[1] | Biemont C, Vieira C (2006) Genetics—Junk DNA as an evolutionary force. Nature 443: 521–524.
|
[2] | Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, et al. (2006) A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature 441: 87–90.
|
[3] | Lerman DN, Michalak P, Helin AB, Bettencourt BR, Feder ME (2003) Modification of heat-shock gene expression in populations via transposable elements. Mol Biol Evol 20: 135–144.
|
[4] | Puig M, Caceres M, Ruiz A (2004) Silencing of a gene adjacent to the breakpoint of a widespread Drosophila inversion by a transposon-induced antisense RNA. Proc Natl Acad Sci U S A 101: 9013–9018.
|
[5] | Bergman CM, Quesneville H, Anxolabehere D, Ashburner M (2006) Recurrent insertion and duplication generate networks of transposable element sequences in the genome. Genome Biol 7: R112.
|
[6] | Duret L, Marais G, Biemont C (2000) Transposons but not retrotransposons are located preferentially in regions of high recombination rate in . Genetics 156: 1661–1669.
|
[7] | 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.
|
[8] | Wright SI, Agrawal N, Bureau TE (2003) Effects of recombination rate and gene density on transposable element distributions in . Genome Res 13: 1897–1903.
|
[9] | Kapitonov VV, Jurka J (2003) Molecular paleontology of transposable elements in the genome. Proc Natl Acad Sci U S A 100: 6569–6574.
|
[10] | Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, et al. (2002) The transposable elements of the euchromatin: a genomics perspective. Genome Biol 3: R84.
|
[11] | Lipatov M, Lenkov K, Petrov DA, Bergman CM (2005) Paucity of chimeric gene-transposable element transcripts in the genome. BMC Biol 3: 24.
|
[12] | Rizzon C, Marais G, Gouy M, Biemont C (2002) Recombination rate and the distribution of transposable elements in the genome. Genome Res 12: 400–407.
|
[13] | Hoogland C, Biémont C (1996) Chromosomal distribution of transposable elements in : test of the ectopic recombination model for maintenance of insertion site number. Genetics 144: 197–204.
|
[14] | Bartolome C, Maside X, Charlesworth B (2002) On the abundance and distribution of transposable elements in the genome of . Mol Biol Evol 19: 926–937.
|
[15] | Montgomery EA, Huang SM, Langley CH, Judd BH (1991) Chromosome rearrangement by ectopic recombination in —Genome structure and evolution. Genetics 129: 1085–1098.
|
[16] | Charlesworth B, Langley CH (1989) The population-genetics of Drosophila transposable elements. Annu Rev Genet 23: 251–287.
|
[17] | Bellen HJ, Levis RW, Liao GC, He YC, Carlson JW, et al. (2004) The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila genes. Genetics 167: 761–781.
|
[18] | Shilova VY, Garbuz DG, Myasyankina EN, Chen B, Evgen'ev MB, et al. (2006) Remarkable site specificity of local transposition into the HsP70 promoter of . Genetics 173: 809–820.
|
[19] | Guimond N, Bideshi DK, Pinkerton AC, Atkinson PW, O'Brochta DA (2003) Patterns of Hermes transposition in . Mol Genet Genomics 268: 779–790.
|
[20] | Ladeveze V, Aulard S, Chaminade N, Biemont C, Periquet G, et al. (2001) Dynamics of the hobo transposable element in transgenic lines of Drosophila melanogaster. Genetical Res 77: 135–142.
|
[21] | Bownes M (1990) Preferential insertion of P-elements into genes expressed in the germ-line of . Mol Gen Genet 222: 457–460.
|
[22] | Liao GC, Rehm EJ, Rubin GM (2000) Insertion site preferences of the P transposable element in . Proc Natl Acad Sci U S A 97: 3347–3351.
|
[23] | Timakov B, Liu X, Turgut I, Zhang P (2002) Timing and targeting of P-element local transposition in the male germline cells of . Genetics 160: 1011–1022.
|
[24] | Quesneville H, Bergman CM, Andrieu O, Autard D, Nouaud D, et al. (2005) Combined evidence annotation of transposable elements in genome sequences. PLoS Comput Biol 1: 166–175. doi: 10.1371/journal.pcbi.0010022.
|
[25] | Chintapalli VR, Wang J, Dow JAT (2007) Using FlyAtlas to identify better Drosophila melanogaster models of human disease. Nature Genet 39: 715–720.
|
[26] | Blumenstiel JP, Hartl DL, Lozovsky ER (2002) Patterns of insertion and deletion in contrasting chromatin domains. Mol Biol Evol 19: 2211–2225.
|
[27] | Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou MM, et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15: 1034–1050.
|
[28] | Haddrill PR, Charlesworth B, Halligan DL, Andolfatto P (2005) Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content. Genome Biol 6: R67.
|
[29] | Halligan DL, Keightley PD (2006) Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison. Genome Res 16: 875–884.
|
[30] | Ometto L, Stephan W, De Lorenzo D (2005) Insertion/deletion and nucleotide polymorphism data reveal constraints in introns and intergenic regions. Genetics 169: 1521–1527.
|
[31] | Wright S (1933) Inbreeding and homozygosis. Proc Natl Acad Sci U S A 19: 411–420.
|
[32] | Castillo-Davis CI, Mekhedov SL, Hartl DL, Koonin EV, Kondrashov FA (2002) Selection for short introns in highly expressed genes. Nature Genet 31: 415–418.
|
[33] | Pozzoli U, Menozzi G, Comi GP, Cagliani R, Bresolin N, et al. (2007) Intron size in mammals: complexity comes to terms with economy. Trends Genet 23: 20–24.
