Alternative Splicing: New Insights from Global Analyses
Tài liệu tham khảo
Ars, 2000, Mutations affecting mRNA splicing are the most common molecular defects in patients with neurofibromatosis type 1, Hum. Mol. Genet., 9, 237, 10.1093/hmg/9.2.237
Baek, 2005, Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing, Proc. Natl. Acad. Sci. USA, 102, 12813, 10.1073/pnas.0506139102
Beffert, 2005, Modulation of synaptic plasticity and memory by Reelin involves differential splicing of the lipoprotein receptor Apoer2, Neuron, 47, 567, 10.1016/j.neuron.2005.07.007
Bentley, 2005, Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors, Curr. Opin. Cell Biol., 17, 251, 10.1016/j.ceb.2005.04.006
Black, 2003, Mechanisms of alternative pre-messenger RNA splicing, Annu. Rev. Biochem., 72, 291, 10.1146/annurev.biochem.72.121801.161720
Blanchette, 2005, Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila, Genes Dev., 19, 1306, 10.1101/gad.1314205
Boucher, 2001, A genome-wide survey of RS domain proteins, RNA, 7, 1693
Brett, 2002, Alternative splicing and genome complexity, Nat. Genet., 30, 29, 10.1038/ng803
Brudno, 2001, Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing, Nucleic Acids Res., 29, 2338, 10.1093/nar/29.11.2338
Cartegni, 2002, Listening to silence and understanding nonsense: exonic mutations that affect splicing, Nat. Rev. Genet., 3, 285, 10.1038/nrg775
Chen, 2006, The molecular diversity of Dscam is functionally required for neuronal wiring specificity in Drosophila, Cell, 125, 607, 10.1016/j.cell.2006.03.034
Chern, 2006, A simple physical model predicts small exon length variations, PLoS Genet., 2, e45, 10.1371/journal.pgen.0020045
Davis, 2000, Test of intron predictions reveals novel splice sites, alternatively spliced mRNAs and new introns in meiotically regulated genes of yeast, Nucleic Acids Res., 28, 1700, 10.1093/nar/28.8.1700
Dulac, 2005, Sex and the single splice, Cell, 121, 664, 10.1016/j.cell.2005.05.017
Dye, 2006, Exon tethering in transcription by RNA polymerase II, Mol. Cell, 21, 849, 10.1016/j.molcel.2006.01.032
Fairbrother, 2002, Predictive identification of exonic splicing enhancers in human genes, Science, 297, 1007, 10.1126/science.1073774
Forch, 2003, Splicing regulation in Drosophila sex determination, Prog. Mol. Subcell. Biol., 31, 127, 10.1007/978-3-662-09728-1_5
Graveley, 2005, Mutually exclusive splicing of the insect Dscam pre-mRNA directed by competing intronic RNA secondary structures, Cell, 123, 65, 10.1016/j.cell.2005.07.028
Gromak, 2003, The PTB interacting protein raver1 regulates alpha-tropomyosin alternative splicing, EMBO J., 22, 6356, 10.1093/emboj/cdg609
Hiller, 2004, Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity, Nat. Genet., 36, 1255, 10.1038/ng1469
Horiuchi, 2006, Alternative trans-splicing: a novel mode of pre-mRNA processing, Biol. Cell., 98, 135, 10.1042/BC20050002
Hughes, 2005, Gene duplication and the properties of biological networks, J. Mol. Evol., 61, 758, 10.1007/s00239-005-0037-z
Ibrahim el, 2005, Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers, Proc. Natl. Acad. Sci. USA, 102, 5002, 10.1073/pnas.0500543102
Johnson, 2003, Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays, Science, 302, 2141, 10.1126/science.1090100
Kanadia, 2003, A muscleblind knockout model for myotonic dystrophy, Science, 302, 1978, 10.1126/science.1088583
Keene, 2005, Post-transcriptional operons and regulons co-ordinating gene expression, Chromosome Res., 13, 327, 10.1007/s10577-005-0848-1
Kim, 2004, Estimating rates of alternative splicing in mammals and invertebrates, Nat. Genet., 36, 915, 10.1038/ng0904-915
Kopelman, 2005, Alternative splicing and gene duplication are inversely correlated evolutionary mechanisms, Nat. Genet., 37, 588, 10.1038/ng1575
