The (r)evolution of SINE versus LINE distributions in primate genomes: Sex chromosomes are important

Genome Research

Volumn 20, Issue 5, 2010, Pages 600-613

  Kvikstad, Erika M ^a,b   Makova, Kateryna D ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b UNIVERSITÉ LYON 1   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ALU GENE; ARTICLE; CHROMOSOME ANALYSIS; COMPARATIVE STUDY; CONTROLLED STUDY; DENSITY; DNA BASE COMPOSITION; DOUBLE STRANDED DNA BREAK; EVOLUTION; FEMALE; GENE; GENE DELETION; GENETIC ANALYSIS; GENETIC RECOMBINATION; GENOME; GENOMIC INSTABILITY; HUMAN; LONG INTERSPERSED REPEAT; MALE; MULTIPLE REGRESSION; PRIMATE; PRIORITY JOURNAL; SEX CHROMOSOME; SHORT INTERSPERSED REPEAT; STATISTICAL MODEL; TRANSPOSON;

ALU ELEMENTS; ANIMALS; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN, X; CHROMOSOMES, HUMAN, Y; EVOLUTION, MOLECULAR; FEMALE; GENOME; HUMANS; LONG INTERSPERSED NUCLEOTIDE ELEMENTS; MALE; MODELS, GENETIC; PRIMATES; SEX CHROMOSOMES; SHORT INTERSPERSED NUCLEOTIDE ELEMENTS;

PRIMATES;

EID: 77951810932     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.099044.109     Document Type: Article

References (75)

