Genome-wide detection of tissue-specific alternative splicing in the human transcriptome.

We have developed an automated method for discovering tissue-specific regulation of alternative splicing through a genome-wide analysis of expressed sequence tags (ESTs). Using this approach, we have identified 667 tissue-specific alternative splice forms of human genes. We validated our muscle-specific and brain-specific splice forms for known genes. A high fraction (8/10) were reported to have a matching tissue specificity by independent studies in the published literature. The number of tissue-specific alternative splice forms is highest in brain, while eye-retina, muscle, skin, testis and lymph have the greatest enrichment of tissue-specific splicing. Overall, 10-30% of human alternatively spliced genes in our data show evidence of tissue-specific splice forms. Seventy-eight percent of our tissue-specific alternative splices appear to be novel discoveries. We present bioinformatics analysis of several tissue-specific splice forms, including automated protein isoform sequence and domain prediction, showing how our data can provide valuable insights into gene function in different tissues. For example, we have discovered a novel kidney-specific alternative splice form of the WNK1 gene, which appears to specifically disrupt its N-terminal kinase domain and may play a role in PHAII hypertension. Our database greatly expands knowledge of tissue-specific alternative splicing and provides a comprehensive dataset for investigating its functional roles and regulation in different human tissues.

[1]  W. Gilbert.  Why genes in pieces? , 1978, Nature.

[2]  D. Crawford,et al.  Multiple splice forms of ribonuclease-inhibitor mRNA differ in the 5'-untranslated region. , 1989, Gene.

[3]  H. Künsch.  The Jackknife and the Bootstrap for General Stationary Observations , 1989 .

[4]  Martin Hofmann,et al.  A new variant of glycoprotein CD44 confers metastatic potential to rat carcinoma cells , 1991, Cell.

[5]  G. Grabowski,et al.  Gaucher disease: A G+1----A+1 IVS2 splice donor site mutation causing exon 2 skipping in the acid beta-glucosidase mRNA. , 1992, American journal of human genetics.

[6]  C. Burd,et al.  hnRNP proteins and the biogenesis of mRNA. , 1993, Annual review of biochemistry.

[7]  Michael Ruogu Zhang,et al.  A sequence compilation and comparison of exons that are alternatively spliced in neurons. , 1994, Nucleic acids research.

[8]  S. Emr,et al.  Coatomer is essential for retrieval of dilysine-tagged proteins to the endoplasmic reticulum , 1994, Cell.

[9]  L. Iverson,et al.  Tissue-specific alternative splicing of hybrid Shaker/lacZ genes correlates with kinetic differences in Shaker K+ currents in vivo , 1995, Neuron.

[10]  W. Tsang,et al.  Neuronatin mRNA: alternatively spliced forms of a novel brain-specific mammalian developmental gene , 1995, Brain Research.

[11]  Xiang-Dong Fu,et al.  The superfamily of arginine/serine-rich splicing factors. , 1995, RNA.

[12]  F. Wieland,et al.  Nonclathrin coat protein gamma, a subunit of coatomer, binds to the cytoplasmic dilysine motif of membrane proteins of the early secretory pathway. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[13]  J. Manley,et al.  SR proteins and splicing control. , 1996, Genes & development.

[14]  D. Kwiatkowski,et al.  Genomic organization and chromosomal location of murine Cdc42. , 1996, Genomics.

[15]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[16]  R. Durbin,et al.  Pfam: A comprehensive database of protein domain families based on seed alignments , 1997, Proteins.

[17]  G. Schuler.  Pieces of the puzzle: expressed sequence tags and the catalog of human genes , 1997, Journal of Molecular Medicine.

[18]  D. Slamon,et al.  Differential subcellular localization, expression and biological toxicity of BRCA1 and the splice variant BRCA1-Δ11b , 1997, Oncogene.

[19]  Erik L. L. Sonnhammer,et al.  A Hidden Markov Model for Predicting Transmembrane Helices in Protein Sequences , 1998, ISMB.

[20]  A. J. Lopez,et al.  Alternative splicing of pre-mRNA: developmental consequences and mechanisms of regulation. , 1998, Annual review of genetics.

[21]  N. Reich,et al.  Interferon Regulatory Factor 3 and CREB-Binding Protein/p300 Are Subunits of Double-Stranded RNA-Activated Transcription Factor DRAF1 , 1998, Molecular and Cellular Biology.

