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Powers TR, Virk SM, Trujillo-Provencio C, Serrano EE. Probing the Xenopus laevis inner ear transcriptome for biological function. BMC Genomics 2012; 13:225. [PMID: 22676585 PMCID: PMC3532188 DOI: 10.1186/1471-2164-13-225] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 05/21/2012] [Indexed: 01/27/2023] Open
Abstract
Background The senses of hearing and balance depend upon mechanoreception, a process that originates in the inner ear and shares features across species. Amphibians have been widely used for physiological studies of mechanotransduction by sensory hair cells. In contrast, much less is known of the genetic basis of auditory and vestibular function in this class of animals. Among amphibians, the genus Xenopus is a well-characterized genetic and developmental model that offers unique opportunities for inner ear research because of the amphibian capacity for tissue and organ regeneration. For these reasons, we implemented a functional genomics approach as a means to undertake a large-scale analysis of the Xenopus laevis inner ear transcriptome through microarray analysis. Results Microarray analysis uncovered genes within the X. laevis inner ear transcriptome associated with inner ear function and impairment in other organisms, thereby supporting the inclusion of Xenopus in cross-species genetic studies of the inner ear. The use of gene categories (inner ear tissue; deafness; ion channels; ion transporters; transcription factors) facilitated the assignment of functional significance to probe set identifiers. We enhanced the biological relevance of our microarray data by using a variety of curation approaches to increase the annotation of the Affymetrix GeneChip® Xenopus laevis Genome array. In addition, annotation analysis revealed the prevalence of inner ear transcripts represented by probe set identifiers that lack functional characterization. Conclusions We identified an abundance of targets for genetic analysis of auditory and vestibular function. The orthologues to human genes with known inner ear function and the highly expressed transcripts that lack annotation are particularly interesting candidates for future analyses. We used informatics approaches to impart biologically relevant information to the Xenopus inner ear transcriptome, thereby addressing the impediment imposed by insufficient gene annotation. These findings heighten the relevance of Xenopus as a model organism for genetic investigations of inner ear organogenesis, morphogenesis, and regeneration.
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Affiliation(s)
- TuShun R Powers
- Biology Department, New Mexico State University, Las Cruces, USA
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McDermott BM, Asai Y, Baucom JM, Jani SD, Castellanos Y, Gomez G, McClintock JM, Starr CJ, Hudspeth AJ. Transgenic labeling of hair cells in the zebrafish acousticolateralis system. Gene Expr Patterns 2010; 10:113-8. [PMID: 20085825 DOI: 10.1016/j.gep.2010.01.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2009] [Revised: 01/07/2010] [Accepted: 01/09/2010] [Indexed: 02/01/2023]
Abstract
The zebrafish provides a useful experimental system for investigations of aural development. To permit the controlled expression of transgenes in developing hair cells, we isolated the genomic control regions of the parvalbumin 3a (pvalb3a) and parvalbumin 3b (pvalb3b) genes. Deletion analysis and somatic-cell transgenesis restricted the cis-acting control regions for hair cells to as little as 484base pairs for pvalb3a and 650base pairs for pvalb3b. Using both meganuclease-mediated and standard methods, we produced transgenic animals that transmit transgenes through their germ lines. These fish express GFP in hair cells in the inner ear and lateral line. Two stable transgenic lines express GFP prior to hair-bundle formation, so the associated promoter constructs are suitable for manipulating gene expression during bundle development. We additionally identified a transgenic line that offers variable labeling of supporting cells.
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Affiliation(s)
- Brian M McDermott
- Laboratory of Sensory Neuroscience and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue New York, NY 10065, USA
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McDermott BM, Baucom JM, Hudspeth AJ. Analysis and functional evaluation of the hair-cell transcriptome. Proc Natl Acad Sci U S A 2007; 104:11820-5. [PMID: 17606911 PMCID: PMC1905926 DOI: 10.1073/pnas.0704476104] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
An understanding of the molecular bases of the morphogenesis, organization, and functioning of hair cells requires that the genes expressed in these cells be identified and their functions ascertained. After purifying zebrafish hair cells and detecting mRNAs with oligonucleotide microarrays, we developed a subtractive strategy that identified 1,037 hair cell-expressed genes whose cognate proteins subserve functions including membrane transport, synaptic transmission, transcriptional control, cellular adhesion and signal transduction, and cytoskeletal organization. To assess the validity of the subtracted hair-cell data set, we verified the presence of 11 transcripts in inner-ear tissue. Functional evaluation of two genes from the subtracted data set revealed their importance in hair bundles: zebrafish larvae bearing the seahorse and ift 172 mutations display specific kinociliary defects. Moreover, a search for candidate genes that underlie heritable deafness identified a human ortholog of a zebrafish hair-cell gene whose map location is bracketed by the markers of a deafness locus.
