Differential chromatin accessibility, gene expression and mRNA splicing between developing cochlear inner and outer hair cells [RNA-Seq]

The mammalian cochlea has two types of low abundance and highly specialized inner (IHC) and outer (OHC) mechanosensory hair cells. Their malfunction or death are common causes of congenital and acquired deafness. We separately collected developing IHCs and OHCs to identify their mRNAs and chromatin state. We examined their transcriptomes by RNA-seq to reveal differences in gene expression and alternative mRNA splicing. We examined their chromatin conformation by ATAC-seq to reveal open vs closed promoter and enhancer elements. Combining both approaches we find that developing IHCs and OHCs have differentially accessible promoters in differentially expressed genes, differ in both levels of gene expression, extent of mRNA splicing and transcription start sites, and utilize unique promoters and mRNA isoforms absent in other cell types. We provide a resource for the identification of promoter and mRNA isoforms of every gene expressed by IHCs or OHCs.