Alternative splicing increases complexity of stem cell transcriptome

Cell Cycle

Volumn 5, Issue 4, 2006, Pages 347-351

  Lemischka, Ihor R ^a   Pritsker, Moshe ^a  

^a PRINCETON UNIVERSITY   (United States)

Author keywords

Alternative splicing; Embryonic; Evolution; Exon; Hematopoietic; Intron; Stem cells

Indexed keywords

CD34 ANTIGEN; CD38 ANTIGEN; COMPLEMENTARY DNA; DNA; ISOPROTEIN; MESSENGER RNA; RNA; TRANSCRIPTOME;

ALTERNATIVE RNA SPLICING; CELL POPULATION; DNA FLANKING REGION; EMBRYONIC STEM CELL; EXON; EXPRESSED SEQUENCE TAG; GENE EXPRESSION; GENE FREQUENCY; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENOME ANALYSIS; HEMATOPOIETIC STEM CELL; HOUSEKEEPING GENE; HUMAN; INTERSPERSED REPEAT; INTRON; NONHUMAN; PROTEIN VARIANT; REFERENCE DATABASE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; RNA INTERFERENCE; SEQUENCE ANALYSIS; SEX DETERMINATION; STEM CELL;

EID: 33645218935     PISSN: 15384101     EISSN: 15514005     Source Type: Journal    
DOI: 10.4161/cc.5.4.2424     Document Type: Review

References (56)