[22]  F. Wieland,et al.  A single binding site for dilysine retrieval motifs and p23 within the gamma subunit of coatomer. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[23]  A. Paetau,et al.  A variant of Alzheimer's disease with spastic paraparesis and unusual plaques due to deletion of exon 9 of presenilin 1 , 1998, Nature Medicine.

[24]  D B Davison,et al.  Alternative gene form discovery and candidate gene selection from gene indexing projects. , 1998, Genome research.

[25]  T. Maniatis,et al.  Virus infection induces the assembly of coordinately activated transcription factors on the IFN-beta enhancer in vivo. , 1998, Molecular cell.

[26]  F. Bloom,et al.  Transgenic expression of IFN-alpha in the central nervous system of mice protects against lethal neurotropic viral infection but induces inflammation and neurodegeneration. , 1998, Journal of immunology.

[27]  E. Beutler,et al.  The human Nramp2 gene: characterization of the gene structure, alternative splicing, promoter region and polymorphisms. , 1998, Blood cells, molecules & diseases.

[28]  J Schultz,et al.  SMART, a simple modular architecture research tool: identification of signaling domains. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[29]  E. Nishida,et al.  Direct triggering of the type I interferon system by virus infection: activation of a transcription factor complex containing IRF‐3 and CBP/p300 , 1998, The EMBO journal.

[30]  D Haussler,et al.  Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae. , 1999, RNA.

[31]  D. Helfman,et al.  Binding of hnRNP H to an exonic splicing silencer is involved in the regulation of alternative splicing of the rat beta-tropomyosin gene. , 1999, Genes & development.

[32]  Jane Y. Wu,et al.  Alternative splicing and programmed cell death. , 1999, Proceedings of the Society for Experimental Biology and Medicine. Society for Experimental Biology and Medicine.

[33]  J. Hiscott,et al.  Essential Role of Interferon Regulatory Factor 3 in Direct Activation of RANTES Chemokine Transcription , 1999, Molecular and Cellular Biology.

[34]  M. Fiszman,et al.  Regulated splicing of an alternative exon of beta-tropomyosin pre-mRNAs in myogenic cells depends on the strength of pyrimidine-rich intronic enhancer elements. , 1999, DNA and cell biology.

[35]  M. Gelfand,et al.  Frequent alternative splicing of human genes. , 1999, Genome research.

[36]  Inna Dubchak,et al.  ASDB: database of alternatively spliced genes , 1999, Nucleic Acids Res..

[37]  T. Seya,et al.  Human membrane cofactor protein (MCP, CD46): multiple isoforms and functions. , 1999, The international journal of biochemistry & cell biology.

[38]  P. White,et al.  The human CDC42 gene: genomic organization, evidence for the existence of a putative pseudogene and exclusion as a SJS1 candidate gene , 1999, Human Genetics.

[39]  S. Henriksen,et al.  Structural and functional neuropathology in transgenic mice with CNS expression of IFN-α 1 Published on the World Wide Web on 17 March 1999. 1 , 1999, Brain Research.

[40]  E. Laue,et al.  Structure of the small G protein Cdc42 bound to the GTPase-binding domain of ACK , 1999, Nature.

[41]  M. E. Mangan,et al.  An extensive list of genes that produce alternative transcripts in the mouse , 1999, Bioinform..

[42]  M. Swanson,et al.  hnRNP complexes: composition, structure, and function. , 1999, Current opinion in cell biology.

[43]  W. James Kent,et al.  The Intronerator: exploring introns and alternative splicing in Caenorhabditis elegans , 2000, Nucleic Acids Res..

[44]  L Grate,et al.  Test of intron predictions reveals novel splice sites, alternatively spliced mRNAs and new introns in meiotically regulated genes of yeast. , 2000, Nucleic acids research.

[45]  T. Cooper,et al.  RNA processing and human disease , 2000, Cellular and Molecular Life Sciences CMLS.

[46]  D. Kwiatkowski,et al.  Alternative splicing of the mouse profilin II gene generates functionally different profilin isoforms. , 2000, Journal of cell science.

[47]  J. Valcárcel,et al.  Alternative pre-mRNA splicing: the logic of combinatorial control. , 2000, Trends in biochemical sciences.

[48]  T. Soong,et al.  Heterologous expression, functional characterization and localization of two isoforms of the monkey iron transporter Nramp2. , 2000, The Biochemical journal.

