The chromatin accessibility and transcriptomic landscape of the aging mice cochlea and the identification of potential functional super-enhancers in age-related hearing loss
Authors: Zhang Chanyuan , Yang Ting , Luo Xiaoqin , Zhou Xiaoqing , Feng Menglong , Yuan Wei 
Published: March 2024

Abstract
Background Presbycusis, also referred to as age-related hearing loss (ARHL), is a condition that results from the cumulative effects of aging on an individual's auditory capabilities. Importantly, the aging process affects individuals in diverse ways and is influenced by various factors, including epigenetic factors. Given the limited understanding of epigenetic mechanisms in ARHL, our research focuses on investigating alterations in chromatin-accessible regions, commonly known as peaks.
Methods To accomplish this,we employed assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) in conjunction with unique identifier (UID) mRNA-seq, which provides reciprocal validation from DNA to RNA between young and aging cochleae.Integrated analysis and motif/TF(Transcription factor)-gene prediction were conducted. Additionally,the essential role of super-enhancers (SEs) in the development of ARHL were identified by comparative analysis to previous research.Meanwhile, an ARHL mouse model and an aging mimic hair cell(HC) model were established with a comprehensive identification of various senescence phenotypes to access the role of SEs in ARHL progression.
Results The ATAC-seq analysis revealed that the control cochlear tissue exhibited greater chromatin accessibility than cochlear tissue affected by ARHL.Integrated analyses indicated that peaks found in the promoter and 5'UTR regions have a more pronounced regulatory impact on the expression of neighboring genes in ARHL compared to peaks in other genomic elements. Furthermore, the levels of histone 3 lysine 27 acetylation were significantly depressed in both aging cochlea and aging mimic HEI-OC1 cells, highlighting the essential role of SEs in the development of ARHL.The CCCTC-binding factor (CTCF), a constituent of chromatin loops that restricts the interaction between enhancers and promoters, was identified as the transcription factor with the most abundant binding to its motif. Subsequently, we identified potential ARHL-associated SASEs(senescence associated super-enhancers), most of which exhibited significantly decreased chromatin accessibility.The majority of genes related to the SASEs showed obvious decreases in mRNA expression level in aging HCs. Importantly, the expression of genes regulated by the identified SASEs, such as Atp6v1a, Dcun1d3, Mitf1, and Sdcbp, was noticeably altered following treatment with the BRD4 inhibitor JQ1 (a commonly used SE inhibitor).
Conclusion The analysis of ATAC-seq showed that the chromatin accessibility in control cochlear tissue was higher than that in cochlear tissue affected by ARHL.Additionally, by conjoint analysis and dual model verification,we establishes a framework for understanding epigenetic regulatory mechanisms underlying the development of ARHL in the cochlea and identifies potential SEs involved in HC senescence, which might provide a basis for future therapeutics targeting SEs in ARHL.