Most developmentally important genes have complex expression patterns that show distinct differences in temporal and spatial distribution. How this is achieved is largely unknown but cis-regulatory enhancer and suppressor elements are believed to play an important role. By screening large cohorts of patients with limb malformations via array-CGH we have identified a series of duplications involving non-coding conserved elements (CNEs) that are located in the vicinity of developmentally important genes. Sonic hedgehog (Shh) is a morphogen expressed asymmetrically in the posterior limb bud margin where it contributes to the overall bauplan of the autopod by determining the number and identity of digits. Shh is surrounded by a large gene desert containing numerous conserved elements that presumably act as enhancers. We identified duplications in one of these regions that are associated with duplicated and triphalangeal thumbs. In a large family with brachydactyly type A2 we identified a small (5 kb) duplication 3' of the BMP2 gene. A highly conserved sequence within this duplication was shown to drive expression in the distal digits suggesting that a dosage effect is causative for the phenotype. Furthermore, in a limb malformation syndrome with absent nails and missing middle phalanges (Cooks syndrome) we identified a 1 Mb duplication 5' of the SOX9 gene, a gene previously associated with a lethal skeletal dysplasia with sex reversal. Our findings identified duplications of CNEs as a novel mutation mechanism for human disease. In addition, they show that CNEs are important for fine tuning expression and that alterations in these regions can result in unexpected phenotypes. Alterations of regulatory CNEs are a likely mechanism for evolutionary change. The mechanisms of long range regulation and its pathology are currently being studied in animal models.

Selected publications:

Kurth I, Klopocki E, Stricker S, van Oosterwijk J, Vanek S, Altmann J, Santos HG, van Harssel JJ, de Ravel T, Wilkie AO, Gal A, Mundlos S.
Duplications of noncoding elements 5' of SOX9 are associated with brachydactyly-anonychia.
Nat Genet. 2009 Aug;41(8):862-3.

Dathe K, Kjaer KW, Brehm A, Meinecke P, Nürnberg P, Neto JC, Brunoni D, Tommerup N, Ott CE, Klopocki E, Seemann P, Mundlos S. Duplications involving a conserved regulatory element downstream of BMP2 are associated with brachydactyly type A2. Am J Hum Genet. 2009 Apr;84(4):483-92;

Klopocki E, Schulze H, Strauss G, Ott CE, Hall J, Trotier F, Fleischhauer S, Greenhalgh L, Newbury-Ecob RA, Neumann LM, Habenicht R, König R, Seemanova E, Megarbane A, Ropers HH, Ullmann R, Horn D, Mundlos S.
Complex inheritance pattern resembling autosomal recessive inheritance involving a microdeletion in thrombocytopenia-absent radius syndrome.
Am J Hum Genet. 2007 Feb;80(2):232-40.

Klopocki E, Ott CE, Benatar N, Ullmann R, Mundlos S, Lehmann K.
A microduplication of the long range SHH limb regulator (ZRS) is associated with triphalangeal thumb-polysyndactyly syndrome.
J Med Genet. 2008 Jun;45(6):370-5.