|
[34] | Fox-Walsh KL, Dou YM, Lam BJ, Hung SP, Baldi PF, et al. (2005) The architecture of pre-mRNAs affects mechanisms of splice-site pairing. Proc Natl Acad Sci U S A 102: 16176–16181.
|
[35] | Thygesen HH, Zwinderman AH (2005) Modelling the correlation between the activities of adjacent genes in Drosophila. BMC Bioinformatics 6: 10.
|
[36] | Caballero A (1995) On the effective size of populations with separate sexes, with particular reference to sex-linked genes. Genetics 139: 1007–1011.
|
[37] | Andolfatto P (2001) Contrasting patterns of X-linked and autosomal nucleotide variation in Drosophila melanogaster and . Mol Biol Evol 18: 279–290.
|
[38] | Haddrill PR, Thornton KR, Charlesworth B, Andolfatto P (2005) Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Res 15: 790–799.
|
[39] | Mousset S, Derome N (2004) Molecular polymorphism in and D. simulans: what have we learned from recent studies? Genetica 120: 79–86.
|
[40] | Straub T, Becker PB (2007) Dosage compensation: the beginning and end of generalization. Nat Rev Genet 8: 47–57.
|
[41] | Pasyukova EG, Nuzhdin SV (1993) Doc and copia instability in an isogenic stock. Mol Gen Genet 240: 302–306.
|
[42] | Caron H, van Schaik B, van der Mee M, Baas F, Riggins G, et al. (2001) The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 291: 1289.
|
[43] | Cohen BA, Mitra RD, Hughes JD, Church GM (2000) A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nature Genet 26: 183–186.
|
[44] | Lercher MJ, Hurst LD (2006) Co-expressed yeast genes cluster over a long range but are not regularly spaced. J Mol Biol 359: 825–831.
|
[45] | Roy PJ, Stuart JM, Lund J, Kim SK (2002) Chromosomal clustering of muscle-expressed genes in . Nature 418: 975–979.
|
[46] | Williams EJB, Bowles DJ (2004) Coexpression of neighboring genes in the genome of . Genome Res 14: 1060–1067.
|
[47] | Sproul D, Gilbert N, Bickmore WA (2005) The role of chromatin structure in regulating the expression of clustered genes. Nat Rev Genet 6: 775–781.
|
[48] | Spellman PT, Rubin GM (2002) Evidence for large domains of similarly expressed genes in the Drosophila genome. J Biol 1: 5.
|
[49] | Hurst LD, Pal C, Lercher MJ (2004) The evolutionary dynamics of eukaryotic gene order. Nat Rev Genet 5: 299–310.
|
[50] | Bachtrog D (2003) Adaptation shapes patterns of genome evolution on sexual and asexual chromosomes in Drosophila. Nature Genet 34: 215–219.
|
[51] | Kavi HH, Fernandez HR, Xie WW, Birchler JA (2005) RNA silencing in Drosophila. FEBS Lett 579: 5940–5949.
|
[52] | Slotkin RK, Martienssen R (2007) Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 8: 272–285.
|
[53] | Sun FL, Haynes K, Simpson CL, Lee SD, Collins L, et al. (2004) cis-Acting determinants of heterochromatin formation on chromosome four. Mol Cell Biol 24: 8210–8220.
|
[54] | Brennecke J, Aravin AA, Stark A, Dus M, Kellis M, et al. (2007) Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128: 1089–1103.
|
[55] | Biemont C, Vieira C (2005) What transposable elements tell us about genome organization and evolution: the case of Drosophila. Cytogenet Genome Res 110: 25–34.
|
[56] | Vinogradov AE (2004) Compactness of human housekeeping genes: selection for economy or genomic design? Trends Genet 20: 543–543.
|
[57] | Nelson CE, Hersh BM, Carroll SB (2004) The regulatory content of intergenic DNA shapes genome architecture. Genome Biol 5: R25.
|
[58] | Petrov DA, Chao YC, Stephenson EC, Hartl DL (1998) Pseudogene evolution in Drosophila suggests a high rate of DNA loss. Mol Biol Evol 15: 1562–1567.
|
[59] | Petrov DA, Sangster TA, Johnston JS, Hartl DL, Shaw KL (2000) Evidence for DNA loss as a determinant of genome size. Science 287: 1060–1062.
|
[60] | Gregory TR (2005) Synergy between sequence and size in large-scale genomics. Nat Rev Genet 6: 699–708.
|
[61] | Vinogradov AE (1999) Intron-genome size relationship on a large evolutionary scale. J Mol Evol 49: 376–384.
|
[62] | Betran E, Bai YS, Motiwale M (2006) Fast protein evolution and germ line expression of a Drosophila parental gene and its young retroposed paralog. Mol Biol Evol 23: 2191–2202.
|
[63] | Vinckenbosch N, Dupanloup I, Kaessmann H (2006) Evolutionary fate of retroposed gene copies in the human genome. Cytogenet Genome Res 103: 3220–3225.
|
[64] | Betran E, Thornton K, Long M (2002) Retroposed new genes out of the X in Drosophila. Genome Res 12: 1854–1859.
|
[65] | Emerson JJ, Kaessmann H, Betran E, Long MY (2004) Extensive gene traffic on the mammalian X chromosome. Science 303: 537–540.
|
[66] | Hey J, Kliman RM (2002) Interactions between natural selection, recombination and gene density in the genes of Drosophila. Genetics 160: 595–608.
|
[67] | Parisi M, Nuttall R, Edwards P, Minor J, Naiman D, et al. (2004) A survey of ovary-, testis-, and soma-biased gene expression in adults. Genome Biol 5: R40.
|
[68] | Gupta V, Parisi M, Sturgill D, Nuttall R, Doctolero M, et al. (2006) Global analysis of X-chromosome dosage compensation. J Biol 5: 3.
|