An exon-centric perspective

Biochemistry and Cell Biology

Volumn 90, Issue 5, 2012, Pages 603-612

  Blencowe, Benjamin J ^a  

^a UNIVERSITY OF TORONTO   (Canada)

Author keywords

Alternative splicing; Exon networks; Splicing code; Transcriptomics

Indexed keywords

ALTERNATIVE SPLICING; DATA SETS; DISCRETE NETWORKS; HUMAN GENES; LARGE DATASETS; REGULATORY MECHANISM; REGULATORY PATTERNS; TRANSCRIPTOMES; TRANSCRIPTOMICS;

GENES; MAMMALS; TISSUE;

NETWORK CODING;

RNA POLYMERASE II; TRANSCRIPTOME;

CHROMATIN; EMBRYONIC STEM CELL; EXON; GENE FUNCTION; GENETIC ASSOCIATION; GENETIC TRANSCRIPTION; HIGH THROUGHPUT SEQUENCING; HUMAN; MAMMAL; NONHUMAN; PREDICTION; QUANTITATIVE ANALYSIS; REGULATORY MECHANISM; REVIEW; RNA SEQUENCE; RNA SPLICING; TRANSCRIPTION REGULATION;

ALTERNATIVE SPLICING; ANIMALS; EXONS; GENE EXPRESSION PROFILING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA SPLICING; TRANSCRIPTOME;

EID: 84865270565     PISSN: 08298211     EISSN: 12086002     Source Type: Journal    
DOI: 10.1139/o2012-019     Document Type: Review

References (44)

