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]
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Acetylation of histone H2B marks active enhancers and predicts CBP/p300 target genes
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“This allows the assemblage of protein complex at specific loci, such as promoters and non-coding cisregulatory elements, to regulate gene transcription (Allis and Jenuwein, 2016; Schoenfelder and Fraser, 2019).”
BackgroundIncreased enhancer–promoter interactions during developmental enhancer activation in mammals
Chen, Z., Snetkova, V., Bower, G., Jacinto, S. H., Clock, B., Dizehchi, A., Barozzi, I., Mannion, B. J., Alcaina‐Caro, A., López-Ríos, J., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01681-2 · Cited by 98
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“1 3 “selected” for activation in cis by TFs, following which their contacts with target promoters are then “facilitated” by the underlying chromosomal topology and then further “specified” by parameters of enhancer–promoter compatibility [431].”
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“Apart from promoters and miRNAs, gene expression may depend on the presence of enhancers that could be located kilobases away (Schoenfelder and Fraser, 2019; Vangala et al., 2020).”
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“Cell type enhancers play an essential role in controlling cell-typespecific gene expression programs by engaging in physical contact [28].”
BackgroundResultThe impact of DNA methylation on CTCF-mediated 3D genome organization
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“Unlike TADs, these loops can vary tremendously between cell types and are important for determining cell identity 10 .”
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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