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Free keywords:
Animals
Base Sequence
Bone Diseases, Developmental/*genetics
DNA Copy Number Variations
DNA-Binding Proteins/deficiency/genetics
Enhancer Elements, Genetic/*genetics
Foot Deformities, Congenital/genetics
Gene Deletion
Gene Dosage
Gene Duplication
Gene Expression Regulation, Developmental/*genetics
Gene Knockout Techniques
Genes, Reporter
Hedgehog Proteins/deficiency/genetics/*physiology
Mice
Mice, Inbred C57BL
Osteogenesis/*genetics
Polydactyly/genetics
Regulatory Sequences, Nucleic Acid
Sequence Analysis, DNA
Skull/abnormalities
Transcription, Genetic
Abstract:
Copy number variations (CNVs) often include noncoding sequences and putative enhancers, but how these rearrangements induce disease is poorly understood. Here we investigate CNVs involving the regulatory landscape of IHH (encoding Indian hedgehog), which cause multiple, highly localized phenotypes including craniosynostosis and synpolydactyly. We show through transgenic reporter and genome-editing studies in mice that Ihh is regulated by a constellation of at least nine enhancers with individual tissue specificities in the digit anlagen, growth plates, skull sutures and fingertips. Consecutive deletions, resulting in growth defects of the skull and long bones, showed that these enhancers function in an additive manner. Duplications, in contrast, caused not only dose-dependent upregulation but also misexpression of Ihh, leading to abnormal phalanges, fusion of sutures and syndactyly. Thus, precise spatiotemporal control of developmental gene expression is achieved by complex multipartite enhancer ensembles. Alterations in the composition of such clusters can result in gene misexpression and disease.
