Congenital and acquired sensorineural hearing loss is often due to the absence or the degeneration of hair cells in the cochlea. Understanding the mechanisms regulating the generation of hair cells may therefore ultimately lead to better treatments for hearing disorders. To elucidate developmental mechanisms specifying the progenitor cells (i.e., prosensory cells) that generate the hair cells and support cells critical for hearing function, we propose to map the cis-regulatory elements (e.g., promoters, enhancers) that precisely orchestrate where, when and how genes are expressed during the specification of prosensory cells in the developing cochlear duct. More specifically, we will determine chromatin accessibility with ATAC-seq and define developmentally regulated enhancers with H3K27ac ChIP-seq. In addition, it is our working hypothesis that Sox2 induces prosensory gene expression through direct transcriptional activator activity, and we will test predictions of this hypothesis using ChIP-seq for Sox2. Together, our integrated datasets will elucidate the downstream targets and mediators of Sox2 activity as well as the potential upstream inducers of Sox2 transcription. The data could potentially reveal a contribution of the epigenome to hereditary hearing loss. Through this mentored research plan and related training activities, the applicant will achieve new expertise in hearing research and genomic analysis. Results will reveal many new and complex interactions between gene expression, chromatin structure and transcription factor-binding across cochlear development, which will direct investigations into novel aspects of the fundamental mechanisms guiding the generation of the hair cells and support cells critical for hearing function.

Public Health Relevance

CDC statistics indicate that hearing loss affects 2-3 per 1000 children born as well as an increasingly large fraction of seniors and veterans. The goal of the proposed research is to identify the targets of a key regulator of cochlea development, Sox2, using ChIP-seq, and to identify developmentally important cis-regulatory regions using a combination of ChIP-seq for H3K27ac, and ATAC-seq to show regions of accessible chromatin. This map has potential to identify gene enhancers driving expression of genes important for hair cell generation and, more broadly, other investigators could use our map of gene enhancers to determine whether variants in non-coding regions of the genome that are statistically-associated with deafness are likely to deregulate gene expression during development of the ear.

National Institute of Health (NIH)
National Institute on Deafness and Other Communication Disorders (NIDCD)
Postdoctoral Individual National Research Service Award (F32)
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Special Emphasis Panel (ZDC1)
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Rivera-Rentas, Alberto L
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University of Washington
Anatomy/Cell Biology
Schools of Medicine
United States
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Wilkerson, Brent A; Artoni, Filippo; Lea, Colby et al. (2018) Effects of 3,3'-Iminodipropionitrile on Hair Cell Numbers in Cristae of CBA/CaJ and C57BL/6J Mice. J Assoc Res Otolaryngol 19:483-491