Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Peng, Tao ^a   Xue, Chenghai ^a   Bi, Jianning ^a   Li, Tingting ^a   Wang, Xiaowo ^a   Zhang, Xuegong ^a   Li, Yanda ^a  

^a TSINGHUA UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE RNA SPLICING; ARTICLE; CONTROLLED STUDY; CORRELATION COEFFICIENT; EXON; EXPRESSED SEQUENCE TAG; GENE CASSETTE; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE INTERACTION; GENETIC CORRELATION; GENOME ANALYSIS; HUMAN; HUMAN VERSUS ANIMAL COMPARISON; MOLECULAR EVOLUTION; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; ANIMAL; GENETIC SELECTION; GENETICS; GENOME; GENOMICS; INTRON;

DNA; MESSENGER RNA;

ALTERNATIVE SPLICING; ANIMALS; BASE SEQUENCE; CONSERVED SEQUENCE; DNA; EVOLUTION, MOLECULAR; EXONS; GENOME, HUMAN; GENOMICS; HUMANS; INTRONS; MICE; READING FRAMES; RNA, MESSENGER; SELECTION (GENETICS);

EID: 45749099262     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-191     Document Type: Article

References (54)

1. Graveley BR Alternative splicing: Increasing diversity in the proteomic world Trends Genet 2001, 17(2):100-107. 10.1016/S0168-9525(00)02176-4 11173120
2. Blencowe BJ Alternative splicing: New insights from global analyses Cell 2006, 126(1):37-47. 10.1016/j.cell.2006.06.023 16839875
3. Kriventseva EV Koch I Apweiler R Vingron M Bork P Gelfand MS Sunyaev S Increase of functional diversity by alternative splicing Trends Genet 2003, 19(3):124-128. 10.1016/S0168-9525(03)00023-4 12615003
4. Kan Z Rouchka EC Gish WR States DJ Gene structure prediction and alternative splicing analysis using genomically aligned ESTs Genome Res 2001, 11(5):889-900. 311065 11337482 10.1101/gr.155001
5. Kim E Magen A Ast G Different levels of alternative splicing among eukaryotes Nucleic Acids Res 2007, 35(1):125-131. 1802581 17158149 10.1093/nar/gkl924
6. Modrek B Lee C A genomic view of alternative splicing Nat Genet 2002, 30(1):13-19. 10.1038/ng0102-13 11753382
7. Modrek B Resch A Grasso C Lee C Genome-wide detection of alternative splicing in expressed sequences of human genes Nucleic Acids Res 2001, 29(13):2850-2859. 55780 11433032 10.1093/nar/29.13.2850
8. Buratti E Baralle M Baralle FE Defective splicing, disease and therapy: searching for master checkpoints in exon definition Nucleic Acids Res 2006, 34(12):3494-3510. 1524908 16855287 10.1093/nar/gkl498
9. Caceres JF Kornblihtt AR Alternative splicing: Multiple control mechanisms and involvement in human disease Trends Genet 2002, 18(4):186-193. 10.1016/S0168-9525(01)02626-9 11932019
10. Cartegni L Chew SL Krainer AR Listening to silence and understanding nonsense: Exonic mutations that affect splicing Nat Rev Genet 2002, 3(4):285-298. 10.1038/nrg775 11967553
11. Pagani F Baralle FE Genomic variants in exons and introns: Identifying the splicing spoilers Nat Rev Genet 2004, 5(5):389-396. 10.1038/nrg1327 15168696
12. Goren A Ram O Amit M Keren H Lev-Maor G Vig I Pupko T Ast G Comparative analysis identifies exonic splicing regulatory sequences - The complex definition of enhancers and silencers Molecular cell 2006, 22(6):769-781. 10.1016/j.molcel.2006.05.008 16793546
13. Wang ZF Xiao XS Van Nostrand E Burge CB General and specific functions of exonic splicing silencers in splicing control Molecular cell 2006, 23(1):61-70. 1839040 16797197 10.1016/j.molcel.2006.05.018
14. Ule J Stefani G Mele A Ruggiu M Wang XN Taneri B Gaasterland T Blencowe BJ Darnell RB An RNA map predicting Nova-dependent splicing regulation Nature 2006, 444(7119):580-586. 10.1038/nature05304 17065982
