Characteristics of transposable element exonization within human and mouse

PLoS ONE

Volumn 5, Issue 6, 2010, Pages

  Sela, Noa ^a,c   Mersch, Britta ^b   Hotz Wagenblatt, Agnes ^b   Ast, Gil ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^c UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ANIMAL GENETICS; ARTICLE; CONTROLLED STUDY; EXON; GENE SEQUENCE; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN; HUMAN GENETICS; INTRON; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM; STOP CODON; TRANSPOSON; ANIMAL; MOUSE; RNA EDITING;

MAMMALIA; PRIMATES;

ANIMALS; DNA TRANSPOSABLE ELEMENTS; EXONS; HUMANS; INTRONS; MICE; POLYMORPHISM, SINGLE NUCLEOTIDE; RNA EDITING;

EID: 77956222970     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0010907     Document Type: Article

References (73)

1. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
2. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
3. Sela N, Mersch B, Gal-Mark N, Lev-Maor G, Hotz-Wagenblatt A, et al. (2007) Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome. Genome Biol 8: R127.
4. Sironi M, Menozzi G, Comi GP, Bresolin N, Cagliani R, et al. (2005) Fixation of conserved sequences shapes human intron size and influences transposoninsertion dynamics. Trends Genet 21: 484-488.
5. Sironi M, Menozzi G, Comi GP, Cereda M, Cagliani R, et al. (2006) Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns. Genome Biol 7: R120.
6. Kister KP, Eckert WA (1987) Characterization of an authentic intermediate in the self-splicing process of ribosomal precursor RNA in macronuclei of Tetrahymena thermophila. Nucleic Acids Res 15: 1905-1920.
7. Sorek R (2007) The birth of new exons: mechanisms and evolutionary consequences. Rna 13: 1603-1608.
8. Batzer MA, Deininger PL (2002) Alu repeats and human genomic diversity. Nat Rev Genet 3: 370-379.
9. Kriegs JO, Churakov G, Jurka J, Brosius J, Schmitz J (2007) Evolutionary history of 7SL RNA-derived SINEs in Supraprimates. Trends Genet 23: 158-161.
10. Cordaux R, Hedges DJ, Herke SW, Batzer MA (2006) Estimating the retrotransposition rate of human Alu elements. Gene 373: 134-137.
11. Deininger P, Batzer MA (1993) Evolution of retroposons. Evol Biol 27: 157-196.
12. Deininger PL, Batzer MA (1999) Alu repeats and human disease. Mol Genet Metab 67: 183-193.
13. Ng SK, Xue H (2006) Alu-associated enhancement of single nucleotide polymorphisms in the human genome. Gene 368: 110-116.
14. Makalowski W, Mitchell GA, Labuda D (1994) Alu sequences in the coding regions of mRNA: a source of protein variability. Trends Genet 10: 188-193.
15. Nekrutenko A, Li WH (2001) Transposable elements are found in a large number of human protein-coding genes. Trends Genet 17: 619-621.
16. Sorek R, Ast G, Graur D (2002) Alu-containing exons are alternatively spliced. Genome Res 12: 1060-1067.
17. Gal-Mark N, Schwartz S, Ram O, Eyras E, Ast G (2009) The pivotal roles of TIA proteins in 59 splice-site selection of alu exons and across evolution. PLoS Genet 5: e1000717.
18. Gal-Mark N, Schwartz S, Ast G (2008) Alternative splicing of Alu exons-two arms are better than one. Nucleic Acids Res 36: 2012-2023.
19. Lev-Maor G, Sorek R, Shomron N, Ast G (2003) The birth of an alternatively spliced exon: 39 splice-site selection in Alu exons. Science 300: 1288-1291.
20. Sorek R, Lev-Maor G, Reznik M, Dagan T, Belinky F, et al. (2004) Minimal conditions for exonization of intronic sequences: 59 splice site formation in alu exons. Mol Cell 14: 221-231.
21. Corvelo A, Eyras E (2008) Exon creation and establishment in human genes. Genome Biol 9: R141.
22. Ram O, Schwartz S, Ast G (2008) Multifactorial interplay controls the splicing profile of Alu-derived exons. Mol Cell Biol 28: 3513-3525.
