Mapping of Chromatin Architecture and Enhancer-Promoter Interactions in the Cochlea

Chromatin interactions, particularly those between promoters and distal enhancers, enable precise gene regulation in specialized tissues, like the cochlea in the inner ear. Disruptions in these long-range interactions between enhancers and gene promoters are linked to hereditary hearing loss. For many genes important to cochlear development and function, the distal regulatory elements that control their expression remain unknown. Identifying these elements and studying their regulatory roles is challenging due to their distance from target genes and the spatial complexity of chromatin architecture. To address this, we employed Micro-C, a high-resolution chromatin conformation capture technique that enables nucleosome-level mapping of chromatin interactions, to construct a cochlea-specific chromatin interaction map. We then integrated epigenomic and transcriptomic data to interpret enhancer-promoter interactions involved in gene regulation. Cochlea organs from P0/1 C57Bl/6 animals were disssected and dissociated for Micro-C, ATACseq, histone or CTCF Cut&Run