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Literature DB >> 12136119

Genome-wide comparison of differences in the integration sites of interspersed repeats between closely related genomes.

Ilgar Mamedov¹, Anastasia Batrak, Anton Buzdin, Elena Arzumanyan, Yuri Lebedev, Eugene D Sverdlov.

Abstract

A technique for genome-wide detection of differences in the integration site positions of interspersed repeats in related genomes (DiffIR) is described. The technique is based on a whole- genome selective PCR amplification of the repeats' flanking regions followed by a differential hybridization screening of the arrayed library of the selected amplicons. The technique was successfully applied to the comparison of the integration sites in the human and chimpanzee genomes, allowing us to discover 11 new human-specific integrations of human endogenous retrovirus, K family (HML-2) long terminal repeats.

Entities: Disease Species

Mesh：

Substances：
DNA

Year: 2002 PMID： 12136119 PMCID： PMC135772 DOI： 10.1093/nar/gnf071

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

26 in total

1. Initial sequencing and analysis of the human genome.

Authors: E S Lander; L M Linton; B Birren; C Nusbaum; M C Zody; J Baldwin; K Devon; K Dewar; M Doyle; W FitzHugh; R Funke; D Gage; K Harris; A Heaford; J Howland; L Kann; J Lehoczky; R LeVine; P McEwan; K McKernan; J Meldrim; J P Mesirov; C Miranda; W Morris; J Naylor; C Raymond; M Rosetti; R Santos; A Sheridan; C Sougnez; Y Stange-Thomann; N Stojanovic; A Subramanian; D Wyman; J Rogers; J Sulston; R Ainscough; S Beck; D Bentley; J Burton; C Clee; N Carter; A Coulson; R Deadman; P Deloukas; A Dunham; I Dunham; R Durbin; L French; D Grafham; S Gregory; T Hubbard; S Humphray; A Hunt; M Jones; C Lloyd; A McMurray; L Matthews; S Mercer; S Milne; J C Mullikin; A Mungall; R Plumb; M Ross; R Shownkeen; S Sims; R H Waterston; R K Wilson; L W Hillier; J D McPherson; M A Marra; E R Mardis; L A Fulton; A T Chinwalla; K H Pepin; W R Gish; S L Chissoe; M C Wendl; K D Delehaunty; T L Miner; A Delehaunty; J B Kramer; L L Cook; R S Fulton; D L Johnson; P J Minx; S W Clifton; T Hawkins; E Branscomb; P Predki; P Richardson; S Wenning; T Slezak; N Doggett; J F Cheng; A Olsen; S Lucas; C Elkin; E Uberbacher; M Frazier; R A Gibbs; D M Muzny; S E Scherer; J B Bouck; E J Sodergren; K C Worley; C M Rives; J H Gorrell; M L Metzker; S L Naylor; R S Kucherlapati; D L Nelson; G M Weinstock; Y Sakaki; A Fujiyama; M Hattori; T Yada; A Toyoda; T Itoh; C Kawagoe; H Watanabe; Y Totoki; T Taylor; J Weissenbach; R Heilig; W Saurin; F Artiguenave; P Brottier; T Bruls; E Pelletier; C Robert; P Wincker; D R Smith; L Doucette-Stamm; M Rubenfield; K Weinstock; H M Lee; J Dubois; A Rosenthal; M Platzer; G Nyakatura; S Taudien; A Rump; H Yang; J Yu; J Wang; G Huang; J Gu; L Hood; L Rowen; A Madan; S Qin; R W Davis; N A Federspiel; A P Abola; M J Proctor; R M Myers; J Schmutz; M Dickson; J Grimwood; D R Cox; M V Olson; R Kaul; C Raymond; N Shimizu; K Kawasaki; S Minoshima; G A Evans; M Athanasiou; R Schultz; B A Roe; F Chen; H Pan; J Ramser; H Lehrach; R Reinhardt; W R McCombie; M de la Bastide; N Dedhia; H Blöcker; K Hornischer; G Nordsiek; R Agarwala; L Aravind; J A Bailey; A Bateman; S Batzoglou; E Birney; P Bork; D G Brown; C B Burge; L Cerutti; H C Chen; D Church; M Clamp; R R Copley; T Doerks; S R Eddy; E E Eichler; T S Furey; J Galagan; J G Gilbert; C Harmon; Y Hayashizaki; D Haussler; H Hermjakob; K Hokamp; W Jang; L S Johnson; T A Jones; S Kasif; A Kaspryzk; S Kennedy; W J Kent; P Kitts; E V Koonin; I Korf; D Kulp; D Lancet; T M Lowe; A McLysaght; T Mikkelsen; J V Moran; N Mulder; V J Pollara; C P Ponting; G Schuler; J Schultz; G Slater; A F Smit; E Stupka; J Szustakowki; D Thierry-Mieg; J Thierry-Mieg; L Wagner; J Wallis; R Wheeler; A Williams; Y I Wolf; K H Wolfe; S P Yang; R F Yeh; F Collins; M S Guyer; J Peterson; A Felsenfeld; K A Wetterstrand; A Patrinos; M J Morgan; P de Jong; J J Catanese; K Osoegawa; H Shizuya; S Choi; Y J Chen; J Szustakowki
Journal: Nature Date: 2001-02-15 Impact factor: 49.962

2. Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity.

