Enhancers navigate the three-dimensional genome to direct cell fate decisions

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Summary

The activity and selectivity of transcriptional enhancers determine gene expression patterns that enable a zygote to become a complex organism. How enhancers convey regulatory information is a central conundrum in biology. Here, we discuss recent progress provided by rapidly evolving technologies in understanding enhancer–promoter interactions in the context of overall nuclear genome organization.

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.).

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