Human endogenous retrovirus-H insertion screening

Guliyev,Mehrab; Yilmaz,Sibel; Sahin,Kaniye; Marakli,Sevgi; Gozukirmizi,Nermin

doi:10.3892/mmr.2013.1295

Human endogenous retrovirus-H insertion screening

Authors:
- Mehrab Guliyev
- Sibel Yilmaz
- Kaniye Sahin
- Sevgi Marakli
- Nermin Gozukirmizi
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Affiliations: Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Vezneciler, Istanbul 34134, Turkey
Published online on: January 28, 2013 https://doi.org/10.3892/mmr.2013.1295
Pages: 1305-1309

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Abstract

Endogenous retroviruses (ERVs) and ERV-like sequences comprise 8% of the human genome. We aimed to analyze genome integration polymorphisms of human endogenous retrovirus (HERV)-H by the inter-retrotransposon amplified polymorphism (IRAP) technique using the sequences of LTR7A (450 bp), LTR7B (445 bp) and LTR7C (471 bp). Blood samples from 20 individuals (10 females and 10 males) of diverse ethnic origins were used for the determination of integration variations at the genomic level. Isolated genomic DNA was screened using 3 pairs of primers corresponding to LTR regions of the HERV-H gene. We observed insertion polymorphism patterns between 0-87% in all subjects. The findings obtained contribute to our understanding of the effects of HERV-H on variations within the human genome.