1. Abrusan G, Krambeck H-J. 2006. The distribution of L1 and Alu retroelements in relation to GC content on human sex chromosomes is consistent with the ectopic recombination model. J Mol Evol 63: 484-492. (Pubitemid 44611735)
2. Abrusan G, Giordano J, Warburton PE. 2008. Analysis of transposon interruptions suggests selection for L1 elements on the X chromosome. PLoS Genet 4: e1000172. doi: 10.1371/journal.pgen.1000172.
3. Bailey JA, Carrel L, Chakravarti A, Eichler EE. 2000. Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: The Lyon repeat hypothesis. Proc Natl Acad Sci 97: 6634-6639. (Pubitemid 30412766)
4. Batzer MA, Deininger PL. 2002. Alu repeats and human genomic diversity. Nat Rev Genet 3: 370-380.
5. Belle EMS, Webster MT, Eyre-Walker A. 2005. Why are young and old repetitive elements distributed differently in the human genome? J Mol Evol 60: 290-296.
6. Bennett EA, Coleman LE, Tsui C, Pittard WS, Devine SE. 2004. Natural genetic variation caused by transposable elements in humans. Genetics 168: 933-951. (Pubitemid 39491469)
7. Berry C, Hannenhalli S, Leipzig J, Bushman FD. 2006. Selection of target sites for mobile DNA integration in the human genome. PLoS Comput Biol 2: e157. doi: 10.1371/journal.pcbi.0020157. (Pubitemid 44819930)
8. Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova K, et al. 2007. A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly. Genome Res 17: 960-964. (Pubitemid 46919731)
9. Boissinot S, Entezam A, Furano A. 2001. Selection against deleterious LINE-1-containing loci in the human lineage. Mol Biol Evol 18: 926-935. (Pubitemid 32520464)
10. Burgess R, Yang Z. 2008. Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequencing errors. Mol Biol Evol 25: 1979-1994.
11. Carrel L, Willard HF. 2005. X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature 434: 400-404. (Pubitemid 40469185)
12. Carrel L, Park C, Tyekucheva S, Dunn J, Chiaromonte F, Makova KD. 2006. Genomic environment predicts expression patterns on the human inactive X chromosome. PLoS Genet 2: e151. doi: 10.1371/journal.pgen.0020151. (Pubitemid 44504798)
13. Charlesworth B, Coyne JA, Barton NH. 1987. The relative rates of evolution of sex chromosomes and autosomes. Am Nat 130: 113-146.
14. Chen J-M, Stenson PD, Cooper DN, Ferec C. 2005. A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease. Hum Genet 117: 411-427. (Pubitemid 41236363)
15. Cheng Z, Ventura M, She X, Khaitovich P, Graves T, Osoegawa K, Church D, de Jong P, Wilson RK, Paabo S, et al. 2005. A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature 437: 88-93. (Pubitemid 41613429)
16. The Chimpanzee Sequencing and Analysis Consortium. 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87.
17. Chow JC, Yen Z, Ziesche SM, Brown CJ. 2005. Silencing of the mammalian X chromosome. Annu Rev Genomics Hum Genet 6: 69-92.
18. Conley AB, Miller WJ, Jordan IK. 2008. Human cis natural antisense transcripts initiated by transposable elements. Trends Genet 24: 53-56.
19. Coop G, Przeworski M. 2007. An evolutionary view of human recombination. Nature 8: 23-34.
20. Cost GJ, Feng Q, Jacquier A, Boeke JD. 2002. Human L1 target-primed reverse transcription in vitro. EMBO J 21: 5899-5910. (Pubitemid 35315287)
21. Ellis PJI, Affara NA. 2006. Spermatogenesis and sex chromosome gene content: An evolutionary perspective. Hum Fertil 9: 1-7.
22. Felsenstein J. 1974. The evolutionary advantage of recombination. Genetics 78: 737-756.
23. Glazko G, Nei M. 2003. Estimation of divergence times for major lineages of primate species. Mol Biol Evol 20: 424-434. (Pubitemid 36427177)
24. Goossens B, Chikhi L, Ancrenaz M, Lackman-Ancrenaz I, Andau P, Bruford MW. 2006. Genetic signature of anthropogenic population collapse in orang-utans. PLoS Biol 4: e25. doi: 10.1371/journal.pbio.0040025. (Pubitemid 43275858)
25. Han K, Konkel MK, Xing J, Wang H, Lee J, Meyer TJ, Huang CT, Sandifer E, Hebert K, Barnes EW, et al. 2007. Mobile DNA in OldWorld monkeys: A glimpse through the rhesus macaque genome. Science 316: 238-240. (Pubitemid 46633093)
26. Han K, Lee J, Meyer TJ, Remedios P, Goodwin L, Batzer MA. 2008. L1 recombination-associated deletions generate human genomic variation. Proc Natl Acad Sci 105: 19366-19371.
27. Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ, Weber R, Elnitski L, Li J, O'Connor M, Kolbe D, et al. 2003. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res 13: 13-26.
28. Hellmann I, Prufer K, Ji H, Zody MC, Paabo S, Ptak SE. 2005. Why do human diversity levels vary at a megabase scale? Genome Res 15: 1222-1231.
29. Hughes JF, Skaletsky H, Pyntikova T, Minx PJ, Graves T, Rozen S, Wilson RK, Page DC. 2005. Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee. Nature 437: 101-104. (Pubitemid 41613431)
30. Jones P. 1999. The DNA methylation paradox. Trends Genet 15: 34-37.
31. Jurka J. 1997. Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc Natl Acad Sci 94: 1872-1877. (Pubitemid 27113929)
32. Jurka J, Krnjajic M, Kapitonov V, Stenger JE, Kokhanyy O. 2002. Active Alu elements are passed primarily through paternal germlines. Theor Popul Biol 61: 519-530.
33. Jurka J, Kohany O, Pavlicek A, Kapitonov VV, Jurka MV. 2004. Duplication, coclustering, and selection of human Alu retrotransposons. Proc Natl Acad Sci 101: 1268-1272. (Pubitemid 38182678)
34. Kaessmann H, Wiebe V, Paabo S. 1999. Extensive nuclear DNA sequence diversity among chimpanzees. Science 286: 1159-1162. (Pubitemid 129515810)
35. Kano H, Godoy I, Courtney C, Vetter MR, Gerton GL, Ostertag EM, Kazazian HH Jr. 2009. L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism. Genes & Dev 23: 1303-1312.
36. Karolchik D, Kuhn R, Baertsch R, Barber G, Clawson H, Diekhans M, Giardine B, Harte R, Hinrichs A, Hsu F, et al. 2008. The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res 36: D773-D779. (Pubitemid 351149822)
37. Khan H, Smit A, Boissinot S. 2006. Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Genome Res 16: 78-87. (Pubitemid 43048936)
38. Kloc A, Martienssen R. 2008. RNAi, heterochromatin, and the cell cycle. Trends Genet 24: 511-517.
39. Kong A, Gudbjartsson DF, Sainz J, Jonsdottir GM, Gudjonsson SA, Richardsson B, Sigurdardottir S, Barnard J, Hallbeck B, Masson G, et al. 2002. A high-resolution recombination map of the human genome. Nat Genet 31: 241-247.
40. Kosakovsky Pond S, Frost S, Muse S. 2005. HyPhy: Hypothesis testing using phylogenies. Bioinformatics 21: 676-679. (Pubitemid 40424796)
41. Kuroki Y, Toyoda A, Noguchi H, Taylor TD, Itoh T, Kim D-S, Kim D-W, Choi S-H, Kim I-C, Choi HH, et al. 2006. Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway. Nat Genet 38: 158-167.
42. Kutner MH, Nachtsheim CJ, Neter J, Li W. 2005. Applied linear statistical models. McGraw-Hill, New York.
43. Kvikstad E, Tyekucheva S, Chiaromonte F, Makova K. 2007. A macaque's-eye view of human insertions and deletions: Differences in mechanisms. PLoS Comput Biol. 3: 1772-1782. (Pubitemid 47502981)
44. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921. (Pubitemid 32165345)
45. Lyon M. 1998. X-chromosome inactivation: A repeat hypothesis. Cytogenet Cell Genet 80: 133-137.
46. Mills RE, Bennett EA, Iskow RC, Luttig CT, Tsui C, Pittard WS, Devine SE. 2006. Recently mobilized transposons in the human and chimpanzee genomes. Am J Hum Genet 78: 671-679.
47. Morelli MA, Cohen PE. 2005. Not all germ cells are created equal: Aspects of sexual dimorphism in mammalian meiosis. Reproduction 130: 761-781.
48. Morrish T, Garcia-Perez J, Stamato T, Taccioli G, Sekiguchi J, Moran JV. 2007. Endonuclease-independent LINE-1 retrotransposition at mammalian telomeres. Nature 446: 208-212. (Pubitemid 46398662)
49. Muller HJ. 1964. The relation of recombination to mutational advance. Mutat Res 1: 2-9.
50. Myers S, Bottolo L, Freeman C, McVean G, Donnelly P. 2005. A fine-scale map of recombination rates and hotspots across the human genome. Science 310: 321-324. (Pubitemid 41457199)
51. Myers S, Freeman C, Auton A, Donnelly P, McVean G. 2008. A common sequence motif associated with recombination hot spots and genome instability in humans. Nat Genet 40: 1124-1129.
52. Myers S, Bowden R, Tumian A, Bontrop RE, Freeman C, MacFie TS, McVean G, Donnelly P. 2010. Drive against hotspot motifs in primates implicates the PRDM9 gene in meiotic recombination. Science 327: 876-879.
