Review Article | Published:

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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Acknowledgements

The authors thank L. Chakalova, N. Gonen and M. Osterwalder for insightful comments on the manuscript, and E. Nora for valuable discussions. They apologize to colleagues whose important primary studies they were unable to cite due to space constraints. P.F. was supported by grants from the Medical Research Council UK (MR/L007150/1), the US National Institutes of Health (4D Nucleome 1U01HL129971-01), the European Research Council (340152) and the Biotechnology and Biological Science Research Council UK (BB/J004480/1). S.S. was supported by the Biotechnology and Biological Science Research Council UK (BB/J004480/1) and a Career Progression Fellowship from the Babraham Institute.

Reviewer information

Nature Reviews Genetics thanks P. Farnham and the other, anonymous reviewer(s) for their contribution to the peer review of this work.

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Both authors were responsible for researching data for the article, discussing content, writing the article, and reviewing and/or editing the manuscript before submission.

Competing interests

The authors declare no competing interests.

Correspondence to Stefan Schoenfelder.

Glossary

dCas9

A nuclease-deficient variant of the Cas9 protein. As for Cas9, it can be targeted to defined genomic loci by a guide RNA. dCas9 is commonly used as a fusion protein, thus allowing locus-specific recruitment of domains conferring activities such as transcriptional modulation, chromatin modification or intermolecular dimerization.

Transcription factories

Discrete nuclear foci of concentrated, hyperphosphorylated RNA polymerase II at which nascent transcription occurs. Active genes and their regulatory elements have been shown to coalesce at transcription factories, and the dynamic relocation of genes towards and away from transcription factories correlates with their transcriptional ‘on’ and ‘off’ cycles.

Super-enhancer

A class of regulatory regions in mammalian genomes with an unusually high degree of enrichment for the binding of the transcriptional co-activator mediator complex subunit 1 (MED1), the histone mark H3K27ac or cell-type-specific transcription factors. As they often result from concatenating individual enhancers, super-enhancers on average span considerably larger genomic regions than ‘normal’ enhancers. Super-enhancers are often located in the proximity of lineage-specifying genes, which they have been proposed to control. The extent to which super-enhancers represent a class of regulatory elements that is functionally distinct from ‘normal’ enhancers is under debate.

Expression quantitative trait loci

(eQTLs). Genomic loci in which genetic variants can be causally linked to variation of gene expression levels, either in cis or, more rarely, in trans. eQTLs are identified by testing the linkage between variation in expression and genetic polymorphisms. eQTL mapping has become a widely used tool to identify genetic sequence variants that affect gene expression control.

TRIP

Thousands of reporters integrated in parallel (TRIP) is a high-throughput assay based on the random integration of barcoded GFP reporter genes (under the control of a minimal promoter) into the genome, to reveal the effects of cis-regulatory elements and the local chromatin environment on gene expression.

Shadow enhancers

Discovered in Drosophila melanogaster, these ‘secondary’ enhancers appear to act in a largely redundant manner to ‘primary’ enhancers; that is, both enhancers drive similar patterns of expression, and deletion of either enhancer does not result in aberrant phenotypes. The largely overlapping functions of primary and secondary enhancers serve to buffer gene expression patterns against genetic or environmental perturbations, thereby conferring robustness during development.

Pioneer transcription factors

A class of transcription factors that can bind to target sites in compacted (‘closed’) chromatin, which is covered by nucleosomes and is not DNase I hypersensitive. Pioneer transcription factors are thought to remodel the chromatin landscape during early steps of cell fate decisions to facilitate the subsequent recruitment of other (non-pioneer) transcription factors and DNA-modifying and chromatin-modifying enzymes to their target sites.

Phase-separated domains

Distinct subcellular non-membrane-bound domains, in the nucleus or in the cytoplasm. They are dynamic compartments in which the components are concentrated relative to the surroundings. Phase-separated condensates in the nucleus have been implicated in various aspects of genome control, including gene expression and heterochromatin formation.

Low-complexity domains

Protein domains (also known as intrinsically disordered regions) that are often found in the activation domains of transcription factors. They contain repeats of single amino acids or short amino acid motifs that are usually not amenable to crystallography. Interactions between low-complexity domains promote the aggregation of transcription factors and cofactors in droplets in vitro and are required for the formation of phase-separated condensates in the nucleus, which have been proposed to drive transcriptional control.

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Fig. 1: Enhancer–promoter contacts in transcriptional control.
Fig. 2: The Shh limb bud enhancer: a paradigm for long-range enhancer control of gene expression.
Fig. 3: Loop extrusion.
Fig. 4: Dynamic enhancer–promoter contacts in the circadian control of gene expression.
Fig. 5: Additive effects of enhancer contacts promote increased gene expression.
Fig. 6: A ‘selecting–facilitating–specifying’ model for enhancer–promoter contact specificity.