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Affiliation(s)
- Brian M. McDermott
- Howard Hughes Medical Institute and Laboratory of Sensory Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399
| | - Jessica M. Baucom
- Howard Hughes Medical Institute and Laboratory of Sensory Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399
| | - A. J. Hudspeth
- Howard Hughes Medical Institute and Laboratory of Sensory Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399
- To whom correspondence should be addressed. E-mail:
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Im GJ, Jung HH, Chae SW, Cho WS, Kim SJ. Differential gene expression profiles in salicylate ototoxicity of the mouse. Acta Otolaryngol 2007; 127:459-69. [PMID: 17453470 DOI: 10.1080/00016480600801365] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
CONCLUSION This study demonstrated differential gene expression profiles in salicylate ototoxicity with oligonucleotide microarray. This study may also provide basic information on candidate genes associated with hearing loss and/or tinnitus or recovery after salicylate-induced cochlear dysfunction. OBJECTIVES Salicylate ototoxicity is accompanied by temporary hearing loss and tinnitus. The purpose of the present study was to evaluate the gene expression profiles in the mouse cochlea with salicylate ototoxicity using DNA microarray. MATERIALS AND METHODS The subject mice were injected intraperitoneally with 400 mg/kg of sodium salicylate; an approximate 30 dB threshold shift that was observed by auditory brainstem response was achieved 3 h after an injection of sodium salicylate and the hearing threshold returned to within normal range at 3 days. Differential gene expression profiles at 3 h after salicylate injection in comparison to the normal cochlea were analyzed with DNA microarray technology. RESULTS No ultrastructural changes in the mice cochlea were observed by TEM at 3 h after salicylate injection. Microarray revealed that 87 genes were up-regulated twofold or more in the mouse cochlea with salicylate ototoxicity in comparison to the normal cochlea. Among these genes, increased expression levels of 30 functional genes were confirmed by semi-quantitative RT-PCR.
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MESH Headings
- Animals
- Anti-Inflammatory Agents, Non-Steroidal/toxicity
- Auditory Fatigue/drug effects
- Cochlea/drug effects
- Cochlea/pathology
- Evoked Potentials, Auditory, Brain Stem/drug effects
- Gene Expression Profiling
- Hair Cells, Auditory, Outer/drug effects
- Hair Cells, Auditory, Outer/pathology
- Male
- Mice
- Mice, Inbred BALB C
- Microscopy, Electron, Transmission
- Oligonucleotide Array Sequence Analysis
- RNA, Messenger/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Sodium Salicylate/toxicity
- Up-Regulation/drug effects
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Affiliation(s)
- Gi Jung Im
- Department of Otolaryngology-Head and Neck Surgery, Korea University College of Medicine, An Am-Dong 5Ka 126-1, Sungbuk-Ku, Seoul 136-705, Korea
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Hildebrand MS, de Silva MG, Klockars T, Campbell CA, Smith RJH, Dahl HHM. Gene expression profiling analysis of the inner ear. Hear Res 2007; 225:1-10. [PMID: 17300888 DOI: 10.1016/j.heares.2007.01.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2006] [Revised: 01/01/2007] [Accepted: 01/02/2007] [Indexed: 11/20/2022]
Abstract
Recent developments in molecular genetics, including progress in the human genome project, have allowed identification of genes at an unprecedented rate. To date gene expression profiling studies have focused on identifying transcripts that are specifically or preferentially enriched within the inner ear on the assumption that they are more likely to be important for auditory and vestibular function. It is now apparent that some genes preferentially expressed in the cochleo-vestibular system are not crucial for hearing or balance or their functions are compensated for by other genes. In addition, transcripts expressed at low abundance in the inner ear are generally under-represented in gene profiling studies. In this review, we highlight the limitations of current gene expression profiling strategies as a discovery tool for genes involved in cochleo-vestibular development and function. We argue that expression profiling based on hierarchical clustering of transcripts by gene ontology, combined with tissue enrichment data, is more effective for inner ear gene discovery. This approach also provides a framework to assist and direct the functional characterization of gene products.