1. Barash Y. Blencowe B.J. Frey B.J. 2010 a. Model-based detection of alternative splicing signals. Bioinformatics, 26 (12): i325-i333. 10.1093/bioinformatics/btq200 20529924
2. Barash Y. Calarco J.A. Gao W. Pan Q. Wang X. Shai O. et al. 2010 b. Deciphering the splicing code. Nature, 465 (7294): 53-59. 10.1038/nature09000 20445623
3. Ben-Dov C. Hartmann B. Lundgren J. Valcarcel J. 2008. Genome-wide analysis of alternative pre-mRNA splicing. J. Biol. Chem. 283 (3): 1229-1233. 10.1074/jbc.R700033200 18024428
4. Blencowe B.J. 2006. Alternative splicing: new insights from global analyses. Cell, 126 (1): 37-47. 10.1016/j.cell.2006.06.023 16839875 (Pubitemid 44040990)
5. Calarco J.A. Saltzman A.L. Ip J.Y. Blencowe B.J. 2007 a. Technologies for the global discovery and analysis of alternative splicing. Adv. Exp. Med. Biol. 623: 64-84. 10.1007/978-0-387-77374-2-5 18380341
6. Calarco J.A. Xing Y. Caceres M. Calarco J.P. Xiao X. Pan Q. et al. 2007 b. Global analysis of alternative splicing differences between humans and chimpanzees. Genes Dev. 21 (22): 2963-2975. 10.1101/gad.1606907 17978102 (Pubitemid 350133443)
7. Calarco J.A. Superina S. OHanlon D. Gabut M. Raj B. Pan Q. et al. 2009. Regulation of vertebrate nervous system alternative splicing and development by an SR-related protein. Cell, 138 (5): 898-910. 10.1016/j.cell.2009.06.012 19737518
8. C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science, 282 (5396): 2012-2018. 10.1126/science.282.5396.2012 9851916 (Pubitemid 29001251)
9. Ellis J.D. Barrios-Rodiles M. Colak R. Kim T. Calarco J.A. Irimia M. et al. 2012. Tissue-specific alternative splicing remodels protein-protein interaction networks. Mol. Cell, 46 (6): 884-892. 10.1016/j.molcel.2012.05.037
10. Fagnani M. Barash Y. Ip J. Misquitta C. Pan Q. Saltzman A.L. et al. 2007. Functional coordination of alternative splicing in the mammalian central nervous system. Genome Biol. 8 (6): R108. 10.1186/gb-2007-8-6-r108 17565696 (Pubitemid 351903173)
11. Fairbrother W.G. Yeh R.F. Sharp P.A. Burge C.B. 2002. Predictive identification of exonic splicing enhancers in human genes. Science, 297 (5583): 1007-1013. 10.1126/science.1073774 12114529 (Pubitemid 34856033)
12. Gabut M. Samavarchi-Tehrani P. Wang X. Slobodeniuc V. OHanlon D. Sung H.K. et al. 2011. An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming. Cell, 147 (1): 132-146. 10.1016/j.cell.2011.08. 023 21924763
13. Gracheva E.O. Cordero-Morales J.F. González-Carcacía J.A. Ingolia N.T. Manno C. Aranguren C.I. et al. 2011. Ganglion-specific splicing of TRPV1 underlies infrared sensation in vampire bats. Nature, 476 (7358): 88-91. 10.1038/nature10245 21814281
14. Graveley B.R. 2011. Splicing up Pluripotency. Cell, 147 (1): 22-24. 10.1016/j.cell.2011.09.004 21962502
15. Hughes T.R. Mao M. Jones A.R. Burchard J. Marton M.J. Shannon K.W. et al. 2001. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol. 19 (4): 342-347. 10.1038/86730 11283592 (Pubitemid 32275343)
16. Ip J.Y. Tong A. Pan Q. Topp J.D. Blencowe B.J. Lynch K.W. 2007. Global analysis of alternative splicing during T-cell activation. RNA, 13 (4): 563-572. 10.1261/rna.457207 17307815 (Pubitemid 46506939)
17. Irimia M. Blencowe B.J. 2012. Alternative splicing: decoding an expansive regulatory layer. Curr. Opin. Cell Biol.,. In press. 10.1016/j.ceb.2012.03.005 22465326
18. Johnson J.M. Castle J. Garrett-Engele P. Kan Z. Loerch P.M. Armour C.D. et al. 2003. Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science, 302 (5653): 2141-2144. 10.1126/science.1090100 14684825 (Pubitemid 38017950)
19. Keene J.D. Tenenbaum S.A. 2002. Eukaryotic mRNPs may represent posttranscriptional operons. Mol. Cell, 9 (6): 1161-1167. 10.1016/S1097-2765(02) 00559-2 12086614 (Pubitemid 34722296)
20. Kornblihtt A.R. de la Mata M. Fededa J.P. Munoz M.J. Nogues G. 2004. Multiple links between transcription and splicing. RNA, 10 (10): 1489-1498. 10.1261/rna.7100104 15383674 (Pubitemid 39288183)
21. Lander E.S. Linton L.M. Birren B. Nusbaum C. Zody M.C. Baldwin J. et al. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature, 409 (6822): 860-921. 10.1038/35057062 11237011 (Pubitemid 32165345)
22. Le K. Mitsouras K. Roy M. Wang Q. Xu Q. Nelson S.F. Lee C. 2004. Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data. Nucleic Acids Res. 32 (22): e180. 10.1093/nar/gnh173 15598820