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1	Lander ES, Linton LM, Birren B, et al: Initial sequencing and analysis of the human genome. Nature. 409:860–921. 2001. View Article : Google Scholar : PubMed/NCBI
2	Jern P and Coffin JM: Effects of retroviruses on host genome function. Annu Rev Genet. 42:709–732. 2008. View Article : Google Scholar : PubMed/NCBI
3	Jern P, Sperber GO, Ahlsén G and Blomberg J: Sequence variability, gene structure, and expression of full-length human endogenous retrovirus H. J Virol. 79:6325–6337. 2005. View Article : Google Scholar : PubMed/NCBI
4	Tristem M: Identification and characterization of novel human endogenous retrovirus families by phylogenetic screening of the human genome mapping project database. J Virol. 74:3715–3730. 2000. View Article : Google Scholar
5	de Parseval N, Casella J, Gressin L and Heidmann T: Characterization of the three HERV-H proviruses with an open envelope reading frame encompassing the immunosuppressive domain and evolutionary history in primates. Virology. 279:558–569. 2001.PubMed/NCBI
6	Hirose Y, Takamatsu M and Harada F: Presence of env genes in members of the RTVL-H family of human endogenous retrovirus-like elements. Virology. 192:52–61. 1993.
7	Goodchild N, Wilkinson DA and Mager D: Recent evolutionary expansion of a subfamily of RTVL-H human endogenous retrovirus-like elements. Virology. 196:778–788. 1993. View Article : Google Scholar : PubMed/NCBI
8	Anderssen S, Sjøttem E, Svineng G and Johansen T: Comparative analyses of LTRs of the ERV-H family of primate-specific retrovirus-like elements isolated from marmoset, African green monkey, and man. Virology. 234:14–30. 1997. View Article : Google Scholar : PubMed/NCBI
9	Yi JM and Kim HS: Evolutionary implications of human endogenous retrovirus HERV-H family. J Hum Genet. 49:215–219. 2004. View Article : Google Scholar : PubMed/NCBI
10	Schulman AH and Kalendar R: A movable feast: diverse retrotransposons and their contribution to barley genome dynamics. Cytogenet Genome Res. 110:598–605. 2005. View Article : Google Scholar : PubMed/NCBI
11	Kalendar R, Grob T, Regina M, Suoniemi A and Schulman A: IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theor Appl Genet. 98:704–711. 1999. View Article : Google Scholar
12	Guo D, Zhang H and Luo Z: Genetic relationships of Diospyros kaki Thunb. and related species revealed by IRAP and REMAP analysis. Plant Sci. 170:528–533. 2006.
13	Manninen O, Kalendar R, Robinson J and Schulman AH: Application of BARE-1 retrotransposon markers to the mapping of a major resistance gene for net blotch in barley. Mol Gen Genet. 264:325–334. 2000.
14	Muhammad AJ and Othman RY: Characterization of Fusarium wilt-resistant and Fusarium wilt-susceptible somaclones of banana cultivar rastali (Musa AAB) by random amplified polymorphic DNA and retrotransposon markers. Plant Mol Biol Rep. 23:241–249. 2005.
15	Evrensel C, Yılmaz S, Temel A and Gozukirmizi N: Variations in BARE-1 insertion patterns in barley callus cultures. Genet Mol Res. 10:980–987. 2011.
16	Bayram E, Yilmaz S, Hamat-Mecbur H, Kartal-Alacam G and Gozukirmizi N: Nikita retrotransposon movements in callus cultures of barley (Hordeum vulgare L.). POJ. 5:211–215. 2012.
17	Grandbastien MA, Audeon C, Bonnivard E, et al: Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae. Cytogenet Genome Res. 110:229–241. 2005. View Article : Google Scholar : PubMed/NCBI
18	Li XQ: Developmental and environmental variation in genomes. Heredity (Edinb). 102:323–329. 2009. View Article : Google Scholar : PubMed/NCBI
19	Yi JM, Kim HM and Kim HS: Human endogenous retrovirus HERV-H family in human tissues and cancer cells: expression, identification and phylogeny. Cancer Lett. 231:228–239. 2006. View Article : Google Scholar : PubMed/NCBI
20	Laska MJ, Brudek T, Nissen KK, Christensen T, Møller-Larsen A, Petersen T and Nexø BA: Expression of HERV-Fc1, a human endogenous retrovirus, is increased in patients with active multiple sclerosis. J Virol. 86:3713–3722. 2012. View Article : Google Scholar : PubMed/NCBI
21	Mamedov I, Lebedev Y, Hunsmann G, Khusnutdinova E and Sverdlov E: A rare event of insertion polymorphism of a HERV-K LTR in the human genome. Genomics. 84:596–599. 2004. View Article : Google Scholar : PubMed/NCBI
22	Belshaw R, Dawson AL, Woolven-Allen J, Redding J, Burt A and Tristem M: Genomewide screening reveals high levels of insertional polymorphism in the human endogenous retrovirus family HERV-K (HML2): implications for present-day activity. J Virol. 79:12507–12514. 2005. View Article : Google Scholar : PubMed/NCBI
23	Moyes D, Griffiths DJ and Venables PJ: Insertional polymorphisms: a new lease of life for endogenous retroviruses in human disease. Trends Genet. 23:326–333. 2007. View Article : Google Scholar : PubMed/NCBI
24	Liang P and Tang W: Database documentation of retrotransposon insertion polymorphisms. Front Biosci (Elite Ed). 4:1542–1555. 2012. View Article : Google Scholar : PubMed/NCBI
25	Batzer MA and Deininger PL: Alu repeats and human genomic diversity. Nat Rev Genet. 3:370–379. 2002. View Article : Google Scholar : PubMed/NCBI
26	Watkins WS, Rogers AR, Ostler C, et al: Genetic variation among world populations: inference from 100 Alu insertion polymorphisms. Genome Res. 13:1607–1618. 2003. View Article : Google Scholar : PubMed/NCBI
27	Bamshad MJ, Wooding S, Watkins WS, Ostler CT, Batzer MA and Jorde LB: Human population genetic structure and inference of group membership. Am J Hum Genet. 72:578–589. 2003. View Article : Google Scholar : PubMed/NCBI
28	Roy-Engel AM, Carroll ML, El-Sawy M, Salem AH, Garber RK, Nguyen SV, Deininger PL and Batzer MA: Non-traditional Alu evolution and primate genomic diversity. J Mol Biol. 316:1033–1040. 2002. View Article : Google Scholar : PubMed/NCBI
29	Vincent BJ, Myers JS, Ho HJ, Kilroy GE, Walker JA, Watkins WS, Jorde LB and Batzer MA: Following the LINEs: an analysis of primate genomic variation at human-specific LINE-1 insertion sites. Mol Biol Evol. 20:1338–1348. 2003. View Article : Google Scholar : PubMed/NCBI
30	Carroll ML, Roy-Engel AM, Nguyen SV, et al: Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity. J Mol Biol. 311:17–40. 2001. View Article : Google Scholar : PubMed/NCBI
31	Myers JS, Vincent BJ, Udall H, et al: A comprehensive analysis of recently integrated human Ta L1 elements. Am J Hum Genet. 71:312–326. 2002. View Article : Google Scholar : PubMed/NCBI
32	Mager DL and Freeman JD: HERV-H endogenous retroviruses: prescence in the New World branch but amplification in the Old World primate lineage. Virology. 213:395–404. 1995. View Article : Google Scholar : PubMed/NCBI
33	Lindeskog M, Mager DL and Blomberg J: Isolation of a human endogenous retroviral HERV-H element with an open env reading frame. Virology. 258:441–450. 1999. View Article : Google Scholar : PubMed/NCBI
34	Huang AY, Gulden PH, Woods AS, et al: The immunodominant major histocompatibility complex class I-restricted antigen of a murine colon tumor derives from an endogenous retroviral gene product. Proc Natl Acad Sci USA. 93:9730–9735. 1996. View Article : Google Scholar
35	Sin HS, Huh JH, Kim WY, et al: Long terminal repeats of human endogenous retrovirus H family provide alternative poly-adenylation signals to NADSYN1 gene. Korean J Genet. 29:395–401. 2007.