Nonsense-mediated decay enables intron gain in Drosophila

PLoS Genetics

Volumn 6, Issue 1, 2010, Pages

  Farlow, Ashley ^a   Meduri, Eshwar ^a   Dolezal, Marlies ^a   Hua, Liushuai ^a   Schlötterer, Christian ^a  

^a UNIVERSITY OF VETERINARY MEDICINE   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CODON; DROSOPHILA; EVOLUTION; GENE INSERTION; INTRON; NONHUMAN; SPLICEOSOME; AMINO ACID SEQUENCE; ANIMAL; CHEMISTRY; GENETICS; METABOLISM; MOLECULAR GENETICS; RNA SPLICING; SEQUENCE ALIGNMENT; STOP CODON;

EUKARYOTA;

DROSOPHILA PROTEIN;

AMINO ACID SEQUENCE; ANIMALS; CODON, NONSENSE; DROSOPHILA; DROSOPHILA PROTEINS; INTRONS; MOLECULAR SEQUENCE DATA; RNA SPLICING; SEQUENCE ALIGNMENT; SPLICEOSOMES;

EID: 76749130220     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1000819     Document Type: Article

References (45)

1. Tarrio R, Ayala FJ, Rodriguez-Trelles F (2008) Alternative splicing: a missing piece in the puzzle of intron gain. Proc Natl Acad Sci U S A 105: 7223-7228.
2. Coulombe-Huntington J, Majewski J (2007) Intron Loss and Gain in Drosophila. Molecular Biology and Evolution 24: 2842-2850.
3. Irimia M, Rukov JL, Penny D, Vinther J, Garcia-Fernandez J, et al. (2008) Origin of introns by 'intronization' of exonic sequences. Trends Genet 24: 378-381.
4. Ragg H, Kumar A, Koster K, Bentele C, Wang Y, et al. (2009) Multiple gains of spliceosomal introns in a superfamily of vertebrate protease inhibitor genes. BMC Evol Biol 9: 208.
5. Cavalier-Smith T (1991) Intron phylogeny: a new hypothesis. Trends Genet 7: 145-148.
6. Toor N, Keating K, Taylor S, Pyle A (2008) Crystal Structure of a Self-Spliced Group II Intron. Science. pp 77-82.
7. Catania F, Lynch M (2008) Where do introns come from? PLoS Biol 6: e283. doi:10.1371/journal.pbio.0060283.
8. Zhang C, Li WH, Krainer AR, Zhang MQ (2008) RNA landscape of evolution for optimal exon and intron discrimination. Proc Natl Acad Sci U S A 105: 5797-5802.
9. Wahl MC, Will CL, Luhrmann R (2009) The spliceosome: design principles of a dynamic RNP machine. Cell 136: 701-718.
10. Cavalier-Smith T (1985) Selfish DNA and the origin of introns. Nature 315: 283-284.
11. Roy SW, Irimia M (2009) Mystery of intron gain: new data and new models. Trends Genet 25: 67-73.
12. Pavesi G, Zambelli F, Caggese C, Pesole G (2008) Exalign: a new method for comparative analysis of exon-intron gene structures. Nucleic Acids Res 36: e47.
13. Gao X, Lynch M (2009) Ubiquitous internal gene duplication and intron creation in eukaryotes. Proc Natl Acad Sci U S A.
14. Li, Tucker, Sung, Thomas k, Lynch (2009) Extensive, Recent Intron Gains in Daphnia Population. Science 326: 1260-1262.
15. Catania F, Gao X, Scofield DG (2009) Endogenous mechanisms for the origins of spliceosomal introns. J Hered 100: 591-596.
16. Sayani S, Janis M, Lee CY, Toesca I, Chanfreau GF (2008) Widespread impact of nonsense-mediated mRNA decay on the yeast intronome. Mol Cell 31: 360-370.
17. Hansen KD, Lareau LF, Blanchette M, Green RE, Meng Q, et al. (2009) Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila. PLoS Genet 5: e1000525. doi:10.1371/journal.pgen.1000525.
18. Nielsen C, Friedman B, Birren B, Burge C, Galagan J (2004) Patterns of Intron Gain and Loss in Fungi. Plos Biol 2: e422. doi:10.1371/journal.pbio. 0020422.
19. Rogozin IB, Wolf YI, Sorokin AV, Mirkin BG, Koonin EV (2003) Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr Biol 13: 1512-1517.
20. Palmer JD, Logsdon JM, Jr. (1991) The recent origins of introns. Curr Opin Genet Dev 1: 470-477.
