine control of gene expression, in addition to the regulation mediated by transcription factors and other epigenetic modifications”
From Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration (2023) · cites this paper as [27]
Citations
Cites
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., Lander, E. S., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.021 · Cited by 9,212
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829
Histone H3K27ac separates active from poised enhancers and predicts developmental state
Creyghton, M. P., Cheng, A. W., Welstead, G. G., Kooistra, T., Carey, B. W., Steine, E. J., Hanna, J., Lodato, M. A., Frampton, G. M., Sharp, P. A., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1016071107 · Cited by 4,302
Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
Maurano, M. T., Humbert, R., Rynes, E., Thurman, R. E., Haugen, E., Wang, H., Reynolds, A. P., Sandstrom, R., Qu, H., Brody, J., et al. (2012) · Science · doi:10.1126/science.1222794 · Cited by 3,716
Capturing Chromosome Conformation
Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002) · Science · doi:10.1126/science.1067799 · Cited by 3,652
Spatial partitioning of the regulatory landscape of the X-inactivation centre
Nora, E. P., Lajoie, B. R., Schulz, E. G., Giorgetti, L., Okamoto, I., Servant, N., Piolot, T., van Berkum, N. L., Meisig, J., Sedat, J., et al. (2012) · Nature · doi:10.1038/nature11049 · Cited by 2,895
Coactivator condensation at super-enhancers links phase separation and gene control
Sabari, B. R., Dall’Agnese, A., Boija, A., Klein, I. A., Coffey, E. L., Shrinivas, K., Abraham, B. J., Hannett, N. M., Zamudio, A. V., Manteiga, J. C., et al. (2018) · Science · doi:10.1126/science.aar3958 · Cited by 2,595
A unique chromatin signature uncovers early developmental enhancers in humans
Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S. A., Flynn, R. A., & Wysocka, J. (2011) · Nature · doi:10.1038/nature09692 · Cited by 2,233
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Mahara, S., Prüssing, S., Smialkovska, V., Krall, S., Holliman, S., Blum, B., Dachtler, V., Borgers, H., Sollier, E., Plass, C., et al. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.10.005 · Cited by 9
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Martín, G. M., Santoro, F., Blanco, E., Figueroa, G. P. G., Dily, F. L., Frigè, G., Vidal, E., Mugianesi, F., Ballaré, C., Gutiérrez, A., et al. (2022) · Genes & Development · doi:10.1101/gad.349115.121 · Cited by 5
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Pumo, G., & Rijli, F. M. (2025) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2025.103024 · Cited by 5
Venu, V., Small, E. M., Roth, C., Adikari, S., Vlot, A. H. C., Sullivan, K. A., Abeyratne, C. R., Jacobson, D., Starkenburg, S. R., Sanbonmatsu, K. Y., et al. (2025) · Epigenetics & Chromatin · doi:10.1186/s13072-025-00631-4 · Cited by 6
Farhangdoost, N., Pietrantonio, A., Liu, Y., Liao, C., Rochefort, D. L., Pacis, A., Alda, M., Dion, P. A., Chaumette, B., Khayachi, A., et al. (2025) · Scientific Reports · doi:10.1038/s41598-025-21716-w · Cited by 4
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Forte, G., Brackley, C., Gilbert, N., & Marenduzzo, D. (2026) · Current Opinion in Genetics and Development · doi:10.1016/j.gde.2025.102426 · Cited by 3
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Metadata
- Authors
- Schoenfelder, S., & Fraser, P.
- Affiliations
- Babraham Institute (GB)
- Florida State University (US)
- Corresponding author
- Schoenfelder, Stefan
- Venue
- Nature Reviews Genetics
- Published
- 2019-05-13
- Volume
- 20
- Issue
- 8
- Pages
- 437-455
- ISSN
- 1471-0056 (ISSN-L)
- 1471-0064
- OpenAlex
- W2945038365
- Semantic Scholar
- d851d5037a1a04033beae17bfcd824e8c27b304e
- Cited by
- 1,102
- References
- 218
- Citations by year
- 2026: 118 · 2025: 144 · 2024: 162 · 2023: 170 · 2022: 163 · 2021: 184 · 2020: 127 · 2019: 32
- FWCI
- 11.70
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Nature Reviews Genetics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Medical Research Council (MR/L007150/1, MR/T016787/1)
- Biotechnology and Biological Sciences Research Council (BB/J004480/1)
- National Heart, Lung, and Blood Institute (U01HL129971)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Keywords
- enhancer-promoter interactions, enhancers, 3D genome organization, chromatin looping, gene expression regulation, developmental gene regulation, disease
- MeSH terms
- Gene Editing, Animals, Enhancer Elements, Genetic, Humans, Mammals, Promoter Regions, Genetic, Gene Expression, Genome, Genomics
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