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 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. Summary: An 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.

[1]  W. Low,et al.  SOX2 is required for inner ear growth and cochlear nonsensory formation before sensory development , 2019, Development.

[2]  M. Montcouquiol,et al.  Development and Patterning of the Cochlea: From Convergent Extension to Planar Polarity. , 2019, Cold Spring Harbor perspectives in medicine.

[3]  R. Fettiplace.  Hair Cell Transduction, Tuning, and Synaptic Transmission in the Mammalian Cochlea. , 2017, Comprehensive Physiology.

[4]  Qin Zhu,et al.  PIVOT: platform for interactive analysis and visualization of transcriptomics data , 2016, BMC Bioinformatics.

[5]  M. Bitner-Glindzicz,et al.  Congenital hearing loss , 2017, Nature Reviews Disease Primers.

[6]  David S. Lorberbaum,et al.  An ancient yet flexible cis-regulatory architecture allows localized Hedgehog tuning by patched/Ptch1 , 2016, eLife.

[7]  Jeff Vierstra,et al.  Genomic footprinting , 2016, Nature Methods.

[8]  A. Groves,et al.  Where hearing starts: the development of the mammalian cochlea , 2016, Journal of anatomy.

[9]  A. Ouhtit,et al.  BRIP1, a potential candidate gene in development of non-BRCA1/2 breast cancer. , 2016, Frontiers in bioscience.

[10]  Héctor Gálvez,et al.  Otx2 is a target of N-myc and acts as a suppressor of sensory development in the mammalian cochlea , 2015, Development.

[11]  E. Golden,et al.  The RNA-binding protein LIN28B regulates developmental timing in the mammalian cochlea , 2015, Proceedings of the National Academy of Sciences.

[12]  M. Scott,et al.  The Eya1 phosphatase promotes Shh signaling during hindbrain development and oncogenesis. , 2015, Developmental cell.

[13]  Stuart L. Johnson,et al.  Absence of plastin 1 causes abnormal maintenance of hair cell stereocilia and a moderate form of hearing loss in mice , 2014, Human molecular genetics.

[14]  Ana Benito-Gonzalez,et al.  Hey1 and Hey2 Control the Spatial and Temporal Pattern of Mammalian Auditory Hair Cell Differentiation Downstream of Hedgehog Signaling , 2014, The Journal of Neuroscience.

[15]  S. Vokes,et al.  Transcriptional regulation of graded Hedgehog signaling. , 2014, Seminars in cell & developmental biology.

[16]  L. Goodrich,et al.  Morphological and physiological development of auditory synapses , 2014, Hearing Research.

[17]  Hugo J. Bellen,et al.  Notch Signaling , 2014, Methods in Molecular Biology.

[18]  Andrea I. Ramos,et al.  Low-affinity transcription factor binding sites shape morphogen responses and enhancer evolution , 2013, Philosophical Transactions of the Royal Society B: Biological Sciences.

[19]  Howard Y. Chang,et al.  Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position , 2013, Nature Methods.

[20]  J. Bok,et al.  Auditory ganglion source of Sonic hedgehog regulates timing of cell cycle exit and differentiation of mammalian cochlear hair cells , 2013, Proceedings of the National Academy of Sciences.

[21]  R. Sandberg,et al.  SoxB1-driven transcriptional network underlies neural-specific interpretation of morphogen signals , 2013, Proceedings of the National Academy of Sciences.

[22]  Alexander van Oudenaarden,et al.  Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning. , 2012, Genes & development.

[23]  J. Ericson,et al.  Mechanistic differences in the transcriptional interpretation of local and long-range Shh morphogen signaling. , 2012, Developmental cell.

[24]  Scott Barolo,et al.  A model of spatially restricted transcription in opposing gradients of activators and repressors , 2012, Molecular systems biology.

[25]  M. Kelley,et al.  Molecular mechanisms of inner ear development. , 2012, Cold Spring Harbor perspectives in biology.

[26]  Ulrich Müller,et al.  Sensing sound: molecules that orchestrate mechanotransduction by hair cells , 2012, Trends in Neurosciences.

