Delayed fusion and altered gene expression contribute to semicircular canal defects in Chd7 deficient mice

► Chd7Gt/+ mice exhibit delayed semicircular canal genesis and Netrin1 expression. ► Expression of Otx1, Jag1 and Sox2 is reduced in Chd7 mutant otocysts. ► Bmp2 expression is reduced in the lateral canal genesis zone of Chd7Gt/+ mice. ► Expression of Bmp4, Gata3, Fgf10, Lmo4, and Msx1 in the developing cristae is sensitive to Chd7 dosage. ► Chd7 may be a selector gene for semicircular canal genesis. Proper morphogenesis of inner ear semicircular canals requires precise regulation of cellular proliferation, epithelial-to-mesenchymal transition, and fusion of epithelial plates. Epigenetic regulation of these processes is not well understood, but is likely to involve chromatin remodeling enzymes. CHD7 is a chromodomain-containing, ATP dependent helicase protein that is highly expressed in the developing ear and is required for semicircular canal development in both humans and mice. Here we report that mice with heterozygous loss of Chd7 function exhibit delayed semicircular canal genesis, delayed Netrin1 expression and disrupted expression of genes that are critical for semicircular canal formation (Bmp2, Bmp4, Msx1 and Fgf10). Complete loss of Chd7 results in aplasia of the semicircular canals and sensory vestibular organs, with reduced or absent expression of Otx1, Hmx3, Jagged1, Lmo4, Msx1 and Sox2. Our results suggest that Chd7 may have critical selector gene functions during inner ear morphogenesis. Detailed analysis of the epigenetic modifications underlying these gene expression changes should provide insights into semicircular canal development and help in the design of therapies for individuals with inner ear malformations.