1. Sharp PA. Split genes and RNA splicing. Cell 1994; 77:805-15.
2. Lopez AJ. Alternative splicing of premRNA: Developmental consequences and mechanisms of regulation. Annu Rev Genet 1998; 32:279-305.
3. Hanke J, Brett D, Zastrow I, Aydin A, Delbruck S, Lehmann G, Luft F, Reich J, Bork P. Alternative splicing of human genes: More the rule than the exception? Trends Genet 1999; 15:389-90.
4. Mironov AA, Fickett JW, Gelfand MS. Frequent alternative splicing of human genes. Genome Res 1999; 9:1288-93.
5. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 2001; 409:860-921.
6. Brett D, Hanke J, Lehmann G, Haase S, Delbruck S, Krueger S, Reich J, Bork P. EST comparison indicates 38% of human mRNAs contain possible alternative splice forms. FEBS Lett 2000; 474:83-6.
7. Croft L, Schandorff S, Clark F, Burrage K, Arctander P, Mattick JS. ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome. Nat Genet 2000; 24:340-1.
8. Kan Z, Rouchka EC, Gish WR, States DJ. Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res 2001; 11:889-900.
9. Modrek B, Resch A, Grasso C, Lee C. Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res 2001; 29:2850-9.
10. Boguski MS, Lowe TM, Tolstoshev CM. dbEST-database for "expressed sequence tags". Nat Genet 1993; 4:332-3.
11. Zavolan M, Kondo S, Schonbach C, Adachi J, Hume DA, Hayashizaki Y, Gaasterland T; RIKEN GER Group; GSL Members. Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome Res 2003; 13:1290-300.
12. Schmucker D, Clemens JC, Shu H, Worby CA, Xiao J, Muda M, Dixon JE, Zipursky SL. Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity. Cell 2000; 101:671-84.
13. Missler M, Sudhof TC. Neurexins: Three genes and 1001 products. Trends Genet 1998; 14:20-6.
14. Rowen L, Young J, Birditt B, Kaur A, Madan A, Philipps DL, Qin S, Minx P, Wilson RK, Hood L, Graveley BR. Analysis of the human neurexin genes: Alternative splicing and the generation of protein diversity. Genomics 2002; 79:587-97.
15. Kim H, Klein R, Majewski J, Ott J. Estimating rates of alternative splicing in mammals and invertebrates. Nat Genet 2004; 36:915-6, (author reply 916-7).
16. Klug CA, Morrison SJ, Masek M, Hahm K, Smale ST, Weissman IL. Hematopoietic stem cells and lymphoid progenitors express different Ikaros isoforms, and Ikaros is localized to heterochromatin in immature lymphocytes. Proc Natl Acad Sci USA 1998; 95:657-62.
17. Salesse S, Dylla SJ, Verfaillie CM. p210BCR/ABL-induced alteration of premRNA splicing in primary human CD34+ hematopoietic progenitor cells. Leukemia 2004; 18:727-33.
18. 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; 102:14290-5.
19. Sharov AA, Piao Y, Matoba R, Dudekula DB, Qian Y, VanBuren V, Falco G, Martin PR, Stagg CA, Bassey UC, Wang Y, Carter MG, Hamatani T, Aiba K, Akutsu H, Sharova L, Tanaka TS, Kimber WL, Yoshikawa T, Jaradat SA, Pantano S, Nagaraja R, Boheler KR, Taub D, Hodes RJ, Longo DL, Schlessinger D, Keller J, Klotz E, Kelsoe G, Umezawa A, Vescovi AL, Rossant J, Kunath T, Hogan BL, Curci A, D'Urso M, Kelso J, Hide W, Ko MS. Transcriptome analysis of mouse stem cells and early embryos. PLoS Biol 2003; 1:E74.
20. Phillips RL, Ernst RE, Brunk B, Ivanova N, Mahan MA, Deanehan JK, Moore KA, Overton GC, Lemischka IR. The genetic program of hematopoietic stem cells. Science 2000; 288:1635-40.
21. Xu Q, Modrek B, Lee C. Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. Nucleic Acids Res 2002; 30:3754-66.
22. Yeo G, Holste D, Kreiman G, Burge CB. Variation in alternative splicing across human tissues. Genome Biol 2004; 5:R74.
23. Kan Z, States D, Gish W. Selecting for functional alternative splices in ESTs. Genome Res 2002; 12:1837-45.
24. Black DL. Mechanisms of alternative premessenger RNA splicing. Annu Rev Biochem 2003; 72:291-336.
25. 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; 34:177-80.
26. Kornblihtt AR. Promoter usage and alternative splicing. Curr Opin Cell Biol 2005; 17:262-8.
27. Graveley BR. Alternative splicing: Increasing diversity in the proteomic world. Trends Genet 2001; 17:100-7.
28. Castillo-Davis CI, Mekhedov SL, Hartl DL, Koonin EV, Kondrashov FA. Selection for short introns in highly expressed genes. Nat Genet 2002; 31:415-8.
29. Sterner DA, Carlo T, Berget SM. Architectural limits on split genes. Proc Natl Acad Sci USA 1996; 93:15081-5.
30. Fox-Walsh KL, Dou Y, Lam BJ, Hung SP, Baldi PF, Hertel KJ. The architecture of premRNAs affects mechanisms of splice-site pairing. Proc Natl Acad Sci USA 2005; 102:16176-81.
31. Thanaraj TA, Clark F, Muilu J. Conservation of human alternative splice events in mouse. Nucleic Acids Res 2003; 31:2544-52.
