Alu elements in primates are preferentially lost fromareas of high GC content

PeerJ

Volumn 2013, Issue 1, 2013, Pages

  Hellen, Elizabeth H B ^a   Brookfield, John F Y ^a  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

Alu; GC content; Human; Insertion bias; Old; Primate; Transposable elements; Transposons; Young

Indexed keywords

ALU SEQUENCE; ARTICLE; CHROMOSOME ANALYSIS; DNA BASE COMPOSITION; DNA FLANKING REGION; GENE FREQUENCY; GENE MUTATION; HUMAN; HUMAN GENOME; NONHUMAN; PRIMATE; SCORING SYSTEM; SEQUENCE ANALYSIS;

EID: 84885109477     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.78     Document Type: Article

References (25)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215:403-410 DOI 10.1016/S0022-2836(05)80360-2.
2. Batzer MA, Deininger PL. 2002. Alu repeats and human genomic diversity. Nature Reviews Genetics 3:370-379 DOI 10.1038/nrg798.
3. Belle EMS, Webster MT, Eyre-Walker A. 2005. Why are young and old repetitive elements distributed differently in the human genome? Journal of Molecular Evolution 60:290-296 DOI 10.1007/s00239-004-0020-0.
4. Boone PM, Liu P, Zhang F, Carvalho CM, Towne CF, Batish SD, Lupski JR. 2001. Alu-specific microhomology-mediated deletion of the final exon of SPAST in three unrelated subjects with hereditary spastic paraplegia. Genetic Medicine 13:582-592 DOI 10.1097/GIM.0b013e3182106775.
5. Brookfield JFY. 2001. Selection on Alu sequences? Current Biology 11:R900-R901 DOI 10.1016/S0960-9822(01)00547-4.
6. Callinan PA, Batzer MA. 2006. Retrotransposable elements and human disease. Genome Dynamics 1:104-115 DOI 10.1159/000092503.
7. Conley AB, Miller WJ, Jordan IK. 2008. Human cis natural antisense transcripts initiated by transposable elements. Trends in Genetics 24:53-56 DOI 10.1016/j.tig.2007.11.008.
8. Cordaux R, Batzer MA. 2009. The Impact of retrotransposons on human genome evolution. Nature Reviews Genetics 10:691-703 DOI 10.1038/nrg2640.
9. Costantini M, Auletta F, Bernardi G. 2012. The distribution of "new" and "old" Alu sequences in the human genome: the solution of a "mystery'. Molecular Biology and Evolution 29:421-427 DOI 10.1093/molbev/msr242.
10. Cowley M, Oakey RJ. 2013. Transposable elements re-wire and fine-tune the transcriptome. PLoS Genetics 9:e1003234 DOI 10.1371/journal.pgen.1003234.
11. Dreszer TR, Karolchik D, Zweig AS, Hinrichs AS, Raney BJ, Kuhn RM, Meyer LR, Wong M, Sloan CA, RosenbloomKR. 2012. The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Research 40:D918-D923 DOI 10.1093/nar/gkr1055.
12. Gallus GN, Cardaioli E, Rufa A, Da Pozzo P, Bianchi S, D'Eramo C, Collura M, Tumino M, Pavone L, Federico A. 2010. Alu-element insertion in an OPA1 intron sequence associated with autosomal dominant optic atrophy. Molecular Vision 16:178-183.
13. Hedges SB, Dudley J, Kumar S. 2006. Timetree: a public knowledge-base of divergence times among organism. Bioinformatics 22:2971-2972 DOI 10.1093/bioinformatics/btl505.
14. Hellen EHB, Brookfield JFY. 2013. The diversity of Class II transposable elements in mammalian genomes has arisen from ancestral phylogenetic splits during ancient waves of proliferation through the genome. Molecular Biology and Evolution 30:100-108 DOI 10.1093/molbev/mss206.
15. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. 2005. Repbase Update, a database of eukaryotic repetitive elements. Cytogenetic Genome Research 110:462-467 DOI 10.1159/000084979.
16. Kapitonov V, Jurka J. 1996. The age of Alu subfamilies. Journal of Molecular Evolution 42:59-65 DOI 10.1007/BF00163212.
17. Kimura M. 1962. On the probability of fixation of mutant genes in a population. Genetics 47:713-719.
18. Kumar S, Hedges SB. 2011. TimeTree2: species divergence times on the iphone. Bioinformatics 27:2023-2024 DOI 10.1093/bioinformatics/btr315.
19. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng Jan-Fang, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Rosenthal André, Platzer M, Nyakatura G, Taudien S, Rump A, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen H-C, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JGR, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AFA, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang S-P, Yeh R-F, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Patrinos A, Morgan MJ. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921 DOI 10.1038/35057062.
20. Laperriere D, Wang TT, White JH, Mader S. 2007. Widespread Alu repeat-driven expansion of consensus DR2 retinoic acid response elements during primate evolution. BMC Genomics 8:23 DOI 10.1186/1471-2164-8-23.
21. Li WH, Gu Z, Wang H, Nekrutenko A. 2001. Evolutionary analyses of the human genome. Nature 409:847-849 DOI 10.1038/35057039.
22. Nekrutenko A, Li WH. 2001. Transposable elements are found in a large number of human protein-coding genes. Trends in Genetics 17:619-621 DOI 10.1016/S0168-9525(01)02445-3.
23. Polak P, Domany E. 2006. Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes. BMC Genomics 7:133 DOI 10.1186/1471-2164-7-133.
24. Stewart C, Kural D, Stromberg MP, Walker JA, Konkel MK, Stütz AM, Urban AE, Grubert F, Lam HYK, LeeW-P, Busby M, Indap AR, Garrison E, HuffC, Xing J, Snyder MP, Jorde LB, Batzer MA, Korbel JO, Marth GT. 2011. A comprehensive map of mobile element insertion polymorphisms in humans. PLoS Genetics 7:e1002236 DOI 10.1371/journal.pgen.1002236.
25. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA. 2001. The sequence of the human genome. Science 292:1838 DOI 10.1126/science.292.5523.1838.