A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish

Using adult zebrafish inner ears as a model for sensorineural regeneration, we performed a targeted ablation of the mechanosensory receptors in the saccule and utricle and characterized the single-cell epigenome and transcriptome at consecutive time-points following hair cell death. Overall design: To elucidate the transcriptional regulatory network that controls tissue regeneration, we characterized the gene expression profiles (scRNA-seq) and the map of accessible regions (scATAC-seq) associated with the response to hair cell ablation in adult zebrafish sensory epithelia. We dissected out saccules and utricles at three time points: Days 4, 5 and 7 post-DT, and each were processed separately in both scRNA-seq and scATAC-seq experiments. Untreated Tg(myo6b:DTR) transgenic zebrafish and wild-type DT injected (and untreated) zebrafish lacking the Tg(myo6b:DTR) transgene were used as non-regenerating controls. Cell suspensions of isolated sensory epithelia were subjected to single cell sequencing for both their transcriptome and open chromatin regions using 10X Genomics Chromium Single Cell Gene Expression and Single Cell ATAC Sequencing. We also include biological triplicates of untreated wild-type saccules and utricles for bulk ATAC-seq.