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Affiliation(s)
- Michael S Hildebrand
- Department of Otolaryngology - Head and Neck Surgery, University of Iowa, Iowa City, IA 52242, USA.
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De Silva MG, Hildebrand MS, Christopoulos H, Newman MR, Bell K, Ritchie M, Smyth GK, Dahl HHM. Gene expression changes during step-wise differentiation of embryonic stem cells along the inner ear hair cell pathway. Acta Otolaryngol 2006; 126:1148-57. [PMID: 17050306 DOI: 10.1080/00016480600702118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
CONCLUSION Our study outlines an alternative approach for the selection and investigation of genes involved in inner ear function. OBJECTIVE To gain understanding of the gene pathways involved in the development of the normal cochlea. MATERIALS AND METHODS Microarray technology currently offers the most efficient approach to investigate gene expression and identify pathways involved in cell differentiation. Epidermal growth factor (EGF) induces cultures derived from the organ of Corti to proliferate and produce new hair cells. Since pluripotent embryonic stem (ES) cells have the capacity to generate all tissues, we induced murine ES cells to differentiate towards ectodermal and neuroectodermal cell types and from there investigated their commitment towards the hair cell lineage in the presence of EGF. Cells were collected at three points along the differentiation pathway and their expression profiles were determined using the Soares NMIE mouse inner ear cDNA library printed in microarray format. RESULTS Three genes up-regulated after addition of EGF (serine (or cysteine) proteinase inhibitor, clade H, member 1 (Serpinh1), solute carrier family 2 (facilitated glucose transporter), member 10 (Slc2a10) and secreted acidic cysteine-rich glycoprotein (Sparc)) were selected for further analysis and characterization. Of the three genes, Serpinh1 and Slc2a10 have never been implicated in the hearing process.
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Affiliation(s)
- Michelle G De Silva
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Vic 3052, Australia.
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Roche JP, Wackym PA, Cioffi JA, Kwitek AE, Erbe CB, Popper P. In silico analysis of 2085 clones from a normalized rat vestibular periphery 3' cDNA library. Audiol Neurootol 2005; 10:310-22. [PMID: 16103642 PMCID: PMC1421512 DOI: 10.1159/000087348] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2005] [Accepted: 03/21/2005] [Indexed: 11/19/2022] Open
Abstract
The inserts from 2400 cDNA clones isolated from a normalized Rattus norvegicus vestibular periphery cDNA library were sequenced and characterized. The Wackym-Soares vestibular 3' cDNA library was constructed from the saccular and utricular maculae, the ampullae of all three semicircular canals and Scarpa's ganglia containing the somata of the primary afferent neurons, microdissected from 104 male and female rats. The inserts from 2400 randomly selected clones were sequenced from the 5' end. Each sequence was analyzed using the BLAST algorithm compared to the Genbank nonredundant, rat genome, mouse genome and human genome databases to search for high homology alignments. Of the initial 2400 clones, 315 (13%) were found to be of poor quality and did not yield useful information, and therefore were eliminated from the analysis. Of the remaining 2085 sequences, 918 (44%) were found to represent 758 unique genes having useful annotations that were identified in databases within the public domain or in the published literature; these sequences were designated as known characterized sequences. 1141 sequences (55%) aligned with 1011 unique sequences had no useful annotations and were designated as known but uncharacterized sequences. Of the remaining 26 sequences (1%), 24 aligned with rat genomic sequences, but none matched previously described rat expressed sequence tags or mRNAs. No significant alignment to the rat or human genomic sequences could be found for the remaining 2 sequences. Of the 2085 sequences analyzed, 86% were singletons. The known, characterized sequences were analyzed with the FatiGO online data-mining tool (http://fatigo.bioinfo.cnio.es/) to identify level 5 biological process gene ontology (GO) terms for each alignment and to group alignments with similar or identical GO terms. Numerous genes were identified that have not been previously shown to be expressed in the vestibular system. Further characterization of the novel cDNA sequences may lead to the identification of genes with vestibular-specific functions. Continued analysis of the rat vestibular periphery transcriptome should provide new insights into vestibular function and generate new hypotheses. Physiological studies are necessary to further elucidate the roles of the identified genes and novel sequences in vestibular function.