23. Schwartz S, Gal-Mark N, Kfir N, Oren R, Kim E, et al. (2009) Alu exonization events reveal features required for precise recognition of exons by the splicing machinery. PLoS Comput Biol 5: e1000300.
24. Krull M, Petrusma M, Makalowski W, Brosius J, Schmitz J (2007) Functional persistence of exonized mammalian-wide interspersed repeat elements (MIRs). Genome Res 17: 1139-1145.
25. Lin L, Jiang P, Shen S, Sato S, Davidson BL, et al. (2009) Large-scale analysis of exonized mammalian-wide interspersed repeats (MIRs) in primate genomes. Hum Mol Genet.
26. Lin L, Shen S, Tye A, Cai JJ, Jiang P, et al. (2008) Diverse splicing patterns of exonized alu elements in human tissues. PLoS Genet 4: e1000225.
27. Mersch B, Sela N, Ast G, Suhai S, Hotz-Wagenblatt A (2007) SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements. BMC Genet 8: 78.
28. Goren A, Kim E, Amit M, Bochner R, Lev-Maor G, et al. (2008) Alternative approach to a heavy weight problem. Genome Res 18: 214-220.
29. Kwan T, Benovoy D, Dias C, Gurd S, Provencher C, et al. (2008) Genomewide analysis of transcript isoform variation in humans. Nat Genet 40: 225-231.
30. Graveley BR (2007) The haplo-spliceo-transcriptome: common variations in alternative splicing in the human population. Trends Genet.
31. Hull J, Campino S, Rowlands K, Chan MS, Copley RR, et al. (2007) Identification of common genetic variation that modulates alternative splicing. PLoS Genet 3: e99.
32. Kwan T, Benovoy D, Dias C, Gurd S, Serre D, et al. (2007) Heritability of alternative splicing in the human genome. Genome Res 17: 1210-1218.
33. Zhang XH, Chasin LA (2006) Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons. Proc Natl Acad Sci U S A 103: 13427-13432.
34. Amit M, Sela N, Keren H, Melamed Z, Muler I, et al. (2007) Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene. BMC Mol Biol 8: 109.
35. Ast G (2004) How did alternative splicing evolve? Nat Rev Genet 5: 773-782.
36. Hillman RT, Green RE, Brenner SE (2004) An unappreciated role for RNA surveillance. Genome Biol 5: R8.
37. Magen A, Ast G (2005) The importance of being divisible by three in alternative splicing. Nucleic Acids Res 33: 5574-5582.
38. Resch A, Xing Y, Alekseyenko A, Modrek B, Lee C (2004) Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation. Nucleic Acids Res 32: 1261-1269.
39. Levy A, Sela N, Ast G (2008) TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates. Nucleic Acids Res 36: D47-52.
40. Roy M, Kim N, Xing Y, Lee C (2008) The effect of intron length on exon creation ratios during the evolution of mammalian genomes. Rna 14: 2261-2273.
41. Singer SS, Mannel DN, Hehlgans T, Brosius J, Schmitz J (2004) From ''junk'' to gene: curriculum vitae of a primate receptor isoform gene. J Mol Biol 341: 883-886.
42. Chang YF, Imam JS, Wilkinson MF (2007) The nonsense-mediated decay RNA surveillance pathway. Annu Rev Biochem 76: 51-74.
43. Lo WS, Lau CF, Xuan Z, Chan CF, Feng GY, et al. (2004) Association of SNPs and haplotypes in GABAA receptor beta2 gene with schizophrenia. Mol Psychiatry 9: 603-608.
44. Labuda D, Striker G (1989) Sequence conservation in Alu evolution. Nucleic Acids Res 17: 2477-2491.
45. Yang JO, Kim W-Y, Bhak J (2009) ssSNPTarget: genome-wide splice-site single nucleotide polymorphism database. Human Mutation 30: E1010-E1020.
46. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, et al. (2002) The human genome browser at UCSC. Genome Res 12: 996-1006.
47. Lev-Maor G, Sorek R, Levanon EY, Paz N, Eisenberg E, et al. (2007) RNAediting- mediated exon evolution. Genome Biol 8: R29.
48. Moller-Krull M, Zemann A, Roos C, Brosius J, Schmitz J (2008) Beyond DNA: RNA editing and steps toward Alu exonization in primates. J Mol Biol 382: 601-609.
