CHD7 and SOX2 act in a common gene regulatory network during mammalian semicircular canal and cochlear development.

Abstract

Inner ear morphogenesis requires tightly regulated epigenetic and transcriptional control of gene expression. CHD7, an ATP-dependent chromodomain helicase DNA-binding protein, and SOX2, an SRY-related HMG box pioneer transcription factor, are known to contribute to vestibular and auditory system development, but their genetic interactions in the ear have not been explored. Here, we analyzed inner ear development and the transcriptional regulatory landscapes in mice with variable dosages of <i>Chd7</i> and/or <i>Sox2</i>. We show that combined haploinsufficiency for <i>Chd7</i> and <i>Sox2</i> results in reduced otic cell proliferation, severe malformations of semicircular canals, and shortened cochleae with ectopic hair cells. Examination of mice with conditional, inducible <i>Chd7</i> loss by <i>Sox2^CreER</i> reveals a critical period (~E9.5) of susceptibility in the inner ear to combined <i>Chd7</i> and <i>Sox2</i> loss. Data from genome-wide RNA-sequencing and CUT&Tag studies in the otocyst show that CHD7 regulates <i>Sox2</i> expression and acts early in a gene regulatory network to control expression of key otic patterning genes, including <i>Pax2</i> and <i>Otx2</i>. CHD7 and SOX2 directly bind independently and cooperatively at transcription start sites and enhancers to regulate otic progenitor cell gene expression. Together, our findings reveal essential roles for <i>Chd7</i> and <i>Sox2</i> in early inner ear development and may be applicable for syndromic and other forms of hearing or balance disorders.