Kornblihtt, 2005, Promoter usage and alternative splicing, Curr. Opin. Cell Biol., 17, 262, 10.1016/j.ceb.2005.04.014
Kornblihtt, 2006, Chromatin, transcript elongation and alternative splicing, Nat. Struct. Mol. Biol., 13, 5, 10.1038/nsmb0106-5
Lander, 2001, Initial sequencing and analysis of the human genome, Nature, 409, 860, 10.1038/35057062
Le, 2004, Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data, Nucleic Acids Res., 32, e180, 10.1093/nar/gnh173
Lee, 2003, ASAP: the Alternative Splicing Annotation Project, Nucleic Acids Res., 31, 101, 10.1093/nar/gkg029
Lev-Maor, 2003, The birth of an alternatively spliced exon: 3′ splice-site selection in Alu exons, Science, 300, 1288, 10.1126/science.1082588
Lewis, 2003, Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans, Proc. Natl. Acad. Sci. USA, 100, 189, 10.1073/pnas.0136770100
Li, 2006, Two-dimensional transcriptome profiling: identification of messenger RNA isoform signatures in prostate cancer from archived paraffin-embedded cancer specimens, Cancer Res., 66, 4079, 10.1158/0008-5472.CAN-05-4264
Lipscombe, 2005, Neuronal proteins custom designed by alternative splicing, Curr. Opin. Neurobiol., 15, 358, 10.1016/j.conb.2005.04.002
Martinez-Contreras, 2006, Intronic binding sites for hnRNP A/B and hnRNP F/H proteins stimulate pre-mRNA splicing, PLoS Biol., 4, e21, 10.1371/journal.pbio.0040021
Matlin, 2005, Understanding alternative splicing: towards a cellular code, Nat. Rev. Mol. Cell Biol., 6, 386, 10.1038/nrm1645
Miki, 2001, Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays, Proc. Natl. Acad. Sci. USA, 98, 2199, 10.1073/pnas.041605498
Minovitsky, 2005, The splicing regulatory element, UGCAUG, is phylogenetically and spatially conserved in introns that flank tissue-specific alternative exons, Nucleic Acids Res., 33, 714, 10.1093/nar/gki210
Modrek, 2002, A genomic view of alternative splicing, Nat. Genet., 30, 13, 10.1038/ng0102-13
Modrek, 2003, Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss, Nat. Genet., 34, 177, 10.1038/ng1159
Modrek, 2001, Genome-wide detection of alternative splicing in expressed sequences of human genes, Nucleic Acids Res., 29, 2850, 10.1093/nar/29.13.2850
Ohler, 2005, Recognition of unknown conserved alternatively spliced exons, PLoS Comput. Biol., 1, 113, 10.1371/journal.pcbi.0010015
Pagani, 2004, Genomic variants in exons and introns: identifying the splicing spoilers, Nat. Rev. Genet., 5, 389, 10.1038/nrg1327
Pan, 2004, Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform, Mol. Cell, 16, 929, 10.1016/j.molcel.2004.12.004
Pan, 2005, Alternative splicing of conserved exons is frequently species-specific in human and mouse, Trends Genet., 21, 73, 10.1016/j.tig.2004.12.004
Pan, 2006, Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression, Genes Dev., 20, 153, 10.1101/gad.1382806
Philipps, 2004, A computational and experimental approach toward a priori identification of alternatively spliced exons, RNA, 10, 1838, 10.1261/rna.7136104
Resch, 2004, Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation, Nucleic Acids Res., 32, 1261, 10.1093/nar/gkh284
Resch, 2004, Assessing the impact of alternative splicing on domain interactions in the human proteome, J. Proteome Res., 3, 76, 10.1021/pr034064v
Schmucker, 2000, Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity, Cell, 101, 671, 10.1016/S0092-8674(00)80878-8
Senapathy, 1990, Splice junctions, branch point sites, and exons: sequence statistics, identification, and applications to genome project, Methods Enzymol., 183, 252, 10.1016/0076-6879(90)83018-5
Shai, 2006, Inferring global levels of alternative splicing isoforms using a generative model of microarray data, Bioinformatics, 22, 606, 10.1093/bioinformatics/btk028