53. Nergadze SG, Santagostino M, Salzano A, Mondello C, Giulotto E. 2007. Contribution of telomerase RNA retrotranscription to DNA double-strand break repair during mammalian genome evolution. Genome Biol 8: R260. doi: 10.1186/gb-2007-8-12-r260. (Pubitemid 351917514)
54. Ozsolak F, Song J, Liu X, Fisher D. 2007. High-throughput mapping of the chromatin structure of human promoters. Nat Biotechnol 25: 244-248. (Pubitemid 46227125)
55. R Development Core Team. 2005. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna.
56. Rhesus Macaque Genome Sequencing and Analysis Consortium. 2007. Evolutionary and biomedical insights from the rhesus macaque genome. Science 13: 222-234. (Pubitemid 46633091)
57. Rodriguez F, Oliver JL, Marin A, Medina J. 1990. The general stochastic model of nucleotide substitution. J Theor Biol 142: 485-501. (Pubitemid 20108270)
58. Ross MT, Grafham DV, Coffey AJ, Scherer S, McLay K, Muzny D, Platzer M, Howell GR, Burrows C, Bird CP, et al. 2005. The DNA sequence of the human X chromosome. Nature 434: 325-337.
59. Rozen S, Skaletsky H, Marszalek JD, Minx PJ, Cordum HS, Waterston RH, Wilson RK, Page DC. 2003. Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. Nature 423: 873-876. (Pubitemid 36781279)
60. Rubin C, VandeVoort C, Teplitz R, Schmid C. 1994. Alu repeated DNAs are differentially methylated in primate germ cells. Nucleic Acids Res 22: 5121-5127.
61. Seleme MC, Vetter MR, Cordaux R, Bastone L, Batzer MA, Kazazian HH. Jr. 2006. Extensive individual variation in L1 retrotransposition capability contributes to human genetic diversity. Proc Natl Acad Sci 103: 6611-6616.
62. Sen SK, Han K, Wang J, Lee J, Wang H, Callinan PA, Dyer M, Cordaux R, Liang P, Batzer MA. 2006. Human genomic deletions mediated by recombination between Alu elements. Am J Hum Genet 79: 41-53. (Pubitemid 43927375)
63. Sen SK, Huang CT, Han K, Batzer M. 2007. Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome. Nucleic Acids Res 35: 3741-3751. (Pubitemid 47244667)
64. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. 2005. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15: 1034-1050. (Pubitemid 41126859)
65. Simons C, Pheasant M, Makunin IV, Mattick JS. 2006. Transposon-free regions in mammalian genomes. Genome Res 16: 164-172.
66. Sironi M, Menozzi G, Comi G, Cereda M, Cagliani R, Bresolin N, Pozzoli U. 2006. Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns. Genome Biol 7: R120. doi: 10.1186/gb-2006-7-12-r120. (Pubitemid 46995595)
67. Skaletsky H, Kuroda-Kawaguchi T, Minx PJ, Cordum HS, Hillier L, Brown LG, Repping S, Pyntikova T, Ali J, Bieri T, et al. 2003. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423: 825-837. (Pubitemid 36781267)
68. Smit A, Toth G, Riggs A, Jurka J. 1995. Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences. J Mol Biol 246: 401-417.
69. Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, Orth AP, Vega RG, Sapinoso LM, Moqrich A, et al. 2002. Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci 99: 4465-4470. (Pubitemid 34286008)
70. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, et al. 2004. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci 101: 6062-6067. (Pubitemid 38520528)
71. Tyekucheva S, Makova KD, Karro JE, Hardison RC, Miller W, Chiaromonte F. 2008. Human-macaque comparisons illuminate variation in neutral substitution rates. Genome Biol 9: R76. doi: 10.1186/gb-2008-9-4-r76. (Pubitemid 351974302)
72. van de Lagemaat L, Gagnier L, Medstrand P, Mager D. 2005. Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates. Genome Res 15: 1243-1249. (Pubitemid 41247914)
73. Walser J-C, Ponger L, Furano A. 2008. CpG dinucleotides and the mutation rate of non-CpG DNA. Genome Res 18: 1403-1414.
74. Woodfine K, Fiegler H, Beare DM, Collins JE, McCann OT, Young BD, Debernardi S, Mott R, Dunham I, Carter NP. 2004. Replication timing of the human genome. Hum Mol Genet 13: 191-202.
75. Yang S, Smit AF, Schwartz S, Chiaromonte F, Roskin KM, Haussler D, Miller W, Hardison RC. 2004. Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes. Genome Res 14: 517-527. (Pubitemid 38500222)