32. Nurtdinov RN, Artamonova II, Mironov AA, Gelfand MS. Low conservation of alternative splicing patterns in the human and mouse genomes. Hum Mol Genet 2003; 12:1313-20.
33. Yeo GW, Van Nostrand E, Holste D, Poggio T, Burge CB. Identification and analysis of alternative splicing events conserved in human and mouse. Proc Natl Acad Sci USA 2005; 102:2850-5.
34. Kan Z, Garrett-Engele PW, Johnson JM, Castle JC. Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles. Nucleic Acids Res 2005; 33:5659-66.
35. Sorek R, Shamir R, Ast G. How prevalent is functional alternative splicing in the human genome? Trends Genet 2004; 20:68-71.
36. Graham P, Penn JK, Schedl P. Masters change, slaves remain. Bioessays 2003; 25:1-4.
37. Bell LR, Maine EM, Schedl P, Cline TW. Sex-lethal, a Drosophila sex determination switch gene, exhibits sex-specific RNA splicing and sequence similarity to RNA binding proteins. Cell 1988; 55:1037-46.
38. Meise M, Hilfiker-Kleiner D, Dubendorfer A, Brunner C, Nothiger R, Bopp D. Sex-lethal, the master sex-determining gene in Drosophila, is not sex-specifically regulated in Musca domestica. Development 1998; 125:1487-94.
39. Saccone G, Peluso I, Artiaco D, Giordano E, Bopp D, Polito LC. The Ceratitis capitata homologue of the Drosophila sex-determining gene sex-lethal is structurally conserved, but not sex-specifically regulated. Development 1998; 125:1495-500.
40. Ivanova NB, Dimos JT, Schaniel C, Hackney JA, Moore KA, Lemischka IR. A stem cell molecular signature. Science 2002; 298:601-4.
41. Ramalho-Santos M, Yoon S, Matsuzaki Y, Mulligan RC, Melton DA. "Stemness": Transcriptional profiling of embryonic and adult stem cells. Science 2002; 298:597-600.
42. Venezia TA, Merchant AA, Ramos CA, Whitehouse NL, Young AS, Shaw CA, Goodell MA. Molecular signatures of proliferation and quiescence in hematopoietic stem cells. PLoS Biol 2004; 2:e301.
43. Forsberg EC, Prohaska SS, Katzman S, Heffner GC, Stuart JM, Weissman IL. Differential expression of novel potential regulators in hematopoietic stem cells. PLoS Genet 2005; 1:e28.
44. Daheron L, Opitz SL, Zaehres H, Lensch WM, Andrews PW, Itskovitz-Eldor J, Daley GQ. LIF/STAT3 signaling fails to maintain self-renewal of human embryonic stem cells. Stem Cells 2004; 22:770-8.
45. Clark TA, Sugnet CW, Ares Jr M. Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 2002; 296:907-10.
46. Yeakley JM, Fan JB, Doucet D, Luo L, Wickham E, Ye Z, Chee MS, Fu XD. Profiling alternative splicing on fiber-optic arrays. Nat Biotechnol 2002; 20:353-8.
47. Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, Fodor SP, Gingeras TR. Large-scale transcriptional activity in chromosomes 21 and 22. Science 2002; 296:916-9.
48. Johnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM, Armour CD, Santos R, Schadt EE, Stoughton R, Shoemaker DD. Genome-wide survey of human alternative premRNA splicing with exon junction microarrays. Science 2003; 302:2141-4.
49. Pan Q, Shai O, Misquitta C, Zhang W, Saltzman AL, Mohammad N, Babak T, Siu H, Hughes TR, Morris QD, Frey BJ, Blencowe BJ. Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol Cell 2004; 16:929-41.
50. Castle J, Garrett-Engele P, Armour CD, Duenwald SJ, Loerch PM, Meyer MR, Schadt EE, Stoughton R, Parrish ML, Shoemaker DD, Johnson JM. Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing. Genome Biol 2003; 4:R66.
51. Watahiki A, Waki K, Hayatsu N, Shiraki T, Kondo S, Nakamura M, Sasaki D, Arakawa T, Kawai J, Harbers M, Hayashizaki Y, Carninci P. Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas. Nat Methods 2004; 1:233-9.
52. Huang Q, Raya A, DeJesus P, Chao SH, Quon KC, Caldwell JS, Chanda SK, Izpisua-Belmonte JC, Schultz PG. Identification of p53 regulators by genome-wide functional analysis. Proc Natl Acad Sci USA 2004; 101:3456-61.
53. Paddison PJ, Silva JM, Conklin DS, Schlabach M, Li M, Aruleba S, Balija V, O'Shaughnessy A, Gnoj L, Scobie K, Chang K, Westbrook T, Cleary M, Sachidanandam R, McCombie WR, Elledge SJ, Hannon GJ. A resource for large-scale RNA-interference-based screens in mammals. Nature 2004; 428:427-31.
54. Berns K, Hijmans EM, Mullenders J, Brummelkamp TR, Velds A, Heimerikx M, Kerkhoven RM, Madiredjo M, Nijkamp W, Weigelt B, Agami R, Ge W, Cavet G, Linsley PS, Beijersbergen RL, Bernards R. A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 2004; 428:431-7.
55. Park JW, Parisky K, Celotto AM, Reenan RA, Graveley BR. Identification of alternative splicing regulators by RNA interference in Drosophila. Proc Nad Acad Sci USA 2004; 101:15974-9.
56. Ule J, Ule A, Spencer J, Williams A, Hu JS, Cline M, Wang H, Clark T, Fraser C, Ruggiu M, Zeeberg BR, Kane D, Weinstein JN, Blume J, Darnell RB. Nova regulates brain-specific splicing to shape the synapse. Nat Genet 2005; 37:844-52.