15. Modrek B Lee CJ Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss Nat Genet 2003, 34(2):177-180. 10.1038/ng1159 12730695
16. Ast G How did alternative splicing evolve? Nat Rev Genet 2004, 5(10):773-782. 10.1038/nrg1451 15510168
17. Yeo GW Van Nostrand E Holste D Poggio T Burge CB Identification and analysis of alternative splicing events conserved in human and mouse P Natl Acad Sci USA 2005, 102(8):2850-2855. 10.1073/pnas.0409742102 15708978 548664
18. Wang BB Brendel V Genomewide comparative analysis of alternative splicing in plants Proc Natl Acad Sci USA 2006, 103(18):7175-7180. 1459036 16632598 10.1073/pnas.0602039103
19. Sugnet CW Kent WJ Ares M Jr Haussler D Transcriptome and genome conservation of alternative splicing events in humans and mice Pacific Symposium on Biocomputing 2004:66-77. 14992493
20. Koren E Lev-Maor G Ast G The emergence of alternative 3′ and 5′ splice site exons from constitutive exons PLoS computational biology 2007, 3(5):e95. 1876488 17530917 10.1371/journal.pcbi.0030095
21. Fededa JP Petrillo E Gelfand MS Neverov AD Kadener S Nogues G Pelisch F Baralle FE Muro AF Kornblihtt AR A polar mechanism coordinates different regions of alternative splicing within a single gene Molecular cell 2005, 19(3):393-404. 10.1016/j.molcel.2005.06.035 16061185
22. Xing Y Resch A Lee C The multiassembly problem: Reconstructing multiple transcript isoforms from EST fragment mixtures Genome Res 2004, 14(3):426-441. 353230 14962984 10.1101/gr.1304504
23. Emerick MC Parmigiani G Agnew WS Multivariate Analysis and Visualization of Splicing Correlations in Single-Gene Transcriptomes BMC Bioinformatics 2007, 8(1):16. 1785386 17233916 10.1186/1471-2105-8-16
24. Fagnani M Barash Y Ip J Misquitta C Pan Q Saltzman AL Shai O Lee L Rozenhek A Mohammad N Functional coordination of alternative splicing in the mammalian central nervous system Genome Biol 2007, 8(6):R108. 10.1186/gb-2007-8-6-r108 17565696 2394768
25. Stamm S Riethoven JJ Le Texier V Gopalakrishnan C Kumanduri V Tang YS Barbosa-Morais NL Thanaraj TA ASD: A bioinformatics resource on alternative splicing Nucleic Acids Res 2006, 34:D46-D55. 1347394 16381912 10.1093/nar/gkj031
26. Kim N Alekseyenko AV Roy M Lee C The ASAP II database: Analysis and comparative genomics of alternative splicing in 15 animal species Nucleic Acids Res 2007, 35(Database):D93-98. 1669709 17108355 10.1093/ nar/gkl884
27. Carmel I Tal S Vig I Ast G Comparative analysis detects dependencies among the 5′ splice-site positions Rna-a Publication of the Rna Society 2004, 10(5):828-840.
28. Sorek R Shemesh R Cohen Y Basechess O Ast G Shamir R A non-EST-based method for exon-skipping prediction Genome Res 2004, 14(8):1617-1623. 509271 15289480 10.1101/gr.2572604
29. Xia H Bi J Li Y Identification of alternative 5′/3′ splice sites based on the mechanism of splice site competition Nucleic Acids Res 2006, 34(21):6305-6313. 1669764 17098928 10.1093/nar/gkl900
30. Smith CWJ Alternative splicing - When two's a crowd Cell 2005, 123(1):1-3. 10.1016/j.cell.2005.09.010 16213205
31. Fox-Walsh KL Dou Y Lam BJ Hung SP Baldi PF Hertel KJ The architecture of pre-mRNAs affects mechanisms of splice-site pairing Proc Natl Acad Sci USA 2005, 102(45):16176-16181. 1283478 16260721 10.1073/pnas.0508489102
32. Sorek R Shamir R Ast G How prevalent is functional alternative splicing in the human genome? Trends Genet 2004, 20(2):68-71. 10.1016/ j.tig.2003.12.004 14746986
