| Experiment Id | GSE150000 | Name | Epigenetic analysis of perinatal maturation of supporting cells in the organ of Corti |
| Experiment Type | RNA-Seq | Study Type | Baseline |
| Source | GEO | Curation Date | 2023-07-21 |
| description | Sensory hair cells cannot be regenerated through transdifferentiation of neighboring supporting cells in the organ of Corti in mature mammalian animals, but limited regeneration capacity exists in supporting cells at neonatal stage in mouse and this transdifferentiation potential is rapidly lost during the first week of postnatal maturtion. We hypothesized that epigenetic decommissioning of hair cell gene enhancers in supporting cells during postnatal maturation leads the permanent silencing of hair cell genes and the loss of transdifferentiation potential. To test this hypothesis, we FACS purified hair cells and supporting cells from cochleae at different developmental stages for transcritomic analysis (RNAseq), chromatin accessibility assay (ATACseq) and histone modification profiling (ChIPseq or CUT&RUN). We first defined hair cell genes and predicted their potential active enhancers. We found that hair cell gene promoters and enhancers were kept in a primed-but-silenced status (H3K4me1/3+, low H3K27ac but high H3K27me3) in supporting cells at neonatal stage. During postnatal maturation, hair cell gene enhancers are decommissioned through H3K4me1 removal, leading to the permanent silencing of hair cells genes. We also found that hair cell gene enhancer decommissioning process correlated with the base-to-apex wave of transdifferentiation potential loss. In addition, hair cell gene enhancer commissioning status is preserved in mature utricular supporting cells, which can regenerate hair cells through transdifferentiation even at adult stage. Those data together suggest that decommissioning of hair cell gene enhancers in supporting cells during postnatal maturation is the epigenetic mechanism underlying the loss of regeneration capacity in the organ of Corti. Sensory hair cells (Atoh1-GFP+) were purified from postnatal day 1 (P1) animals for RNAseq, ATACseq, ChIPseq or CUT&RUN for hair cell gene identification and putative active enhancer prediction. Supporting cells (Lfng-GFP+) were purified from embryonic day 17.5 (E17.5), P1 and P6 animals for RNAseq, ATACseq, ChIPseq and CUT&RUN to interrogate the epigenetic modification changes surrounding hair cell gene regulatory elements during perinatal matruation. To compare the epigenetic status of supporting cells between apical half and basal half of cochlea, organs were cut into two halves after dissection and then supporting cells were purfied from each half for H3K4me1 CUT&RUN. To compare enhancer commissioning status in cochlear and utricular supporting cells at mature stage, supporting cells were purified from cochleae or utricles at 3 week old stage for H3K4me1 profiling by CUT&RUN and chromatin accessibility assay by ATACseq. |
