Regulation of disease-associated gene expression in the 3D genome

Key Points

  • The human genome harbours a dizzying array of regulatory sequences, such as enhancers with a priori unpredictable, promiscuous and context-dependent behaviour.

  • More than 90% of disease-associated variants lie in non-coding DNA, accumulating in presumptive enhancers. Therefore, a picture is emerging in which diseases and traits are often the consequence of erroneous wiring of regulatory circuitry between enhancers and their target genes.

  • Enhancers communicate with distant target genes through chromatin loops. Such transcription regulatory loops are formed within topologically associated domains (TADs), the structural and functional units of the chromosomes.

  • Disrupting enhancer–promoter loops, as well as TAD boundaries, can lead to gene dysregulation and disease, the latter due to previously insulated genes and enhancers being released to form new regulatory chromatin loops.

  • Technological advances and the availability of increasingly detailed genomic contact maps generated by Hi-C are enabling the elucidation of the physical contacts between genes and non-coding sequences in different cell types, which greatly facilitates the assigning of function to disease-associated genetic variation.

  • We present a roadmap — from disease-associated genetic variants to molecular mechanisms causing disease — that proposes to integrate epigenetic data with detailed 3D genome information and haplotype-resolved expression analysis to help move results descriptive genetic association studies towards the discovery of the molecular mechanisms underlying disease.

Abstract

Genetic variation associated with disease often appears in non-coding parts of the genome. Understanding the mechanisms by which this phenomenon leads to disease is necessary to translate results from genetic association studies to the clinic. Assigning function to this type of variation is notoriously difficult because the human genome harbours a complex regulatory landscape with a dizzying array of transcriptional regulatory sequences, such as enhancers that have unpredictable, promiscuous and context-dependent behaviour. In this Review, we discuss how technological advances have provided increasingly detailed information on genome folding; for example, genome folding forms loops that bring enhancers and target genes into close proximity. We also now know that enhancers function within topologically associated domains, which are structural and functional units of chromosomes. Studying disease-associated mutations and chromosomal rearrangements in the context of the 3D genome will enable the identification of dysregulated target genes and aid the progression from descriptive genetic association results to discovering molecular mechanisms underlying disease.

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Figure 1: Mechanism of gene expression regulation by enhancers.
Figure 2: TADs host de novo and pre-formed regulatory enhancer–promoter loops.
Figure 3: Erroneous regulatory wiring between enhancers and target genes causing disease.
Figure 4: Regulatory detours between TADs.
Figure 5: Disease variants associated with disruptions in TADs and the 3D regulatory landscape.

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Acknowledgements

W.d.L's research is supported by a Netherlands Organisation for Scientific Research-Chemical Sciences (NWO/CW) TOP grant (714.012.002), an NWO-Innovational Research Incentives Scheme (VICI) grant (724.012.003), a European Union grant (2010–259743; Modelling Hepatocellular Carcinoma (MODHEP)) and a grant from The Leducq Foundation (FP058566-01-PR).

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Glossary

Thalassaemias

Inherited blood disorders characterized by the abnormal formation of haemoglobin and caused by the reduced production of globin proteins.

Enhancers

Regulatory DNA elements that can upregulate the transcriptional output of a target gene.

Topologically associated domains

(TADs). Boundary-insulated chromosomal segments within which sequences preferentially contact each other.

Cofactor p300

An enhancer-associated protein with histone acetyltransferase activity that recruits transcriptional-activating proteins and can increase gene expression.

STARR-seq

Self-transcribing active regulatory region sequencing. A massively parallel analysis plasmid based method to interrogate the sequence-intrinsic enhancer capacity of genomic segments.

Housekeeping gene promoter

Promoter of a gene that is expressed in all tissues.

Minimal promoter

The minimal portion of the promoter (the core promoter) required to initiate transcription. When integrated in the genome, it depends on enhancers for detectable levels of transcription.

Enhancer trap assay

Assay in which transcriptional output of a genomic integrated reporter gene under the control of a minimal promoter is used to identify regulatory elements in a given genomic context.

Structural variations

Changes in the linear order of multiple base pairs as a consequence of a chromosomal rearrangement (for example, translocation, inversion, deletion, insertion or duplication).

Nuclear compartments

Nuclear sub-volumes in which chromosomal regions with similar chromatin composition spatially aggregate.

Haplotype

A genomic region that is inherited from one parent that has a sequence composition with genetic variations such as single-nucleotide polymorphisms (SNPs) that can be different from those found in the corresponding genomic region inherited by the other parent.

Chromocentres

Sites in the nuclear interior where heterochromatic pericentromeric regions of different chromosomes cluster.

Polycomb

A family of proteins that remodel chromatin to repress transcription.

SNPs

Single-nucleotide polymorphisms causing genetic variation.

Indels

Short DNA sequence insertions or deletions.

Copy number variations

Changes in the number of copies of a given chromosomal segment in a cell caused by their duplication or deletion.

Drivers

Risk-associated variants that cause disease.

Passengers

Risk-associated variants that do not cause disease.

Linkage disequilibrium

Alleles of SNPs are in linkage disequilibrium when their frequency of association in the population is not random, which indicates that they are physically and/or functionally linked.

Chromosomal breakpoints

The sites where chromosomes were incidentally broken and, as consequence of erroneous DNA repair, now flank a chromosomal rearrangement.

Haploinsufficient

A phenotypic state observed despite a diploid organism still carrying one functional gene.

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Krijger, P., de Laat, W. Regulation of disease-associated gene expression in the 3D genome. Nat Rev Mol Cell Biol 17, 771–782 (2016). https://doi.org/10.1038/nrm.2016.138

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