33. Hsu F Kent WJ Clawson H Kuhn RM Diekhans M Haussler D The UCSC Known Genes Bioinformatics 2006, 22(9):1036-1046. 10.1093/bioinformatics/ btl048 16500937
34. Zhang XHF Chasin LA Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons P Natl Acad Sci USA 2006, 103(36):13427-13432. 10.1073/pnas.0603042103
35. Xing Y Lee CJ Protein modularity of alternatively spliced exons is associated with tissue-specific regulation of alternative splicing PLoS genetics 2005, 1(3):e34. 1201369 16170410 10.1371/journal.pgen.0010034
36. Philipps DL Park JW Graveley BR A computational and experimental approach toward a priori identification of alternatively spliced exons Rna-a Publication of the Rna Society 2004, 10(12):1838-1844.
37. Pritsker M Doniger TT Kramer LC Westcot SE Lemischka IR Diversification of stem cell molecular repertoire by alternative splicing Proc Natl Acad Sci USA 2005, 102(40):14290-14295. 1242282 16183747 10.1073/ pnas.0502132102
38. Xing Y Lee C Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences P Natl Acad Sci USA 2005, 102(38):13526-13531. 10.1073/pnas.0501213102
39. Plass M Eyras E Differentiated evolutionary rates in alternative exons and the implications for splicing regulation BMC Evol Biol 2006, 6:50. 1543662 16792801 10.1186/1471-2148-6-50
40. Kondrashov FA Koonin EV Origin of alternative splicing by tandem exon duplication Hum Mol Genet 2001, 10(23):2661-2669. 10.1093/hmg/10.23.2661 11726553
41. Letunic I Copley RR Bork P Common exon duplication in animals and its role in alternative splicing Hum Mol Genet 2002, 11(13):1561-1567. 10.1093/hmg/11.13.1561 12045209
42. Sorek R Ast G Graur D Alu-containing exons are alternatively spliced Genome Res 2002, 12(7):1060-1067. 186627 12097342 10.1101/gr.229302
43. Lev-Maor G Sorek R Shomron N Ast G The birth of an alternatively spliced exon: 3 ′ splice-site selection in Alu exons Science 2003, 300(5623):1288-1291. 10.1126/science.1082588 12764196
44. Alekseyenko AV Kim N Lee CJ Global analysis of exon creation versus loss and the role of alternative splicing in 17 vertebrate genomes Rna 2007, 13(5):661-670. 1852814 17369312 10.1261/rna.325107
45. Pan Q Shai O Misquitta C Zhang W Saltzman AL Mohammad N Babak T Siu H Hughes TR Morris QD Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform Molecular cell 2004, 16(6):929-941. 10.1016/j.molcel.2004.12.004 15610736
46. Consortium GO The Gene Ontology (GO) database and informatics resource Nucl Acids Res 2004, 32(suppl 1):D258-261. 10.1093/nar/gkh036
47. Castillo-Davis CI Hartl DL GeneMerge-post-genomic analysis, data mining, and hypothesis testing Bioinformatics 2003, 19(7):891-892. 10.1093/ bioinformatics/btg114 12724301
48. Neugebauer KM Please hold - the next available exon will be right with you Nat Struct Mol Biol 2006, 13(5):385-386. 10.1038/nsmb0506-385 16738604
49. Dye MJ Gromak N Proudfoot NJ Exon tethering in transcription by RNA polymerase II Molecular cell 2006, 21(6):849-859. 10.1016/ j.molcel.2006.01.032 16543153
50. Zhu J Shendure J Mitra RD Church GM Single molecule profiling of alternative pre-mRNA splicing Science 2003, 301(5634):836-838. 10.1126/ science.1085792 12907803
51. UCSC Genome Browser http://genome.ucsc.edu/
52. BioMart http://www.biomart.org
53. RepeatMasker Open-3.0 http://www.repeatmasker.org
54. Hedges SB Kumar S Vertebrate genomes compared Science 2002, 297(5585):1283-1285. 10.1126/science.1076231 12193771