Mechanisms and Pathology of Long Range Regulation in Limb Development

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The precise control of gene expression in space and time is an essential component of gene function, and as such an important cause of human diseases. Here we propose to explore some of the mechanisms associated with regulatory pathologies of limb development in humans based on our previous finding that copy number variations (CNVs) involving conserved non-coding sequences (CNEs) can result in congenital malformations. Using an innovative in vivo chromosomal strategy (GROMIT), we will engineer mice with targeted series of deletions and duplications throughout regions associated with limb deformities. We will produce mouse models for Cooks syndrome, a brachydactyly with nail dysplasia, caused by duplications of a 1Mb gene desert 5 of SOX9, and for cleidocranial dysplasia associated with duplications around the MSX2 locus. These mice will enable us to study the developmental pathology of these syndromes and to narrow down the associated regulatory elements and mechanisms. We will use chromatin profiling and conformation capture to identify enhancers and characterize the regulatory landscape they define. By using a combination of bioinformatic tools and wet lab techniques, we will aim at identifying most regulatory sequences involved in limb development. These resources and the knowledge gained by studying in detail specific models will facilitate the identification and understanding of new regulatory mutations in patients with limb malformations.