DNA methylation in the mouse cochlea promotes maturation of supporting cells and contributes to the failure of hair cell regeneration

Abstract

Mammalian hair cells do not functionally regenerate in adulthood but can regenerate at embryonic and neonatal stages in mice by direct transdifferentiation of neighboring supporting cells into new hair cells. Previous work showed loss of transdifferentiation potential of supporting cells is in part due to H3K4me1 enhancer decommissioning of the hair cell gene regulatory network during the first postnatal week. However, inhibiting this decommissioning only partially preserves transdifferentiation potential. Therefore, we explored other repressive epigenetic modifications that may be responsible for this loss of plasticity. We find supporting cells progressively accumulate DNA methylation at promoters of developmentally regulated hair cell genes. Specifically, DNA methylation overlaps with binding sites of Atoh1, a key transcription factor for hair cell fate. We further show that DNA hypermethylation replaces H3K27me3-mediated repression of hair cell genes in mature supporting cells, and is accompanied by progressive loss of chromatin accessibility, suggestive of facultative heterochromatin formation. Another subset of hair cell loci is hypermethylated in supporting cells, but not in hair cells. Ten-eleven translocation (TET) enzyme-mediated demethylation of these hypermethylated sites is necessary for neonatal supporting cells to transdifferentiate into hair cells. We also observe changes in chromatin accessibility of supporting cell subtypes at the single-cell level with increasing age: Gene programs promoting sensory epithelium development loses chromatin accessibility, in favor of gene programs that promote physiological maturation and function of the cochlea. We also find chromatin accessibility is partially recovered in a chronically deafened mouse model, which holds promise for future translational efforts in hearing restoration.

AAV‐mediated Gene Cocktails Enhance Supporting Cell Reprogramming and Hair Cell Regeneration

“…Previous studies have demonstrated that cochlear developmental genes, such as Atoh1, exhibit greater accessibility in HCs and SCs during P1 compared to P8 mice, which display more pronounced methylation in SCs and inhibit HC regeneration in P8 mice. [63] This may account for the reduced maturation of regenerated HCs following AAV-GPAS injection after P7, thereby impeding the restoration of auditory function after DTR injury. Despite the existence of various strategies to promote HC regeneration by multiple genes, [19,20,22] there remains a dearth of research on restoring hearing function through regenerative HCs in cases of HC damage.…”

The Inheritance of Hearing Loss and Deafness: A Historical Perspective

“…Researchers are exploring compounds to regulate epigenetic modification as a potential avenue for alleviating acquired hearing loss. Epigenetic regulation is also crucial for inner ear HC regeneration, which offers an opportunity for hearing loss therapy [69,70].…”