Epigenetic landscape of supporting cell reprogramming toward hair cell regeneration in chick auditory epithelia.

Sensorineural hearing loss is usually intractable because of virtually no capacity for hair cell (HC) regeneration in mammals. In contrast to mammals, lower vertebrates including birds have the capability for HC regeneration. Elucidation of precise mechanisms for HC regeneration in avian auditory epithelia will contribute to exploring key molecules for inducing HC regeneration in mammals. We previously established an explant culture model of the chick auditory epithelium, namely basilar papilla (BP), showing total HC loss and consecutive HC regeneration through direct conversion of supporting cells (SCs) to HCs (Matsunaga, 2020). Single-cell RNA sequencing using this model illustrated dynamic changes in expressed genes in BP SCs during direct conversion, which indicates that reprogramming of SCs to the precursor state occurs before differentiation into HCs (Matsunaga, 2023). To explore mechanisms of SC reprogramming toward hair cell regeneration in chick BP, we performed an integrated analysis of RNA- and ATAC-seq of chick BP explant cultures during the early phase (three time points) of HC regeneration. ATAC sequencing detected 80,366 peaks. Based on the distance from the transcription start site, and correlations between read counts and peak depths and between their alterations in a time course, we determined enhancer candidate loci for differentially expressed genes. We focused on a set of temporally upregulated genes during SC reprogramming in our previous single-cell RNA sequencing data (Matsunaga, 2023). In temporally upregulated genes during SC reprogramming, enhancer candidate loci were identified in nine genes. Motif enrichment analysis of these loci indicated transcription factors that may control chromatin remodeling in SC reprogramming. In the near future, we will examine spaciotemporal expression patterns of these transcription factors in regenerating chick BP. [ABSTRACT FROM AUTHOR]