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Affiliation(s)
- Joseph P. Roche
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisc., USA
| | - P. Ashley Wackym
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisc., USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisc., USA
| | - Joseph A. Cioffi
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisc., USA
| | - Anne E. Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisc., USA
| | - Christy B. Erbe
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisc., USA
| | - Paul Popper
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisc., USA
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Li H, Liu H, Sage C, Huang M, Chen ZY, Heller S. Islet-1 expression in the developing chicken inner ear. J Comp Neurol 2004; 477:1-10. [PMID: 15281076 DOI: 10.1002/cne.20190] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The cell types of the inner ear originate from the otic placode, a thickened layer of ectoderm adjacent to the developing hindbrain. The placode invaginates and forms the otic pit, which pinches off as a small vesicle called the otocyst. Presumptive cochleovestibular neurons delaminate from the anterior ventral part of the otocyst and form the cochleovestibular ganglion of the inner ear. Here we show that the LIM/homeodomain protein islet-1 is expressed in cells of the ventral part of the otic placode and that this ventral expression is maintained at the otic pit and the otocyst stages. Auditory and vestibular neurons originate from this islet-1-positive zone of the otocyst, and these neurons maintain islet-1 expression until adulthood. We also demonstrate that islet-1 becomes up-regulated in the presumptive sensory epithelia of the inner ear in regions that are defined by the expression domains of BMP4. The up-regulation of islet-1 in developing inner ear hair and supporting cells is accompanied by down-regulation of Pax-2 in these cell types. Islet-1 expression in hair and supporting cells persists until early postnatal stages, when the transcriptional regulator is down-regulated in hair cells. Our data is consistent with a role for islet-1 in differentiating inner ear neurons and sensory epithelia cells, perhaps in the specification of cellular subtypes in conjunction with other LIM/homeodomain proteins.
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Affiliation(s)
- Huawei Li
- Department of Otolaryngology and Program in Neuroscience, Harvard Medical School, and Eaton Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts 02114, USA
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Beisel KW, Shiraki T, Morris KA, Pompeia C, Kachar B, Arakawa T, Bono H, Kawai J, Hayashizaki Y, Carninci P. Identification of unique transcripts from a mouse full-length, subtracted inner ear cDNA library. Genomics 2004; 83:1012-23. [PMID: 15177555 DOI: 10.1016/j.ygeno.2004.01.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2003] [Revised: 12/15/2003] [Accepted: 01/25/2004] [Indexed: 11/20/2022]
Abstract
A small-scale full-length library construction approach was developed to facilitate production of a mouse full-length cDNA encyclopedia representing approximately 250 enriched, normalized, and/or subtracted cDNA libraries. One library produced using this approach was a subtracted adult mouse inner ear cDNA library (sIEa). The average size of the inserts was approximately 2.5 kb, with the majority ranging from 0.5 to 7.0 kb. From this library 22,574 sequence reads were obtained from 15,958 independent clones. Sequencing and chromosomal localization established 5240 clusters, with 1302 clusters being unique and 359 representing new ESTs. Our sIEa library contributed 56.1% of the 7773 nonredundant Unigene clusters associated with the four mouse inner ear libraries in the NCBI dbEST. Based on homologous chromosomal regions between human and mouse, we identified 1018 UniGene clusters associated with the deafness locus critical regions. Of these, 59 clusters were found only in our sIEa library and represented approximately 50% of the identified critical regions.
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Affiliation(s)
- Kirk W Beisel
- Department of Biomedical Sciences, Creighton University, 2500 California, Omaha, NE 68178, USA.
