Cis‐Regulatory Mutations in Human Disease

Abstract

Enhancers are cis‐regulatory elements that accurately control the spatiotemporal pattern of gene expression and these can function over large genomic distances to activate the target gene. Genomewide methodologies have revealed general chromatin signatures for enhancers and the human and mouse noncoding genomes have undergone an extensive functional annotation. An increasing number of enhancer mutations are showing association with human disease, and disease mechanisms are being described that result from altered gene expression. Owing to the modular nature of enhancers, mutations can generate disease phenotypes that represent either a subset of the symptoms of coding mutations or due to a change in specificity of enhancer activity, a novel phenotype. Topologically associated domains, also known as TADs, have emerged as a fundamental structural unit to limit enhancer regulatory activity and disruptions of these boundaries result in gene misexpression and disease.

Key Concepts

  • Enhancers function over large genomic distances to activate the target gene.
  • Methodologies have been developed to annotate the functional elements in the noncoding genome.
  • Mutations in enhancers that regulate developmental gene expression can cause congenital abnormalities.
  • Owing to the modular nature of enhancers the disease presentation may be different from mutations in the coding region of the target gene.
  • Disruption of TAD boundaries can result in gene misexpression and disease.

Keywords: cis‐regulatory mutation; enhancer; congenital abnormalities; gene expression; topological associated domains

Figure 1. The roles of enhancers in regulating gene expression in the PAX6, SOX9 and SHH loci. (a) In the PAX6 locus, PAX6 protein binds to the SIMO enhancer leading to its interaction with the PAX6 gene. This maintains an auto regulatory feedback loop resulting in the production of additional PAX6 (i). A G>T point mutation alters the PAX6 binding site within the SIMO enhancer leading to reduced PAX6 binding and loss of the auto regulatory loop (ii). (b) In the SOX9 locus a collection of highly conserved noncoding elements (HCNEs) between the SOX9 and KCNJ2 genes are responsible for regulating optimal SOX9 levels (i). Increased binding of MSX1 (which acts as an inhibitor) at one of these HCNEs due to a T>C point mutation weakens its influence on the SOX9 gene expression leading to a disease phenotype (ii). Removal of this HCNE completely due to a 75 kb deletion also effects SOX9 levels (iii). In contrast, a duplication event may lead to overproduction of SOX9 due to the action of additional HCNEs on the SOX9 gene (iv). (c) In the limb bud the SHH gene is regulated by the ZRS, while in the forebrain it is regulated by SBE2. Within the limb, SHH is maintained in the posterior regions due to the correct ratio of ETS1/GABPα to ETV4/ETV5 proteins bound at the ZRS (i). Point mutations within this enhancer can lead to additional ETS1/GABPα sites at the detriment of ETV4/ETV5 sites, leading to the production of SHH in both anterior and posterior regions and the associated limb phenotypes (ii). Likewise, a 2 kb deletion may remove a silencer acting on the SHH gene leading to ectopic SHH expression (iii). In the forebrain the SHH gene is regulated by SBE2, which is situated roughly equidistant between the ZRS and SHH (iv). An inversion event removes the influence of SBE2, instead allowing an enhancer (HCNE2) within the EMID2 gene to regulate SHH expression, a process referred to as enhancer adoption (v).
Figure 2. Point mutations can effect transcription factor binding sites (TFBSs) within an enhancer leading to alterations in gene expression. (a) The precise quantity and type of transcription factor binding to enhancers are responsible for regulating the normal expression levels of a gene. (b) Point mutations within an enhancer may remove some of these TFBSs leading to reduced binding and reduced expression of the target gene. (c) Sometimes mutations may create sites for repressor proteins, which again leads to a reduction in target gene expression. (d) Alternatively, point mutations may produce additional TFBSs for activator proteins, which may result in ectopic gene expression.
Figure 3. Topological associated domains (TADs) are separated by boundary regions, which, when removed, allow enhancers from previously inaccessible regions to influence the expression of genes within the TAD. (a) Within a TAD, boundary regions such as those provided by CTCF sites restrict the influence of enhancers to genes within a defined area. (b) However, when a TAD boundary is removed, perhaps due to a deletion, enhancers from the adjacent TAD may act on genes within this deconstructed TAD thereby leading to abnormal gene expression levels.
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Further Reading

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Douglas, Adam, Peluso, Silvia, Lettice, Laura A, and Hill, Robert E(Aug 2016) Cis‐Regulatory Mutations in Human Disease. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0024920]