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 (Smoecko) and gain (Shh-P1) of Shh signaling revealed a set of Shh responsive genes partitioned into four expression categories in the ventral half of the otic vesicle. This target gene classification scheme provided novel insights 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.SUMMARY STATEMENTAn integrated genomic approach identifies Shh responsive genes and associated regulatory sequences with known and previously uncharacterized roles in cochlear morphogenesis, including genes that prime the cochlea for sensory development.

Development of the cochlea

“…The inner and outer sulci are derived from Kölliker's organ and LER, respectively, which undergo significant remodeling before the onset of hearing. Anatomical and genetic evidence suggest that the domains discussed above are already specified to varying extents at the time of initial outgrowth (Groves and Fekete, 2012;Muthu et al, 2019) (Fig. 2).…”

“…For instance, Otx2 has been shown to directly repress Sox2 in both the CNS and optic cup (Nishihara et al, 2012;Omodei et al, 2008). Similarly, disruption of Shh signaling, which also suppresses inner ear sensory development, leads to changes in the pattern of Sox2 (Muthu et al, 2019).…”

“…Shh has recently been shown to positively regulate Lin28a expression in the cochlea (Muthu et al, 2019), suggesting a likely mechanism for Shh-mediated regulation of the timing and pattern of HC differentiation.…”

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 – 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.…”

“…The vestibular ear requires a set of transcription genes to initiate the placode formation, starting with Foxi3 [ 168 ] and Fgf3/10 [ 63 , 169 , 170 ]. Downstream are Eya1/Six1 [ 49 , 171 ], Pax2/8 [ 58 , 172 ], Shh [ 78 , 173 ], BMPs [ 174 , 175 ] and Wnt’s [ 176 – 178 ] to form the otocyst, among other necessary genes [ 179 ], where they interact to define the dorso/ventral, anterior/posterior and lateral/medial divisions to develop the otocyst [ 180 , 181 ]. Further downstream is the expression for Sox2 upregulation [ 16 , 182 ].…”