Transposable element orientation bias in the Drosophila melanogaster genome

Journal of Molecular Evolution

Volumn 61, Issue 6, 2005, Pages 733-741

  Cutter, Asher D ^a,c   Good, Jeffrey M ^a   Pappas, Christopher T ^a   Saunders, Matthew A ^a   Starrett, Dean M ^b   Wheeler, Travis J ^b  

^a University of Arizona   (United States)

^b University of Arizona   (United States)

^c UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

Codon usage bias; Drosophila melanogaster; Polyadenylation; Transposable elements

Indexed keywords

POLYADENYLIC ACID; RNA;

ARTICLE; DNA BASE COMPOSITION; DNA FLANKING REGION; DROSOPHILA MELANOGASTER; GENETIC TRANSCRIPTION; GENOME ANALYSIS; INSECT GENETICS; INTRON; NONHUMAN; TRANSCRIPTION TERMINATION; TRANSPOSON;

ANIMALS; CODON; DROSOPHILA MELANOGASTER; GENOME, INSECT; INTRONS; POLYADENYLATION; RETROELEMENTS;

DROSOPHILA MELANOGASTER; INSECTA;

EID: 28244471042     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-004-0243-0     Document Type: Article

References (52)

1. Akashi H (1994) Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics 136:927-935
2. Bartolome C, Maside X, Charlesworth B (2002) On the abundance and distribution of transposable elements in the genome of Drosophila melanogaster. Mol Biol Evol 19:926-937
3. Biemont C, Tsitrone A, Vieira C, Hoogland C (1997) Transposable element distribution in Drosophila. Genetics 147:1997-1999
4. Burge C, Campbell AM, Karlin S (1992) Over-representation and under-representation of short oligonucleotides in DNA-sequences. Proc Natl Acad Sci USA 89:1358-1362
5. Carr M, Soloway JR, Robinson TE, Brookfield JFY (2002) Mechanisms regulating the copy numbers of six LTR retrotransposons in the genome of Drosophila melanogaster. Chromosoma 110:511-518
6. Charlesworth B, Charlesworth D (1983) The population-dynamics of transposable elements. Genet Res 42:1-27
7. Charlesworth B, Langley CH (1989) The population-genetics of Drosophila transposable elements. Annu Rev Genet 23:251-287
8. Charlesworth B, Morgan MT, Charlesworth D (1993) The effect of deleterious mutations on neutral molecular variation. Genetics 134:1289-1303
9. Daborn PJ, Yen JL, Bogwitz MR, et al. (2002) A single P450 allele associated with insecticide resistance in Drosophila. Science 297:2253-2256
10. Dieringer D, Schlotterer C (2003) Two distinct modes of microsatellite mutation processes: Evidence from the complete genomic sequences of nine species. Genome Res 13:2242-2251
11. Duret L, Marais G, Biemont C (2000) Transposons but not retrotransposons are located preferentially in regions of high recombination rate in Caenorhabditis elegans. Genetics 156:1661-1669
12. Duret L, Mouchiroud D (1999) Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, Arabidopsis. Proc Natl Acad Sci USA 96:4482-4487
13. Errede B, Company M, Hutchison CA (1987) Ty1 sequence with enhancer and mating-type-dependent regulatory activities. Mol Cell Biol 7:258-265
14. Franchini LF, Ganko EW, McDonald JF (2004) Retrotransposon-gene associations are widespread among D. melanogaster populations. Mol Biol Evol 21:1323-1331
15. Girard L, Freeling M (1999) Regulatory changes as a consequence of transposon insertion. Dev Genet 25:291-296
16. Hey J, Kliman RM (2002) Interactions between natural selection, recombination and gene density in the genes of Drosophila. Genetics 160:595-608
17. Hill WG, Robertson A (1966) Effect of linkage on limits to artificial selection. Genet Res 8:269-294
18. Ikemura T (1985) Codon usage and transfer-RNA content in unicellular and multicellular organisms. Mol Biol Evol 2:13-34
19. Jakubczak JL, Burke WD, Eickbush TH (1991) Retrotransposable elements R1 and R2 interrupt the ribosomal-RNA genes of most insects. Proc Natl Acad Sci USA 88:3295-3299
20. Jiang YW (2002) Transcriptional cosuppression of yeast Ty1 retrotransposons. Genes Dev 16:467-478
21. Kaminker J, Bergman C, Kronmiller B, et al. (2002) The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol 3:research0084.1-20
22. Kidwell MG, Lisch DR (2001) Perspective: Transposable elements, parasitic DNA, and genome evolution. Evolution 55:1-24
23. Kliman RM, Hey J (2003) Hill-Robertson interference in Drosophila melanogaster: reply to Marais, Mouchiroud and Duret. Genet Res 81:89-90
