Composition and dosage of a multipartite enhancer cluster control developmental expression of Ihh (Indian hedgehog)

Nat Genet. 2017 Oct;49(10):1539-1545. doi: 10.1038/ng.3939. Epub 2017 Aug 28.


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.

MeSH terms

  • Animals
  • Base Sequence
  • Bone Diseases, Developmental / genetics*
  • DNA Copy Number Variations
  • DNA-Binding Proteins / deficiency
  • DNA-Binding Proteins / 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
  • Hedgehog Proteins / genetics
  • Hedgehog Proteins / physiology*
  • Mice
  • Mice, Inbred C57BL
  • Osteogenesis / genetics*
  • Polydactyly / genetics
  • Regulatory Sequences, Nucleic Acid
  • Sequence Analysis, DNA
  • Skull / abnormalities
  • Transcription, Genetic


  • DNA-Binding Proteins
  • Hedgehog Proteins
  • XLF protein, mouse
  • ihh protein, mouse