ATACseq, CutnRun and RNAseq data from sensory progenitors and hair cells, from wild type and Pou4f3-mutant cochlea

Hearing and balance are mediated in vertebrates by inner ear mechanosensory hair cells. Hair cell development, maturation and survival require POU4F3, a class IV POU domain transcription factor that is expressed in hair cells shortly after they start to differentiate. Here, we show that POU4F3 has pioneer factor activity, and is necessary to promote chromatin accessibility at approximately half of the distal regulatory elements that appear as hair cells differentiate. Pou4f3 expression in the inner ear is initiated by ATOH1, a bHLH transcription factor that is also necessary for hair cell differentiation and survival. We show that ATOH1 also binds a large number of POU4F3-dependent distal regulatory elements, suggesting a synergistic feed-forward model in which ATOH1 induces POU4F3, which then acts to promote ATOH1-dependent hair cell differentiation. In the present study, we used CUT&RUN (Skene and Henikoff, 2017) to identify the distal regulatory elements of differentiating hair cells that bind ATOH1. We used ATACseq (Buenrostro et al., 2013) to show that the majority of these ATOH1-bound distal elements fall within nucleosome-occupied, silent chromatin in sensory progenitors from which hair cells derive. We use RNAseq to show that POU4F3-dependent ATOH1 targets control the expression of deaf-related genes in the developing hair cells