Gene Expression by Mouse Inner Ear Hair Cells During Development

Hair cells of the inner ear are essential for hearing and balance. As a consequence, pathogenic variants in genes specifically expressed in hair cells often cause hereditary deafness. Hair cells are few in number and not easily isolated from the adjacent supporting cells, so the biochemistry and molecular biology of hair cells can be difficult to study. To study gene expression in hair cells, we developed a protocol for hair cell isolation by FACS sorting. With nearly pure hair cells and surrounding cells, from cochlea and utricle and from embryonic day 16 to postnatal day 7, we performed a comprehensive cell-type-specific RNA-Seq study of gene expression during mouse inner ear development. Expression profiling revealed new hair-cell genes with distinct expression patterns: some are specific for vestibular hair cells, others for cochlear hair cells, and some are expressed just before or after maturation of mechanosensitivity. We found that many of the known hereditary deafness genes are much more highly expressed in hair cells than surrounding cells, suggesting that genes preferentially expressed in hair cells are good candidates for unknown deafness genes. Overall design: 3' tags of mRNA profiles of hair cells and surrounding cells from E16, P0, P4, and P7 cochlear and utricular sensory epithelia were generated by deep sequencing, using Illumina GAIIx