Duplications Involving a Conserved Regulatory Element Downstream of BMP2 Are Associated with Brachydactyly Type A2

Abstract

Autosomal-dominant brachydactyly type A2 (BDA2), a limb malformation characterized by hypoplastic middle phalanges of the second and fifth fingers, has been shown to be due to mutations in the Bone morphogenetic protein receptor 1B (BMPR1B) or in its ligand Growth and differentiation factor 5 (GDF5). A linkage analysis performed in a mutation-negative family identified a novel locus for BDA2 on chromosome 20p12.3 that incorporates the gene for Bone morphogenetic protein 2 (BMP2). No point mutation was identified in BMP2, so a high-density array CGH analysis covering the critical interval of approximately 1.3 Mb was performed. A microduplication of approximately 5.5 kb in a noncoding sequence approximately 110 kb downstream of BMP2 was detected. Screening of other patients by qPCR revealed a similar duplication in a second family. The duplicated region contains evolutionary highly conserved sequences suggestive of a long-range regulator. By using a transgenic mouse model we can show that this sequence is able to drive expression of a X-Gal reporter construct in the limbs. The almost complete overlap with endogenous Bmp2 expression indicates that a limb-specific enhancer of Bmp2 is located within the identified duplication. Our results reveal an additional functional mechanism for the pathogenesis of BDA2, which is duplication of a regulatory element that affects the expression of BMP2 in the developing limb.

17p13.3 microduplications are associated with split-hand/foot malformation and long-bone deficiency (SHFLD)

“…6,7,9,[28][29][30] Similar to the findings reported herein, the primary genetic findings in patients with SHFM3 are genomic duplications. Those duplications involve a minimal 325 kb region that includes BTRC, POLL, and a portion of the FBXW4 (human dactylin) gene.…”

“…Duplications of regulatory elements have been shown to be responsible for at least three different limb phenotypes; a tandem duplication of a 5.5 kb region 3¢ of BMP2 is associated with brachydactyly type A2 30 and microduplications of the ZRS, a long-range cis-acting regulatory element of sonic hedgehog (SHH), lead to triphalangeal thumbpolysyndactyly syndrome and syndactyly type IV. 28,29 Within the duplicated region described here, evolutionarily conserved sequences of unknown function (Figure 4) may represent cis-acting regulatory elements altering the activity of a neighbouring gene, or the duplications may disrupt the interaction between a nearby enhancer and its target gene.…”

Genotype–phenotype relationship in three cases with overlapping 19p13.12 microdeletions

“…[21][22][23] Thus, we also considered genes flanking the SRO as potentially responsible for the abnormal phenotypes.…”

TGF-β Family Signaling in Connective Tissue and Skeletal Diseases

“…Inactivating mutations in genes coding for the BMPRIB receptor or its ligand GDF-5 (Nishitoh et al 1996;Lehmann et al 2003Lehmann et al , 2006 cause BDA2, which is characterized by short middle phalanges in the second and fifth digits. A microduplication in a downstream regulatory element of BMP-2, which is thought to affect limb-specific expression, was also found in some patients with BDA2 (Dathe et al 2009). GDF5 mutations also can cause BDC, characterized by short or absent middle phalanges in second, third, and fifth fingers, short first metacarpal and hypersegmentation of the second and/or third finger Robin et al 1997;Galjaard et al 2001;Everman et al 2002;Savarirayan et al 2003;Holder-Espinasse et al 2004;Schwabe et al 2004).…”