[27]  R. Lovell-Badge,et al.  Disruption of SoxB1-dependent Sonic hedgehog expression in the hypothalamus causes septo-optic dysplasia. , 2012, Developmental cell.

[28]  Jianbo Sun,et al.  Eya1-Six1 interaction is sufficient to induce hair cell fate in the cochlea by activating Atoh1 expression in cooperation with Sox2. , 2012, Developmental cell.

[29]  Alexander S. Brown,et al.  Otic ablation of smoothened reveals direct and indirect requirements for Hedgehog signaling in inner ear development , 2011, Development.

[30]  Brian P. Brunk,et al.  Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM) , 2011, Bioinform..

[31]  L. Puelles,et al.  Meis gene expression patterns in the developing chicken inner ear , 2011, The Journal of comparative neurology.

[32]  A. Dror,et al.  Hearing Impairment: A Panoply of Genes and Functions , 2010, Neuron.

[33]  Ulrich Müller,et al.  The cell biology of hearing , 2010, The Journal of cell biology.

[34]  Cory Y. McLean,et al.  GREAT improves functional interpretation of cis-regulatory regions , 2010, Nature Biotechnology.

[35]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[36]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[37]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[38]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[39]  L. Biesecker,et al.  Hedgehog Signaling Regulates Sensory Cell Formation and Auditory Function in Mice and Humans , 2008, The Journal of Neuroscience.

[40]  N. Segil,et al.  Notch signaling augments the canonical Wnt pathway to specify the size of the otic placode , 2008, Development.

[41]  B. Hogan,et al.  Bmp4 Is Essential for the Formation of the Vestibular Apparatus that Detects Angular Head Movements , 2008, PLoS genetics.

[42]  U. Rüther,et al.  Opposing gradients of Gli repressor and activators mediate Shh signaling along the dorsoventral axis of the inner ear , 2007, Development.

[43]  Yongsu Jeong,et al.  Activation of Class I transcription factors by low level Sonic hedgehog signaling is mediated by Gli2-dependent and independent mechanisms. , 2007, Developmental biology.

[44]  Inna Dubchak,et al.  VISTA Enhancer Browser—a database of tissue-specific human enhancers , 2006, Nucleic Acids Res..

[45]  Julian Lewis,et al.  Notch ligands with contrasting functions: Jagged1 and Delta1 in the mouse inner ear , 2006, Development.

[46]  A. Kiernan,et al.  The Notch Ligand JAG1 Is Required for Sensory Progenitor Development in the Mammalian Inner Ear , 2006, PLoS genetics.

[47]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[48]  Karen P. Steel,et al.  Sox2 is required for sensory organ development in the mammalian inner ear , 2005, Nature.

[49]  T. Lufkin,et al.  Hmx2 and Hmx3 homeobox genes direct development of the murine inner ear and hypothalamus and can be functionally replaced by Drosophila Hmx. , 2004, Developmental cell.

[50]  K. Ikeda,et al.  Six1 controls patterning of the mouse otic vesicle , 2004, Development.

[51]  A. Joyner,et al.  All mouse ventral spinal cord patterning by hedgehog is Gli dependent and involves an activator function of Gli3. , 2004, Developmental cell.

[52]  Weiming Zheng,et al.  The role of Six1 in mammalian auditory system development , 2003, Development.

[53]  M. Daly,et al.  PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes , 2003, Nature Genetics.

[54]  M. Mulheisen,et al.  Specification of the mammalian cochlea is dependent on Sonic hedgehog. , 2002, Genes & development.

[55]  H. Fuchs,et al.  The Notch ligand Jagged1 is required for inner ear sensory development , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[56]  N. Segil,et al.  p27(Kip1) links cell proliferation to morphogenesis in the developing organ of Corti. , 1999, Development.

[57]  W. House,et al.  Congenital malformations of the inner ear: A classification based on embryogenesis , 1987, The Laryngoscope.

[58]  R. Ruben.  Development of the inner ear of the mouse: a radioautographic study of terminal mitoses. , 1967, Acta oto-laryngologica.

[59]  C. S. Hallpike.  Mammalian Cochlea , 1965, Nature.