Soergel, 2005, Regulation of gene expression by coupling of alternative splicing and NMD, 175
Sorek, 2004, How prevalent is functional alternative splicing in the human genome?, Trends Genet., 20, 68, 10.1016/j.tig.2003.12.004
Stolc, 2004, A gene expression map for the euchromatic genome of Drosophila melanogaster, Science, 306, 655, 10.1126/science.1101312
Su, 2006, Evolution of alternative splicing after gene duplication, Genome Res., 16, 182, 10.1101/gr.4197006
Sugnet, 2006, Unusual intron conservation near tissue-regulated exons found by splicing microarrays, PLoS Comput. Biol., 2, e4, 10.1371/journal.pcbi.0020004
Sun, 2000, Multiple splicing defects in an intronic false exon, Mol. Cell. Biol., 20, 6414, 10.1128/MCB.20.17.6414-6425.2000
Teraoka, 1999, Splicing defects in the ataxia-telangiectasia gene, ATM: underlying mutations and consequences, Am. J. Hum. Genet., 64, 1617, 10.1086/302418
Thanaraj, 2004, ASD: the Alternative Splicing Database, Nucleic Acids Res., 32, D64, 10.1093/nar/gkh030
Ule, 2006, RNA binding proteins and the regulation of neuronal synaptic plasticity, Curr. Opin. Neurobiol., 16, 102, 10.1016/j.conb.2006.01.003
Ule, 2003, CLIP identifies Nova-regulated RNA networks in the brain, Science, 302, 1212, 10.1126/science.1090095
Ule, 2005, Nova regulates brain-specific splicing to shape the synapse, Nat. Genet., 37, 844, 10.1038/ng1610
Wang, 2003, Gene structure-based splice variant deconvolution using a microarray platform, Bioinformatics, 19, i315, 10.1093/bioinformatics/btg1044
Wang, 2004, Systematic identification and analysis of exonic splicing silencers, Cell, 119, 831, 10.1016/j.cell.2004.11.010
Wang, 2005, Structural genomics analysis of alternative splicing and application to isoform structure modeling, Proc. Natl. Acad. Sci. USA, 102, 18920, 10.1073/pnas.0506770102
Wang, 2006, General and specific functions of exonic splicing silencers in splicing control, Mol. Cell, 23, 61, 10.1016/j.molcel.2006.05.018
Watahiki, 2004, Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas, Nat. Methods, 1, 233, 10.1038/nmeth719
Watson, 2005, Extensive diversity of Ig-superfamily proteins in the immune system of insects, Science, 309, 1874, 10.1126/science.1116887
Wu, 2002, Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters, Nat. Genet., 31, 255, 10.1038/ng906
Xing, 2005, Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences, Proc. Natl. Acad. Sci. USA, 102, 13526, 10.1073/pnas.0501213102
Xing, 2005, Protein modularity of alternatively spliced exons is associated with tissue-specific regulation of alternative splicing, PLoS Genet., 1, e34, 10.1371/journal.pgen.0010034
Yeakley, 2002, Profiling alternative splicing on fiber-optic arrays, Nat. Biotechnol., 20, 353, 10.1038/nbt0402-353
Yeo, 2004, Variation in alternative splicing across human tissues, Genome Biol., 5, R74, 10.1186/gb-2004-5-10-r74
Yeo, 2005, Identification and analysis of alternative splicing events conserved in human and mouse, Proc. Natl. Acad. Sci. USA, 102, 2850, 10.1073/pnas.0409742102
Zavolan, 2003, Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome, Genome Res., 13, 1290, 10.1101/gr.1017303
Zhang, 2006, Profiling alternatively spliced mRNA isoforms for prostate cancer classification, BMC Bioinformatics, 7, 202, 10.1186/1471-2105-7-202
Zhang, 2004, The functional landscape of mouse gene expression, J. Biol., 3, 21, 10.1186/jbiol16
Zhang, 2004, Computational definition of sequence motifs governing constitutive exon splicing, Genes Dev., 18, 1241, 10.1101/gad.1195304
Zheng, 2005, MAASE: an alternative splicing database designed for supporting splicing microarray applications, RNA, 11, 1767, 10.1261/rna.2650905