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Keresztes G, Mutai H, Hibino H, Hudspeth AJ, Heller S. Expression patterns of the RGS9-1 anchoring protein R9AP in the chicken and mouse suggest multiple roles in the nervous system. Mol Cell Neurosci 2004; 24:687-95. [PMID: 14664818 DOI: 10.1016/s1044-7431(03)00231-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
In retinal photoreceptors, the duration of G protein signalling is tightly regulated by the GTPase-activating protein RGS9-1. RGS9-1 is anchored to the disk membranes of photoreceptor outer segments by association with the membrane-spanning protein R9AP. Here we report the cloning of chicken R9AP from an inner ear cDNA library and the isolation of a murine R9AP cDNA from a retinal library. In the chicken, R9AP appears to be expressed in a variety of neuronal tissues, particularly in sensory cells including inner ear hair cells, photoreceptors, and dorsal root ganglion neurons. In the mouse, R9AP is detectable predominantly in photoreceptors, but it is also weakly expressed in other areas of the central nervous system. The expression of R9AP beyond photoreceptors led us to examine potential alternative roles for R9AP besides anchoring RGS9-1 and we found sequence homology and structural similarity of the protein with members of the SNARE protein family. Expression of chicken and mouse R9AP interfered with intracellular trafficking of an indicator protein in an in vitro assay, suggesting a more active role of the protein, possibly in targeting. GTPase-activating proteins to specific membranous compartments.
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MESH Headings
- Adaptor Proteins, Signal Transducing
- Animals
- Cell Compartmentation/physiology
- Cell Membrane/metabolism
- Chickens
- DNA, Complementary/analysis
- DNA, Complementary/genetics
- Ganglia, Spinal/cytology
- Ganglia, Spinal/metabolism
- Hair Cells, Auditory/cytology
- Hair Cells, Auditory/metabolism
- Membrane Proteins/genetics
- Membrane Proteins/isolation & purification
- Membrane Proteins/metabolism
- Mice
- Molecular Sequence Data
- Nervous System/cytology
- Nervous System/metabolism
- Neurons, Afferent/cytology
- Neurons, Afferent/metabolism
- Photoreceptor Cells/cytology
- Photoreceptor Cells/metabolism
- Protein Transport/physiology
- RGS Proteins/metabolism
- SNARE Proteins
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
- Vesicular Transport Proteins
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Affiliation(s)
- Gabor Keresztes
- Department of Otolaryngology and Program in Neuroscience, Harvard Medical School, Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA
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Abstract
The vertebrate inner ear is a marvel of structural and functional complexity, which is all the more remarkable because it develops from such a simple structure, the otic placode. Analysis of inner ear development has long been a fascination of experimental embryologists, who sought to understand cellular mechanisms of otic placode induction. More recently, however, molecular and genetic approaches have made the inner ear a useful model system for studying a much broader range of basic developmental mechanisms, including cell fate specification and differentiation, axial patterning, epithelial morphogenesis, cytoskeletal dynamics, stem cell biology, neurobiology, physiology, etc. Of course, there has also been tremendous progress in understanding the functions and processes peculiar to the inner ear. The goal of this review is to recount how historical approaches have shaped our understanding of the signaling interactions controlling early otic development; to discuss how new findings have led to fundamental new insights; and to point out new problems that need to be resolved in future research.
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Affiliation(s)
- Bruce B Riley
- Biology Department, Texas A&M University, College Station, TX 77843-3258, USA.
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Abstract
Our senses of touch, hearing, and balance are mediated by mechanosensitive ion channels. In vertebrates, little is known about the molecular composition of these mechanoreceptors, an example of which is the transduction channel of the inner ear's receptor cells, hair cells. Members of the TRP family of ion channels are considered candidates for the vertebrate hair cell's mechanosensitive transduction channel and here we review the evidence for this candidacy. We start by examining the results of genetic screens in invertebrates that identified members of the TRP gene family as core components of mechanoreceptors. In particular, we discuss the Caenorhabditis elegans OSM-9 channel, an invertebrate TRPV channel, and the Drosophila melanogaster TRP channel NOMPC. We then evaluate basic features of TRPV4, a vertebrate member of the TRPV subfamily, which is gated by a variety of physical and chemical stimuli including temperature, osmotic pressure, and ligands. Finally, we compare the characteristics of all discussed mechanoreceptive TRP channels with the biophysical characteristics of hair cell mechanotransduction, speculating about the possible make-up of the elusive inner ear mechanoreceptor.
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Affiliation(s)
- Hideki Mutai
- Department of Otolaryngology and Program in Neuroscience, Harvard Medical School, Division of Health Sciences and Technology, Harvard University-Massachusetts Institute of Technology, Boston, MA 02114, USA
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