Alternative Isoform Regulation in Human Tissue Transcriptomes

Through alternative processing of pre-messenger RNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes on the basis of deep sequencing of complementary DNA fragments, yielding a digital inventory of gene and mRNA isoform expression. Analyses in which sequence reads are mapped to exon–exon junctions indicated that 92–94% of human genes undergo alternative splicing, ∼86% with a minor isoform frequency of 15% or more. Differences in isoform-specific read densities indicated that most alternative splicing and alternative cleavage and polyadenylation events vary between tissues, whereas variation between individuals was approximately twofold to threefold less common. Extreme or ‘switch-like’ regulation of splicing between tissues was associated with increased sequence conservation in regulatory regions and with generation of full-length open reading frames. Patterns of alternative splicing and alternative cleavage and polyadenylation were strongly correlated across tissues, suggesting coordinated regulation of these processes, and sequence conservation of a subset of known regulatory motifs in both alternative introns and 3′ untranslated regions suggested common involvement of specific factors in tissue-level regulation of both splicing and polyadenylation.

[1]  B. O’Malley,et al.  The ovalbumin gene: cloning and molecular organization of the entire natural gene. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[2]  M. Mckeown.  Regulation of alternative splicing. , 1990, Genetic engineering.

[3]  S. Karlin,et al.  Prediction of complete gene structures in human genomic DNA. , 1997, Journal of molecular biology.

[4]  International Human Genome Sequencing Consortium.  Initial sequencing and analysis of the human genome , 2001, Nature.

[5]  W. Hahn,et al.  Human breast cancer cells generated by oncogenic transformation of primary mammary epithelial cells. , 2001, Genes & development.

[6]  T. Cooper,et al.  Finding signals that regulate alternative splicing in the post-genomic era , 2002, Genome Biology.

[7]  S. Brenner,et al.  Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[8]  P. Grabowski,et al.  Function of quaking in myelination: Regulation of alternative splicing , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Christopher J. Lee,et al.  Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. , 2002, Nucleic acids research.

[10]  B. Blencowe,et al.  SRm160 Splicing Coactivator Promotes Transcript 3′-End Cleavage , 2002, Molecular and Cellular Biology.

[11]  T. Maniatis,et al.  An extensive network of coupling among gene expression machines , 2002, Nature.

[12]  David Haussler,et al.  Combining phylogenetic and hidden Markov models in biosequence analysis , 2003, RECOMB '03.

[13]  D. Black.  Mechanisms of alternative pre-messenger RNA splicing. , 2003, Annual review of biochemistry.

[14]  J. Castle,et al.  Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction Microarrays , 2003, Science.

[15]  Werner Dubitzky,et al.  A Practical Approach to Microarray Data Analysis , 2003, Springer US.

[16]  Christopher B. Burge,et al.  Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals , 2003, RECOMB '03.

[17]  J. Kelso,et al.  Allele‐specific transcript isoforms in human , 2004, FEBS letters.

[18]  Gene W. Yeo,et al.  Variation in alternative splicing across human tissues , 2004, Genome Biology.

[19]  S. Haas,et al.  Strengths and weaknesses of EST-based prediction of tissue-specific alternative splicing , 2004, BMC Genomics.

[20]  M. Wollerton,et al.  Polypyrimidine Tract Binding Protein Modulates Efficiency of Polyadenylation , 2004, Molecular and Cellular Biology.

[21]  B. Frey,et al.  Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. , 2004, Molecular cell.

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

[23]  Christopher J. Lee,et al.  Protein Modularity of Alternatively Spliced Exons Is Associated with Tissue-Specific Regulation of Alternative Splicing , 2005, PLoS genetics.

[24]  Michael Recce,et al.  PolyA_DB: a database for mammalian mRNA polyadenylation , 2004, Nucleic Acids Res..

[25]  S. Richard,et al.  Target RNA motif and target mRNAs of the Quaking STAR protein , 2005, Nature Structural &Molecular Biology.

[26]  C. Burge,et al.  Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets , 2005, Cell.

[27]  F. Clark,et al.  Understanding alternative splicing: towards a cellular code , 2005, Nature Reviews Molecular Cell Biology.

[28]  Peter Stoilov,et al.  Homologues of the Caenorhabditis elegans Fox-1 Protein Are Neuronal Splicing Regulators in Mammals , 2005, Molecular and Cellular Biology.

[29]  D. Black,et al.  Structure of PTB Bound to RNA: Specific Binding and Implications for Splicing Regulation , 2005, Science.

[30]  S. Kawamoto,et al.  Tissue-dependent isoforms of mammalian Fox-1 homologs are associated with tissue-specific splicing activities , 2005, Nucleic acids research.

[31]  B. Blencowe.  Alternative Splicing: New Insights from Global Analyses , 2006, Cell.

[32]  B. Blencowe,et al.  An RNA map predicting Nova-dependent splicing regulation , 2006, Nature.

[33]  Maqc Consortium.  The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements , 2006, Nature Biotechnology.

[34]  R. Paz,et al.  Increased expression of activity-dependent genes in cerebellar glutamatergic neurons of patients with schizophrenia. , 2006, The American journal of psychiatry.

[35]  Zefeng Wang,et al.  General and specific functions of exonic splicing silencers in splicing control. , 2006, Molecular cell.

[36]  David Haussler,et al.  Unusual Intron Conservation near Tissue-Regulated Exons Found by Splicing Microarrays , 2005, PLoS Comput. Biol..

[37]  D. Black,et al.  Molecular basis of RNA recognition by the human alternative splicing factor Fox‐1 , 2006, The EMBO journal.

[38]  S. Kohlwein,et al.  Mitochondrial phosphate-carrier deficiency: a novel disorder of oxidative phosphorylation. , 2007, American journal of human genetics.

[39]  Uwe Ohler,et al.  Spatial preferences of microRNA targets in 3' untranslated regions , 2007, BMC Genomics.

[40]  Tyson A. Clark,et al.  HITS-CLIP yields genome-wide insights into brain alternative RNA processing , 2008, Nature.

[41]  Jacek Majewski,et al.  Genome-wide analysis of transcript isoform variation in humans , 2008, Nature Genetics.

[42]  M. Gorospe,et al.  GU-rich RNA: expanding CUGBP1 function, broadening mRNA turnover. , 2008, Molecular cell.

[43]  Marcel H. Schulz,et al.  A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome , 2008, Science.

[44]  Brenton R Graveley,et al.  The haplo-spliceo-transcriptome: common variations in alternative splicing in the human population. , 2008, Trends in genetics : TIG.

[45]  J. Wilusz,et al.  The RNA-binding Protein CUGBP1 Regulates Stability of Tumor Necrosis Factor mRNA in Muscle Cells , 2008, Journal of Biological Chemistry.

[46]  David Haussler,et al.  The UCSC Genome Browser Database: 2008 update , 2007, Nucleic Acids Res..

[47]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[48]  R. Rosenfeld.  Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.