[49]  Robert B Darnell,et al.  Nova-1 Regulates Neuron-Specific Alternative Splicing and Is Essential for Neuronal Viability , 2000, Neuron.

[50]  J. Erickson,et al.  The γ-subunit of the coatomer complex binds Cdc42 to mediate transformation , 2000, Nature.

[51]  P Bork,et al.  EST comparison indicates 38% of human mRNAs contain possible alternative splice forms , 2000, FEBS letters.

[52]  Michael Ruogu Zhang,et al.  An alternative-exon database and its statistical analysis. , 2000, DNA and cell biology.

[53]  W. Rizzo,et al.  Genomic organization, expression, and alternate splicing of the mouse fatty aldehyde dehydrogenase gene. , 2000, Molecular genetics and metabolism.

[54]  C. Ampe,et al.  Profilin II Is Alternatively Spliced, Resulting in Profilin Isoforms That Are Differentially Expressed and Have Distinct Biochemical Properties , 2000, Molecular and Cellular Biology.

[55]  E. Goldsmith,et al.  WNK1, a Novel Mammalian Serine/Threonine Protein Kinase Lacking the Catalytic Lysine in Subdomain II* , 2000, The Journal of Biological Chemistry.

[56]  Kevin Burrage,et al.  ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome , 2000, Nature Genetics.

[57]  A. Karpova,et al.  Dual utilization of an acceptor/donor splice site governs the alternative splicing of the IRF-3 gene. , 2000, Genes & development.

[58]  D. Black,et al.  Cooperative Assembly of an hnRNP Complex Induced by a Tissue-Specific Homolog of Polypyrimidine Tract Binding Protein , 2000, Molecular and Cellular Biology.

[59]  Human variant glucose-6-phosphate transporter is active in microsomal transport , 2000, Human Genetics.

[60]  D. Black,et al.  Alternative RNA splicing in the nervous system , 2001, Progress in Neurobiology.

[61]  Qing Zhou,et al.  AsMamDB: an alternative splice database of mammals , 2001, Nucleic Acids Res..

[62]  J. Erickson,et al.  Multiple roles for Cdc42 in cell regulation. , 2001, Current opinion in cell biology.

[63]  Christopher J. Lee,et al.  The GeneMine system for genome/proteome annotation and collaborative data mining , 2001, IBM Syst. J..

[64]  Peter Jordan,et al.  WNK kinases, a novel protein kinase subfamily in multi-cellular organisms , 2001, Oncogene.

[65]  W. Gish,et al.  Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. , 2001, Genome research.

[66]  L. Ronco,et al.  Functional Characterization of Interferon Regulatory Factor 3a (IRF-3a), an Alternative Splice Isoform of IRF-3 , 2001, Molecular and Cellular Biology.

[67]  S. Tsui,et al.  Characterization of tissue‐specific LIM domain protein (FHL1C) which is an alternatively spliced isoform of a human LIM‐only protein (FHL1) , 2001, Journal of Cellular Biochemistry.

[68]  T. Jatkoe,et al.  Predicting splice variant from DNA chip expression data. , 2001, Genome research.

[69]  W. Rizzo,et al.  Fatty aldehyde dehydrogenase: genomic structure, expression and mutation analysis in Sjögren-Larsson syndrome. , 2001, Chemico-biological interactions.

[70]  Robert J. Unwin,et al.  Human Hypertension Caused by Mutations in WNK Kinases , 2001, Science.

[71]  I-Min A. Dubchak,et al.  Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing. , 2001, Nucleic acids research.

[72]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[73]  T. Dörk,et al.  A new type of mutation causes a splicing defect in ATM , 2002, Nature Genetics.

[74]  A. Skandalis,et al.  Spontaneous frequency of exon skipping in the human HPRT gene. , 2002, Mutation research.

[75]  Christopher J. Lee,et al.  A genomic view of alternative splicing , 2002, Nature Genetics.

[76]  Tyson A. Clark,et al.  Genomewide Analysis of mRNA Processing in Yeast Using Splicing-Specific Microarrays , 2002, Science.

[77]  Xiang-Dong Fu,et al.  Profiling alternative splicing on fiber-optic arrays , 2002, Nature Biotechnology.

[78]  H. Takada,et al.  Quantitative analysis of glucose-6-phosphate translocase gene expression in various human tissues and haematopoietic progenitor cells , 2000, Journal of Inherited Metabolic Disease.