Genomic architecture of Shh dependent cochlear morphogenesis

Abstract

The mammalian cochlea develops from a ventral outgrowth of the otic vesicle in response to Shh signaling. Mouse embryos lacking Shh or its essential signal transduction components display cochlear agenesis; however, a detailed understanding of the transcriptional network mediating this process is unclear. Here, we describe an integrated genomic approach to identify Shh-dependent genes and associated regulatory sequences that promote cochlear duct morphogenesis. A comparative transcriptome analysis of otic vesicles from mouse mutants exhibiting loss (Smo ecko) and gain (Shh-P1) of Shh signaling reveal a set of Shh-responsive genes partitioned into four expression categories in the ventral half of the otic vesicle. This target gene classification scheme provides novel insight into several unanticipated roles for Shh, including priming the cochlear epithelium for subsequent sensory development. We also mapped regions of open chromatin in the inner ear by ATAC-seq that, in combination with Gli2 ChIP-seq, identified inner ear enhancers in the vicinity of Shh-responsive genes. These datasets are useful entry points for deciphering Shh-dependent regulatory mechanisms involved in cochlear duct morphogenesis and establishment of its constituent cell types.

An Integrated Perspective of Evolution and Development: From Genes to Function to Ear, Lateral Line and Electroreception

“…In addition to directly initiating the formation of neurons by Eya1, Sox2, Pax2 and Neurog1/2, another set of genes are regulated to differentiate into Neurod1 [18,20,21,71,73], followed by Isl1, Foxg1, Pou4f1 and Phox2b [71,[74][75][76], which interact with Shh, BMPs and Wnts to define neurons [77,78]. Regional regulation of the distinct vestibular, lateral line, electroreception and auditory neurons are sorted out by downstream genes regulating the distinct innervation.…”

Cannabinoid Signaling in Auditory Function and Development

“…Hartman et al (2015) utilized a >19,000 unique gene microarray to profile gene expression from microdissected otic vesicles, periotic tissues, and the remainder of the embyros of E10.5 mice. Muthu et al (2019) performed RNA-seq on otic vesicles derived from E11.5 mouse embryos. Kolla et al (2020) performed single cell RNA-seq from murine cochlear epithelia isolated at E14, E16, P1, and P7.…”

“…Data from experiments conducted using E10.5 and E11.5 otic vesicles (Hartman et al, 2015;Muthu et al, 2019) suggest that several of the ECS components are not detectable or are expressed at very low levels. However, Cnr1, Trpv4, Napepld, Daglb, Faah, and Abhd12 do appear to be expressed at physiologically relevant levels (Tables 1, 2).…”

“…Most notably, TABLE 2 | Expression of ECS-related transcripts from reported RNA-seq values using E11.5 otic vesicles. Data from E11.5 embryos were obtained from Muthu et al (2019) and is presented as reads per kilobase million (RPKM). The last four rows demonstrate values obtained for transcripts known to be highly expressed (Fbxo2, Gata3) or low to undetectable (Atoh1, Cdkn1b) at these stages of otic vesicle (OV) development.…”

Novel gene discovery for hearing loss and other routes to increased diagnostic rates

“…Emerging resources and tools such as the ENCODE (the Encyclopedia of DNA Elements) dataset (ENCODE; Project Consortium et al 2020), and DESCARTES (the Developmental Single Cell Atlas of Gene Regulation; Cao et al 2020;Domcke et al 2020) will increasingly facilitate to address variants in regulatory regions, although the inner ear was not analysed yet in these projects. In other projects, studies of the inner ear are being performed and data on gene expression and chromatin accessibility are becoming available (Muthu et al 2019;Yizhar-Barnea et al 2018; gEAR portal [https:// umgear. org/]).…”