49. Athanasiadis A, Rich A, Maas S (2004) Widespread A-to-I RNA editing of Alucontaining mRNAs in the human transcriptome. PLoS Biol 2: e391.
50. Blow M, Futreal PA, Wooster R, Stratton MR (2004) A survey of RNA editing in human brain. Genome Res 14: 2379-2387.
51. Kim DD, Kim TT, Walsh T, Kobayashi Y, Matise TC, et al. (2004) Widespread RNA editing of embedded alu elements in the human transcriptome. Genome Res 14: 1719-1725.
52. Levanon EY, Eisenberg E, Yelin R, Nemzer S, Hallegger M, et al. (2004) Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat Biotechnol 22: 1001-1005.
53. He S, Liu C, Skogerbo G, Zhao H, Wang J, et al. (2008) NONCODE v2.0: decoding the non-coding. Nucleic Acids Res 36: D170-172.
54. Liu C, Bai B, Skogerbo G, Cai L, Deng W, et al. (2005) NONCODE: an integrated knowledge database of non-coding RNAs. Nucleic Acids Res 33: D112-115.
55. Nakabayashi K, Bentley L, Hitchins MP, Mitsuya K, Meguro M, et al. (2002) Identification and characterization of an imprinted antisense RNA (MESTIT1) in the human MEST locus on chromosome 7q32. Hum Mol Genet 11: 1743-1756.
56. Nemes JP, Benzow KA, Moseley ML, Ranum LP, Koob MD (2000) The SCA8 transcript is an antisense RNA to a brain-specific transcript encoding a novel actin-binding protein (KLHL1). Hum Mol Genet 9: 1543-1551.
57. Chen WL, Lin JW, Huang HJ, Wang SM, Su MT, et al. (2008) SCA8 mRNA expression suggests an antisense regulation of KLHL1 and correlates to SCA8 pathology. Brain Res 1233: 176-184.
58. Koob MD, Moseley ML, Schut LJ, Benzow KA, Bird TD, et al. (1999) An untranslated CTG expansion causes a novel form of spinocerebellar ataxia (SCA8). Nat Genet 21: 379-384.
59. Xing Y, Lee C (2006) Alternative splicing and RNA selection pressure- evolutionary consequences for eukaryotic genomes. Nat Rev Genet 7: 499-509.
60. Gerber A, O'Connell MA, Keller W (1997) Two forms of human doublestranded RNA-specific editase 1 (hRED1) generated by the insertion of an Alu cassette. Rna 3: 453-463.
61. Gehring NH, Lamprinaki S, Hentze MW, Kulozik AE (2009) The hierarchy of exon-junction complex assembly by the spliceosome explains key features of mammalian nonsense-mediated mRNA decay. PLoS Biol 7: e1000120.
62. Kim E, Magen A, Ast G (2007) Different levels of alternative splicing among eukaryotes. Nucleic Acids Res 35: 125-131.
63. Xie H, Wang M, Bonaldo MD, Smith C, Rajaram V, et al. (2009) Highthroughput sequence-based epigenomic analysis of Alu repeats in human cerebellum. Nucleic Acids Res.
64. Mills RE, Bennett EA, Iskow RC, Devine SE (2007) Which transposable elements are active in the human genome? Trends Genet 23: 183-191.
65. Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, et al. (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science 316: 222-234.
66. Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ, et al. (2007) The UCSC genome browser database: update 2007. Nucleic Acids Res 35: D668-673.
67. Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, et al. (2004) The UCSC Table Browser data retrieval tool. Nucleic Acids Res 32: D493-496.
68. Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, et al. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res 15: 1451-1455.
69. Jurka J (2000) Repbase update: a database and an electronic journal of repetitive elements. Trends Genet 16: 418-420.
70. Smit AFA, Hubley R, Green P. Version: open-3.2.7.
71. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, et al. (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110: 462-467.
72. Kapitonov VV, Jurka J (2008) A universal classification of eukaryotic transposable elements implemented in Repbase. Nat Rev Genet 9: 411-412; author reply 414.
73. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, et al. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29: 308-311.