24. Kreitman M (1983) Nucleotide polymorphism at the alcohol-dehydrogenase locus of Drosophila melanogaster. Nature 304:412-417
25. Langley CH, Montgomery E, Hudson R, Kaplan N, Charlesworth B (1988) On the role of unequal exchange in the containment of transposable element copy number. Genet Res 52:223-235
26. Lerat E, Rizzon C, Biemont C (2003) Sequence divergence within transposable element families in the Drosophila melanogaster genome. Genome Res 13:1889-1896
27. Lerman DN, Michalak P, Helin AB, Bettencourt BR, Feder ME (2003) Modification of heat-shock gene expression in Drosophila melanogaster populations via transposable elements. Mol Biol Evol 20:135-144
28. Li W-H (1997) Molecular evolution. Sinauer Associates, Sunderland, MA
29. Lynch M, Walsh JB (1997) Genetics and analysis of quantitative traits. Sinauer Associates, Sunderland, MA
30. Marais G, Mouchiroud D, Duret L (2001) Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes. Proc Natl Acad Sci USA 98:5688-5692
31. Marais G, Mouchiroud D, Duret L (2003) Neutral effect of recombination on base composition in Drosophila. Genet Res 81:79-87
32. Martin E, Laloux H, Couette G, Alvarez T, Bessou C, Hauser O, Sookhareea S, Labouesse M, Segalat L (2002) Identification of 1088 new transposon insertions of Caenorhabditis elegans: A pilot study toward large-scale screens. Genetics 162:521-524
33. McDonald JF, Matyunina LV, Wilson S, Jordan IK, Bowen NJ, Miller WJ (1997) LTR retrotransposons and the evolution of eukaryotic enhancers. Genetica 100:3-13
34. Medstrand P, van de Lagemaat LN , Mager DL (2002) Retroelement distributions in the human genome: Variations associated with age and proximity to genes. Genome Res 12:1483-1495
35. Montgomery E, Charlesworth B, Langley CH (1987) A test for the role of natural selection in the stabilization of transposable element copy number in a population of Drosophila melanogaster. Genet Res 49:31-41
36. Pardue ML, DeBaryshe PG (1999) Drosophila telomeres: two transposable elements with important roles in chromosomes. Genetica 107:189-196
37. Petrov DA, Lozovskaya ER, Hartl DL (1996) High intrinsic: Rate of DNA loss in Drosophila. Nature 384:346-349
38. Petrov DA, Hartl DL (1998) High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups. Mol Biol Evol 15:293-302
39. Petrov DA, Aminetzach YT, Davis JC, Bensasson D, Hirsh AE (2003) Size matters: Non-LTR retrotransposable elements and ectopic recombination in Drosophila. Mol Biol Evol 20:880-892
40. Rizzon C, Marais G, Gouy M, Biemont C (2002) Recombination rate and the distribution of transposable elements in the Drosophila melanogaster genome. Genome Res 12:400-407
41. Rizzon C, Martin E, Marais G, Duret L, Segalat L, Biemont C (2003) Patterns of selection against transposons, inferred from the distribution of Tc1, Tc3 and Tc5 insertions in the mut-7 line of the nematode Caenorhabditis elegans. Genetics 165:1127-1135
42. Schlenke TA, Begun DJ (2004) Strong selective sweep associated with a transposon insertion in Drosophila simulans. Proc Natl Acad Sci USA 101:1626-1631
43. Semon M, Duret L (2004) Evidence that functional transcription units cover at least half of the human genome. Trends Genet 20:229-232
44. Smit AFA (1999) Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev 9:657-663
45. Sokal RR, Rohlf FJ (1995) Biometry. W.H. Freeman and Company, New York
46. Spradling AC, Stern DM, Kiss I, Roote J, Laverty T, Rubin GM (1995) Gene disruptions using P transposable elements: An integral component of the Drosophila genome project. Proc Natl Acad Sci USA 92:10824-10830
47. Stole V, Gauhar Z, Mason C, et al. (2004) A gene expression map for the euchromatic genome of Drosophila melanogaster. Science 306:655-660
48. van de Lagemaat LN , Landry JR, Mager DL, Medstrand P (2003) Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions. Trends Genet 19:530-536
49. Waterston RH, Lindblad-Toh K, Birney E, et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562
50. Wright SI, Agrawal N, Bureau TE (2003) Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana. Genome Res 13:1897-1903
51. Yu N, Jensen-Seaman MI, Chemnick L, Ryder O, Li W-H (2004) Nucleotide diversity in gorillas. Genetics 166:1375-1383
52. Zhao J, Hyman L, Moore C (1999) Formation of mRNA 3′ ends in eukaryotes: Mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol Mol Biol Rev 63:405-445