Enhancers navigate the three-dimensional genome to direct cell fate decisions
Introduction
Specialized cell types have the same underlying genome but are distinguished by the complement of genes they express. These unique transcriptomes are under the direction of enhancers [1,2]. Mammalian genomes contain thousands of genes but hundreds of thousands of enhancers, which are highly cell type specific. Understanding how enhancers activate target genes has been challenging because they can be located at exceptionally large genomic distances along chromosomes from their targets (up to megabases). Importantly, enhancers appear to be the location of many thousands of genetic variants (single nucleotide polymorphisms) that influence risk for common diseases [3,4]. Thus, understanding how enhancers function and are regulated is critical to understanding normal and disease states.
Chromosomes are sequentially partitioned into active and inactive domains (A and B compartment, respectively). In metazoans, these domains are further subdivided into topologically associating domains (TAD) with borders enriched for the architectural/insulator protein CCCTC-binding factor (CTCF). Sequences within TADs interact preferentially with each other and less often with those in other TADs. Enhancers and the target genes they activate typically lie within the same TAD. The question of the relationship between genome folding and gene expression has been of enduring interest [5,6]. In this context, what underlies enhancer–promoter interaction remains unclear with accepted models becoming less definitive and newer models in need of stronger support. Nuclear architecture studies, genome editing, and imaging approaches have driven remarkable progress in the past few years in understanding the mechanics and function of different levels of genome organization. Here we discuss the latest advances in using these technologies to understand enhancers. Excellent, more comprehensive reviews of enhancers are available elsewhere [2,7,8].
Section snippets
Interaction of remote enhancers with target genes
Enhancers are relatively short (several hundred kb) stretches of DNA crowded with recognition motifs for cell type-specific transcription factors. It is thought that the cooperative binding of complexes of these proteins results in recruitment of co-activators, for example, p300, Mediator and BRG1, and contributes to evicting nucleosomes from DNA to create an open chromatin environment. Mechanisms by which regulatory elements can control genes located far away in the genome have been debated
The role of chromatin topology and CTCF/cohesin in enhancer–promoter interaction
TADs are thought to form through dynamic cohesin complex-mediated extrusion and to be stopped at CTCF sites that are orientated toward each other [17,18] (Figure 2a). Enhancers communicate principally with target genes that lie within the same TAD, and even within the same sub-TAD or insulated neighborhood [19,20] (Figure 2b). Based on this topology, it would seem reasonable to suppose that TADs restrict enhancers to genes within their domains and that their borders contribute to blocking
Enhancer communities
Genes can be regulated by multiple enhancers that are relatively close to each other along the linear genomic sequence and can cluster in three dimensions to form hubs or communities. Variably called LCRs, super enhancers (SEs), or stretch enhancers, they are bound by a high density of transcription factors and co-factors and typically drive expression of key cell identity genes (reviewed in Ref. [37]). The constituent enhancers typically activate a single target gene but how this is
The importance of biomolecular condensates to enhancer–promoter transcription activation
The nucleolus, Cajal bodies, and constitutive heterochromatin are examples of dynamic membrane-less compartments that concentrate related genomic regions, for example, heterochromatin [46] and the proteins and RNA molecules needed for specialized nuclear functions (reviewed in Refs. [47,48]; Figure 3a). These bodies have liquid-like properties suggesting they are condensates that may form by liquid–liquid phase separation (LLPS). Transcription factors, coactivators such as BRD4 and MED1, and
Enhancer RNAs and enhancer function
Enhancer RNAs (eRNAs) are long noncoding RNAs that are transcribed from active enhancers in a cell- and tissue-specific manner (reviewed in Ref. [59]). eRNAs are implicated in the regulation of transcription in diverse ways. eRNA transcripts can recruit transcription factors, co-activators, or cohesin either to promote enhancer looping to a target gene or to otherwise contribute to transcription activation [60, 61, 62, 63, 64]. In other cases, the eRNA may be dispensable for the enhancer effect
Conclusions
This brief review leaves the strong impression that fundamental questions about how enhancers work remain unresolved. Proximity between enhancers and promoters for transcription activation seems to be variable. Formation of condensates may provide an explanation of how enhancer activation can occur without gene proximity, but much remains unclear about the nature and formation of condensates. And eRNAs do not yet seem to have a unified role in enhancer function. Why some enhancers are impacted
Conflict of interest statement
Nothing declared.
Acknowledgement
This work was supported by the Intramural Program of the NIDDK (DK 075033 to A.D.).
References (70)
- et al.
Mechanisms of interplay between transcription factors and the 3D genome
Mol Cell
(2019) - et al.
The 3D genome as moderator of chromosomal communication
Cell
(2016) - et al.
Regulatory landscaping: how enhancer-promoter communication is sculpted in 3D
Mol Cell
(2019) - et al.
Looping and interaction between hypersensitive sites in the active beta-globin locus
Mol Cell
(2002) - et al.
Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1
Mol Cell
(2005) - et al.
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping
Cell
(2014) - et al.
Cohesin loss eliminates all loop domains
Cell
(2017) - et al.
Genetic dissection of the alpha-globin super-enhancer in vivo
Nat Genet
(2016) - et al.
Temporal dissection of an enhancer cluster reveals distinct temporal and functional contributions of individual elements
Mol Cell
(2021) - et al.
LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice
Nature
(2019)
Organization of chromatin by intrinsic and regulated phase separation
Cell
Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences
Genes Dev
Fetal gamma-globin genes are regulated by the BGLT3 long noncoding RNA locus
Blood
Developmental enhancers and chromosome topology
Science
Systematic localization of common disease-associated variation in regulatory DNA
Science
A compendium of promoter-centered long-range chromatin interactions in the human genome
Nat Genet
The relationship between genome structure and function
Nat Rev Genet
Long-range enhancer-promoter contacts in gene expression control
Nat Rev Genet
The active spatial organization of the beta-globin locus requires the transcription factor EKLF
Genes Dev
Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations
Nat Genet
Shh and ZRS enhancer colocalisation is specific to the zone of polarising activity
Development
Decreased enhancer-promoter proximity accompanying enhancer activation
Mol Cell
Dynamic interplay between enhancer-promoter topology and gene activity
Nat Genet
Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity
Elife
Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
Proc Natl Acad Sci U S A
Formation of chromosomal domains by loop extrusion
Cell Rep
Promoter-enhancer communication occurs primarily within insulated neighborhoods
Mol Cell
Transcription factors and 3D genome conformation in cell-fate decisions
Nature
Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization
Cell
Developmentally regulated Shh expression is robust to TAD perturbations
Development
Chromatin topology and the timing of enhancer function at the HoxD locus
Proc Natl Acad Sci U S A
Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression
Nat Genet
Chromatin structure dynamics during the mitosis-to-G1 phase transition
Nature
Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells
Science
Extensive heterogeneity and intrinsic variation in spatial genome organization
Cell
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