Rxivist logo

Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 67,132 bioRxiv papers from 295,346 authors.

Genomic architecture of Shh dependent cochlear morphogenesis

By Victor Muthu, Alex Rohacek, Yao Yao, Staci M. Rakowiecki, Alexander S Brown, Ying-Tao Zhao, James Meyers, Kyoung-Jae Won, Shweta Ramdas, Christopher D Brown, Kevin A. Peterson, Douglas Epstein

Posted 08 Jun 2019
bioRxiv DOI: 10.1101/665091 (published DOI: 10.1242/dev.181339)

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.

Download data

  • Downloaded 175 times
  • Download rankings, all-time:
    • Site-wide: 51,735 out of 67,118
    • In developmental biology: 1,600 out of 1,992
  • Year to date:
    • Site-wide: 29,323 out of 67,118
  • Since beginning of last month:
    • Site-wide: 53,682 out of 67,118

Altmetric data

Downloads over time

Distribution of downloads per paper, site-wide

Sign up for the Rxivist weekly newsletter! (Click here for more details.)