Authors: M L Carroll; A M Roy-Engel; S V Nguyen; A H Salem; E Vogel; B Vincent; J Myers; Z Ahmad; L Nguyen; M Sammarco; W S Watkins; J Henke; W Makalowski; L B Jorde; P L Deininger; M A Batzer
Journal: J Mol Biol Date: 2001-08-03 Impact factor: 5.469

3. Genetics. L1 retrotransposons shape the mammalian genome.

Authors: H H Kazazian
Journal: Science Date: 2000-08-18 Impact factor: 47.728

4. Identification of a genomic island present in the majority of pathogenic isolates of Pseudomonas aeruginosa.

Authors: X Liang; X Q Pham; M V Olson; S Lory
Journal: J Bacteriol Date: 2001-02 Impact factor: 3.490

Review 5. Human L1 retrotransposition: insights and peculiarities learned from a cultured cell retrotransposition assay.

Authors: J V Moran
Journal: Genetica Date: 1999 Impact factor: 1.082

6. Full-sized HERV-K (HML-2) human endogenous retroviral LTR sequences on human chromosome 21: map locations and evolutionary history.

Authors: S G Kurdyukov; Y B Lebedev; I I Artamonova; T N Gorodentseva; A V Batrak; I Z Mamedov; T L Azhikina; S P Legchilina; I G Efimenko; K Gardiner; E D Sverdlov
Journal: Gene Date: 2001-07-25 Impact factor: 3.688

7. A new exon created by intronic insertion of a rearranged LINE-1 element as the cause of chronic granulomatous disease.

Authors: C Meischl; M Boer; A Ahlin; D Roos
Journal: Eur J Hum Genet Date: 2000-09 Impact factor: 4.246

8. Reading between the LINEs: human genomic variation induced by LINE-1 retrotransposition.

Authors: F M Sheen; S T Sherry; G M Risch; M Robichaux; I Nasidze; M Stoneking; M A Batzer; G D Swergold
Journal: Genome Res Date: 2000-10 Impact factor: 9.043

9. Molecular description of three macro-deletions and an Alu-Alu recombination-mediated duplication in the HPRT gene in four patients with Lesch-Nyhan disease.

Authors: E M Brooks; R F Branda; J A Nicklas; J P O'Neill
Journal: Mutat Res Date: 2001-05-09 Impact factor: 2.433

10. Many human endogenous retrovirus K (HERV-K) proviruses are unique to humans.

Authors: M Barbulescu; G Turner; M I Seaman; A S Deinard; K K Kidd; J Lenz
Journal: Curr Biol Date: 1999-08-26 Impact factor: 10.834

16 in total

1. ATLAS: a system to selectively identify human-specific L1 insertions.

Authors: Richard M Badge; Reid S Alisch; John V Moran
Journal: Am J Hum Genet Date: 2003-03-11 Impact factor: 11.025

2. At least 50% of human-specific HERV-K (HML-2) long terminal repeats serve in vivo as active promoters for host nonrepetitive DNA transcription.

Authors: Anton Buzdin; Elena Kovalskaya-Alexandrova; Elena Gogvadze; Eugene Sverdlov
Journal: J Virol Date: 2006-11 Impact factor: 5.103

3. A new set of markers for human identification based on 32 polymorphic Alu insertions.

Authors: Ilgar Z Mamedov; Irina A Shagina; Marya A Kurnikova; Sergey N Novozhilov; Dmitry A Shagin; Yury B Lebedev
Journal: Eur J Hum Genet Date: 2010-02-24 Impact factor: 4.246

4. Genome-wide amplification of proviral sequences reveals new polymorphic HERV-K(HML-2) proviruses in humans and chimpanzees that are absent from genome assemblies.

Authors: Catriona M Macfarlane; Richard M Badge
Journal: Retrovirology Date: 2015-04-28 Impact factor: 4.602

Review 5. Molecular functions of human endogenous retroviruses in health and disease.

Authors: Maria Suntsova; Andrew Garazha; Alena Ivanova; Dmitry Kaminsky; Alex Zhavoronkov; Anton Buzdin
Journal: Cell Mol Life Sci Date: 2015-06-18 Impact factor: 9.261

6. Allelic variation of HERV-K(HML-2) endogenous retroviral elements in human populations.

Authors: Catriona Macfarlane; Peter Simmonds
Journal: J Mol Evol Date: 2004-11 Impact factor: 2.395

7. Evolutionary dynamics of endogenous Jaagsiekte sheep retroviruses proliferation in the domestic sheep, mouflon and Pyrenean chamois.

Authors: M Sistiaga-Poveda; B M Jugo
Journal: Heredity (Edinb) Date: 2014-04-02 Impact factor: 3.821

8. RISCI--Repeat Induced Sequence Changes Identifier: a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify repeat induced sequence changes in closely related genomes.

Authors: Vipin Singh; Rakesh K Mishra
Journal: BMC Bioinformatics Date: 2010-12-26 Impact factor: 3.169

9. Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach.

Authors: Ilgar Z Mamedov; Elena S Arzumanyan; Anna L Amosova; Yuri B Lebedev; Eugene D Sverdlov
Journal: Nucleic Acids Res Date: 2005-01-26 Impact factor: 16.971

10. Detection of Human Endogenous Retrovirus K (HERV-K) Transcripts in Human Prostate Cancer Cell Lines.

Authors: Lorenzo Agoni; Chandan Guha; Jack Lenz
Journal: Front Oncol Date: 2013-07-09 Impact factor: 6.244