Transcriptomic and epigenetic analysis of neonatal supporting cells during Notch inhibition-induced transdifferentiation

Latent regeneration potential has been found in neonatal supporting cells in the organ of Corti in mouse. Upon Notch inhibition by DAPT, postnatal day 1 (P1) supporting cells transdifferentiate into hair cells. To profile the transcriptomic and epigenetic changes in supporting cells during transdifferentiation, we FACS purified supporting cells from DAPT treated cochleae for RNAseq, ATACseq and H3K27ac CUT&RUN. We found that hair cell genes were up-regulated in supporting cells after DAPT treatment and that hair cell gene induction was accompanied by epigentic activation of hair cell gene cis-regulatory elements through chromatin accessibility increase and H3K27ac accumulation, suggesting the regulatory roles of epigenetic activation of hair cell gene elements for hair cell gene expression induction. P1 cochlear organs were cultured and treated by DAPT or DMSO. At 24 hour post treatment, all supporting cells (Lfng-GFP+) were purified for RNAseq. At 48 hours post treatment, supporting cells undergoing transdifferentiation upon DAPT (permissive, Lfng-CreER/TdT+ and Atoh1-GFP+), supporting cells irresponsive to DAPT (nonpermissive, Lfng-CreER/TdT+ only) and DMSO-treated supporting cells (control, Lfng-CreER/TdT+ only) from control organs were purified for transcriptomic analysis (RNAseq), chromatin accessibility assay (ATACseq) and H3K27ac profile (CUT&RUN).