cis-regulatory mutations are a genetic cause of human limb malformations

Abstract

The underlying mutations that cause human limb malformations are often difficult to determine, particularly for limb malformations that occur as isolated traits. Evidence from a variety of studies shows that cis-regulatory mutations, specifically in enhancers, can lead to some of these isolated limb malformations. Here, we provide a review of human limb malformations that have been shown to be caused by enhancer mutations and propose that cis-regulatory mutations will continue to be identified as the cause of additional human malformations as our understanding of regulatory sequences improves.

Fig. 1

Diagram of cis-regulatory elements described in this review. Two different promoters are located next to the two different genes. By binding to Promoter 1, an enhancer actively regulates Gene 1 and leads to its transcription, as indicated by the black arrow above Gene 1. An insulator prevents this enhancer from activating Gene 2, which is not transcribed due to regulation by the silencer.

Fig. 2

Genomic context of zone of polarizing activity regulatory sequence (ZRS) mutations and duplications. A: The ZRS Duplications track shows duplications that include the ZRS and that lead to complex polysyndactylies. Each bar in the track indicates the region that was duplicated in a family with these malformations. While the duplicated regions vary between families, they all include the ZRS. B: The ZRS Mutations track shows point mutations that are distributed throughout a ~750 base pair conserved ZRS region that cause human limb malformations. Genomic coordinates and citations for duplications and SNPs can be found in Table 1. Both UCSC Genome browser tracks are available from http://bts.ucsf.edu/ahituv/limb.html. Images generated using the UCSC genome browser, http://genome.ucsc.edu/ (Kent et al., 2002).

Fig. 3

Phenotypic severity of human limb malformation is correlated with the degree of misexpression determined by the specific ZRS mutation. A: Wild-type (wt) human zone of polarizing activity regulatory sequence (ZRS) enhancer expression is restricted to the ZPA. B: In a mouse enhancer assay, the Cuban mutation shows strong anterior expression (arrowheads) and an expanded posterior expression domain (arrows). C: The Cuban mutation leads to a more severe limb malformation, including bilateral tibial aplasia in addition to polydactyly and triphalangeal thumb in this patient. D: The Belgian2 mutation leads to weak enhancer expression in the anterior portion of the developing limb (D′ arrow). E: The Belgian 2 mutation causes a milder human phenotype with triphalangeal thumbs on both hands (arrows) and an additional digit on the left hand (arrowhead). Images used with permission from (Zguricas et al., 1999; Lettice et al., 2003, 2008).