Signatures from tissue-specific MPSS libraries identify transcripts preferentially expressed in the mouse inner ear.

Specialization in cell function and morphology is influenced by the differential expression of mRNAs, many of which are expressed at low abundance and restricted to certain cell types. Detecting such transcripts in cDNA libraries may require sequencing millions of clones. Massively parallel signature sequencing (MPSS) is well suited to identifying transcripts that are expressed in discrete cell types and in low abundance. We have made MPSS libraries from microdissections of three inner ear tissues. By comparing these MPSS libraries to those of 87 other tissues included in the Mouse Reference Transcriptome online resource, we have identified genes that are highly enriched in, or specific to, the inner ear. We show by RT-PCR and in situ hybridization that signatures unique to the inner ear libraries identify transcripts with highly specific cell-type localizations. These transcripts serve to illustrate the utility of a resource that is available to the research community. Utilization of these resources will increase the number of known transcription units and expand our knowledge of the tissue-specific regulation of the transcriptome.

[1]  C. Petit,et al.  OTOF encodes multiple long and short isoforms: genetic evidence that the long ones underlie recessive deafness DFNB9. , 2000, American journal of human genetics.

[2]  C. V. Jongeneel,et al.  An atlas of human gene expression from massively parallel signature sequencing (MPSS). , 2005, Genome research.

[3]  W. Miller,et al.  Distinguishing regulatory DNA from neutral sites. , 2003, Genome research.

[4]  Ron Shamir,et al.  A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs , 2005, Genome Biology.

[5]  M. Brilliant,et al.  A new allelic series for the underwhite gene on mouse chromosome 15. , 1998, The Journal of heredity.

[6]  K. Lindblad-Toh,et al.  Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals , 2005, Nature.

[7]  Yusuke Nakamura,et al.  Mutation analysis of COL9A3, a gene highly expressed in the cochlea, in hearing loss patients. , 2005, Auris, nasus, larynx.

[8]  I. Khrebtukova,et al.  MPSS profiling of human embryonic stem cells , 2004, BMC Developmental Biology.

[9]  Alex E. Lash,et al.  Gene Expression Omnibus: NCBI gene expression and hybridization array data repository , 2002, Nucleic Acids Res..

[10]  J B Hurley,et al.  Abnormal photoresponses and light-induced apoptosis in rods lacking rhodopsin kinase. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[11]  H. Takeda,et al.  Otolith matrix proteins OMP-1 and Otolin-1 are necessary for normal otolith growth and their correct anchoring onto the sensory maculae , 2005, Mechanisms of Development.

[12]  Erez Y. Levanon,et al.  Widespread occurrence of antisense transcription in the human genome , 2003, Nature Biotechnology.

[13]  Linda B. Buck,et al.  Information coding in the olfactory system: Evidence for a stereotyped and highly organized epitope map in the olfactory bulb , 1994, Cell.

[14]  R. Russell,et al.  Animal MicroRNAs Confer Robustness to Gene Expression and Have a Significant Impact on 3′UTR Evolution , 2005, Cell.

[15]  B. Scheithauer,et al.  Myosin XVA expression in the pituitary and in other neuroendocrine tissues and tumors. , 2001, The American journal of pathology.

[16]  T. Friedman,et al.  Myosin XVa localizes to the tips of inner ear sensory cell stereocilia and is essential for staircase formation of the hair bundle , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[17]  G. Richardson,et al.  Mutations in the human α-tectorin gene cause autosomal dominant non-syndromic hearing impairment , 1998, Nature Genetics.

[18]  C. V. Jongeneel,et al.  Long-range heterogeneity at the 3' ends of human mRNAs. , 2002, Genome research.

[19]  B. Delprat,et al.  Deafness and Cochlear Fibrocyte Alterations in Mice Deficient for the Inner Ear Protein Otospiralin , 2005, Molecular and Cellular Biology.

[20]  Ben Lehner,et al.  Antisense transcripts in the human genome. , 2002, Trends in genetics : TIG.

[21]  W. Miller,et al.  Characterization of the human and mouse unconventional myosin XV genes responsible for hereditary deafness DFNB3 and shaker 2. , 1999, Genomics.

[22]  R. Romand,et al.  Development of the auditory receptors of the rat: a SEM study , 1996, Brain Research.

[23]  J. Beckmann,et al.  An alpha-tectorin gene defect causes a newly identified autosomal recessive form of sensorineural pre-lingual non-syndromic deafness, DFNB21. , 1999, Human molecular genetics.

[24]  E. Rugarli,et al.  UMODL1/Olfactorin is an extracellular membrane‐bound molecule with a restricted spatial expression in olfactory and vomeronasal neurons , 2005, The European journal of neuroscience.

[25]  K. Kinzler,et al.  Serial Analysis of Gene Expression , 1995, Science.

[26]  S. Minoshima,et al.  Initial characterization of an uromodulin-like 1 gene on human chromosome 21q22.3. , 2004, Biochemical and biophysical research communications.

[27]  A. Aszódi,et al.  Type IX collagen knock-out mouse shows progressive hearing loss , 2005, Neuroscience Research.

[28]  D. Higgs,et al.  Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease , 2003, Nature Genetics.

[29]  B. Fakler,et al.  Prestin, the Motor Protein of Outer Hair Cells , 2002, Audiology and Neurotology.

[30]  Jing Zheng,et al.  Prestin is the motor protein of cochlear outer hair cells , 2000, Nature.

[31]  Blake C Meyers,et al.  The use of MPSS for whole-genome transcriptional analysis in Arabidopsis. , 2004, Genome research.

[32]  M. Soares,et al.  Normalization and subtraction: two approaches to facilitate gene discovery. , 1996, Genome research.

[33]  J. Mattick,et al.  Non-coding RNA. , 2006, Human molecular genetics.

[34]  Rithy K. Roth,et al.  Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays , 2000, Nature Biotechnology.

[35]  G. Richardson,et al.  The Mouse Tectorins , 1997, The Journal of Biological Chemistry.

[36]  M. Lathrop,et al.  Otoancorin, an inner ear protein restricted to the interface between the apical surface of sensory epithelia and their overlying acellular gels, is defective in autosomal recessive deafness DFNB22 , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[37]  J. R. Holt,et al.  Developmental acquisition of sensory transduction in hair cells of the mouse inner ear , 2003, Nature Neuroscience.

[38]  M. Cohen-Salmon,et al.  Targeted disruption of Otog results in deafness and severe imbalance , 2000, Nature Genetics.

[39]  W. Reardon,et al.  Hereditary Hearing Loss and its Syndromes , 1995 .

[40]  J. Kawai,et al.  Identification of unique transcripts from a mouse full-length, subtracted inner ear cDNA library. , 2004, Genomics.

[41]  Dennis B. Troup,et al.  NCBI GEO: mining millions of expression profiles—database and tools , 2004, Nucleic Acids Res..

[42]  Piero Carninci,et al.  Tag-based approaches for transcriptome research and genome annotation , 2005, Nature Methods.

[43]  M. Greene,et al.  Fish otolith contains a unique structural protein, otolin-1. , 2002, European Journal of Biochemistry.

[44]  C. V. Jongeneel,et al.  Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[45]  D. Mager,et al.  Otoconin-90, the mammalian otoconial matrix protein, contains two domains of homology to secretory phospholipase A2. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[46]  S. Batalov,et al.  Antisense Transcription in the Mammalian Transcriptome , 2005, Science.

[47]  S. Kuersten,et al.  The power of the 3′ UTR: translational control and development , 2003, Nature Reviews Genetics.