21. Crick F (1979) Split genes and RNA splicing. Science 204: 264-271.
22. Rogers JH (1989) How were introns inserted into nuclear genes? Trends Genet 5: 213-216.
23. Venkatesh B, Ning Y, Brenner S (1999) Late changes in spliceosomal introns define clades in vertebrate evolution. Proc Natl Acad Sci U S A 96: 10267-10271.
24. Knowles DG, McLysaght A (2006) High rate of recent intron gain and loss in simultaneously duplicated Arabidopsis genes. Mol Biol Evol 23: 1548-1557.
25. Sharpton T, Neafsey D, Galagan J, Taylor J (2008) Mechanisms of intron gain and loss in Cryptococcus. Genome Biol 9: R24.
26. Fedorov A, Roy S, Fedorova L, Gilbert W (2003) Mystery of intron gain. Genome Res 13: 2236-2241.
27. Hazkani-Covo E, Covo S (2008) Numt-mediated double-strand break repair mitigates deletions during primate genome evolution. PLoS Genet 4: e1000237. doi:10.1371/journal.pgen.1000237.
28. Tanay A, Siggia ED (2008) Sequence context affects the rate of short insertions and deletions in flies and primates. Genome Biol 9: R37.
29. Roca X, Sachidanandam R, Krainer AR (2005) Determinants of the inherent strength of human 5′ splice sites. Rna 11: 683-698.
30. Freund M, Hicks MJ, Konermann C, Otte M, Hertel KJ, et al. (2005) Extended base pair complementarity between U1 snRNA and the 5′ splice site does not inhibit splicing in higher eukaryotes, but rather increases 5′ splice site recognition. Nucleic Acids Res 33: 5112-5119.
31. Ding W, Lin L, Ren F, Zou H, Duan Z, et al. (2009) Effects of splice sites on the intron retention in histamine H3 receptors from rats and mice. J Genet Genomics 36: 475-482.
32. Jaillon O, Bouhouche K, Gout J, Aury J, Noel B, et al. (2008) Translational control of intron splicing in eukaryotes. Nature 451: 359-362.
33. Brogna S, Wen J (2009) Nonsense-mediated mRNA decay (NMD) mechanisms. Nat Struct Mol Biol 16: 107-113.
34. Stalder L, Muhlemann O (2008) The meaning of nonsense. Trends Cell Biol 18: 315-321.
35. Jeffares D, Mourier T, Penny D (2006) The biology of intron gain and loss. Trends in Genetics 22: 16-22.
36. Lin H, Zhu W, Silva J, Gu X, Buell C (2006) Intron gain and loss in segmentally duplicated genes in rice. Genome Biol 7: R41.
37. Chen JQ, Wu Y, Yang H, Bergelson J, Kreitman M, et al. (2009) Variation in the ratio of nucleotide substitution and indel rates across genomes in mammals and bacteria. Mol Biol Evol 26: 1523-1531.
38. Hahn M, Han M, Han S (2007) Gene Family Evolution across 12 Drosophila Genomes. PLoS Genet 3: e197. doi:10.1371/journal.pgen.0030197.
39. Birney E, Clamp M, Durbin R (2004) GeneWise and Genomewise. Genome Res 14: 988-995.
40. Csuros M, Holey J, Rogozin I (2007) In search of lost introns. Bioinformatics 23: i87-i96.
41. Roy SW, Gilbert W (2005) Rates of intron loss and gain: implications for early eukaryotic evolution. Proc Natl Acad Sci U S A 102: 5773-5778.
42. Stajich JE, Dietrich FS, Roy SW (2007) Comparative genomic analysis of fungal genomes reveals intron-rich ancestors. Genome Biol 8: R223.
43. Stephens RM, Schneider TD (1992) Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites. J Mol Biol 228: 1124-1136.
44. Irimia M, Roy SW (2008) Evolutionary convergence on highly-conserved 3′ intron structures in intron-poor eukaryotes and insights into the ancestral eukaryotic genome. PLoS Genet 4: e1000148. doi:10.1371/journal.pgen. 1000148.
45. Hiller M, Platzer M (2008) Widespread and subtle: alternative splicing at short-distance tandem sites. Trends in Genetics 24: 246-255.