23. Luco R.F. Pan Q. Tominaga K. Blencowe B.J. Pereira-Smith O.M. Misteli T. 2010. Regulation of alternative splicing by histone modifications. Science, 327 (5968): 996-1000. 10.1126/science.1184208 20133523
24. McIlwain D.R. Pan Q. Reilly P.T. Elia A.J. McCracken S. Wakeham A.C. et al. 2010. Smg1 is required for embryogenesis and regulates diverse genes via alternative splicing coupled to nonsense-mediated mRNA decay. Proc. Natl. Acad. Sci. U.S.A. 107 (27): 12186-12191. 10.1073/pnas.1007336107 20566848
25. Modrek B. Lee C.J. 2002. A genomic view of alternative splicing. Nat. Genet. 30 (1): 13-19. 10.1038/ng0102-13 11753382
26. Modrek B. Resch A. Grasso C. Lee C. 2001. Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res. 29 (13): 2850-2859. 10.1093/nar/29.13.2850 11433032 (Pubitemid 32685050)
27. Moore M.J. Silver P.A. 2008. Global analysis of mRNA splicing. RNA, 14 (2): 197-203. 10.1261/rna.868008 18083834 (Pubitemid 351171579)
28. Pan Q. Shai O. Misquitta C. Zhang W. Saltzman A.L. Mohammad N. et al. 2004. Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol. Cell, 16 (6): 929-941. 10.1016/j.molcel.2004.12.004 15610736 (Pubitemid 40018403)
29. Pan Q. Bakowski M.A. Morris Q. Zhang W. Frey B.J. Hughes T.R. Blencowe B.J. 2005. Alternative splicing of conserved exons is frequently species-specific in human and mouse. Trends Genet. 21 (2): 73-77. 10.1016/j.tig.2004.12.004 15661351 (Pubitemid 40127349)
30. Pan Q. Shai O. Lee L.J. Frey B.J. Blencowe B.J. 2008. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 40 (12): 1413-1415. 10.1038/ng.259 18978789
31. Raj B. OHanlon D. Vessey J.P. Pan Q. Ray D. Buckley N.J. et al. 2011. Cross-regulation between an alternative splicing activator and a transcription repressor controls neurogenesis. Mol. Cell, 43 (5): 843-850. 10.1016/j.molcel.2011.08.014 21884984
32. Saltzman A.L. Pan Q. Blencowe B.J. 2011. Regulation of alternative splicing by the core spliceosomal machinery. Genes Dev. 25 (4): 373-384. 10.1101/gad.2004811 21325135
33. Salz H.K. 2011. Sex determination in insects: a binary decision based on alternative splicing. Curr. Opin. Genet. Dev. 21 (4): 395-400. 10.1016/j.gde.2011.03.001 21474300
34. Shai O. Morris Q.D. Blencowe B.J. Frey B.J. 2006. Inferring global levels of alternative splicing isoforms using a generative model of microarray data. Bioinformatics, 22 (5): 606-613. 10.1093/bioinformatics/btk028 16403798 (Pubitemid 43372822)
35. Sorek R. Shamir R. Ast G. 2004. How prevalent is functional alternative splicing in the human genome? Trends Genet. 20 (2): 68-71. 10.1016/j.tig.2003. 12.004 14746986 (Pubitemid 38121356)
36. Terai Y. Morikawa N. Kawakami K. Okada N. 2003. The complexity of alternative splicing of hagoromo mRNAs is increased in an explosively speciated lineage in East African cichlids. Proc. Natl. Acad. Sci. U.S.A. 100 (22): 12798-12803. 10.1073/pnas.2132833100 14569027 (Pubitemid 37339979)
37. Thanaraj T.A. Clark F. Muilu J. 2003. Conservation of human alternative splice events in mouse. Nucleic Acids Res. 31 (10): 2544-2552. 10.1093/nar/gkg355 12736303 (Pubitemid 37441738)
38. Ule J. Ule A. Spencer J. Williams A. Hu J.S. Cline M. et al. 2005. Nova regulates brain-specific splicing to shape the synapse. Nat. Genet. 37 (8): 844-852. 10.1038/ng1610 16041372 (Pubitemid 41077110)
39. Ule J. Stefani G. Mele A. Ruggiu M. Wang X. Taneri B. et al. 2006. An RNA map predicting Nova-dependent splicing regulation. Nature, 444 (7119): 580-586. 10.1038/nature05304 17065982 (Pubitemid 44864431)
40. Venter J.C. Adams M.D. Myers E.W. Li P.W. Mural R.J. Sutton G.G. et al. 2001. The Sequence of the Human Genome. Science, 291 (5507): 1304-1351. 10.1126/science.1058040 11181995 (Pubitemid 32173090)
41. Voineagu I. Wang X. Johnston P. Lowe J.K. Tian Y. Horvath S. et al. 2011. Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature, 474 (7351): 380-384. 10.1038/nature10110 21614001
42. Wang E.T. Sandberg R. Luo S. Khrebtukova I. Zhang L. Mayr C. et al. 2008. Alternative isoform regulation in human tissue transcriptomes. Nature, 456 (7221): 470-476. 10.1038/nature07509 18978772 (Pubitemid 352759009)
43. Zender L. Xue W. Zuber J. Semighini C.P. Krasnitz A. Ma B. et al. 2008. An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer. Cell, 135 (5): 852-864. 10.1016/j.cell.2008.09.061 19012953
44. Zhang X.H. Chasin L.A. 2004. Computational definition of sequence motifs governing constitutive exon splicing. Genes Dev. 18 (11): 1241-1250. 10.1101/gad.1195304 15145827 (Pubitemid 38720592)