Ancient retroviral insertions among human populations

Journal of Human Genetics

Volumn 51, Issue 4, 2006, Pages 353-362

  Herrera, Rene J ^a   Lowery, Robert K ^a   Alfonso, Abraham ^a   McDonald, John F ^c   Luis, Javier R ^a,b  

^a FLORIDA INTERNATIONAL UNIVERSITY   (United States)

^b UNIVERSITY OF VIGO   (Spain)

^c GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Endogenous retrovirus; Forensic; Genetic diversity; HERV K; HML 2; Human evolution; PRVI

Indexed keywords

ARTICLE; BIOGEOGRAPHIC REGION; CAMEROON; CHINA; EGYPT; FOSSIL; GENE FREQUENCY; GENE INSERTION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC MARKER; HUMAN; KENYA; LONG TERMINAL REPEAT; MULTIGENE FAMILY; NORMAL HUMAN; NUCLEOTIDE SEQUENCE; OMAN; PHYLOGENETIC TREE; POLYMERASE CHAIN REACTION; POLYMORPHIC LOCUS; POPULATION GENETICS; PROVIRUS; RETROVIRUS; RETROVIRUS INFECTION; RWANDA; TAIWAN; VIRUS GENOME;

ALLELES; DATA INTERPRETATION, STATISTICAL; DNA; ENDOGENOUS RETROVIRUSES; EVOLUTION, MOLECULAR; GENE FREQUENCY; GENETIC MARKERS; GENETICS, POPULATION; HETEROZYGOTE; HUMANS; MUTAGENESIS, INSERTIONAL; NUCLEIC ACID AMPLIFICATION TECHNIQUES; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; TERMINAL REPEAT SEQUENCES; VARIATION (GENETICS);

HUMAN ENDOGENOUS RETROVIRUSES;

EID: 33646458534     PISSN: 14345161     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10038-006-0370-0     Document Type: Article

References (47)

1. Antunez de Mayolo G, Antunez de Mayolo A, Antunez de Mayolo P, Papiha SS, Hammer M, Yunis JJ, Yunis EJ, Damodaran C, Martinez de Pancorbo M, Caeiro JL, Puzyrev VP, Herrera RJ (2002) Phylogenetics of worldwide human populations as determined by polymorphic Alu insertions. Electrophoresis 23:3346-3356
2. Barbulescu M, Turner G, Seaman MI, Deinard AS, Kidd K, Lenz J (1999) Many human endogenous retrovirus K (HERV-K) proviruses are unique to humans. Curr Biol 9:861-868
3. Black WC IV (1997) BIOSYS-2. A computer program for the analysis of allelic variation in genetics. Colorado State University, Ft. Collins, CO
4. Bock M, Stoye JP (2000) Endogenous retroviruses and the human germline. Curr Opin Genet Dev 10:651-655
5. Brosius J (1999) RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 238:115-134
6. Buzdin A, Ustyugova S, Khodosevich K, Mamedov I, Lebedev Y, Hunsmann G, Sverdlov E (2003) Human-specific subfamilies of HERV-K (HML-2) long terminal repeats: three master genes were active simultaneously during branching of hominoid lineages. Genomics 81:149-156
7. Carmody G (1991) G-Test. Department of Biology, Carleton University. Ottawa
8. Cavalli-Sforza LL, Menozzi P, Piazza A (1994) The history and geography of human genes. Princeton University Press, New Jersey
9. Chen CK, Burns ME, He W, Wensel TG, Baylor DA, Simon MI (2000) Slowed recovery of rod photoresponse in mice lacking the GTPase accelerating protein RGS9-1. Nature 403:557-560
10. Cinnioglu C, King R, Kivisild T, Kalfoglu E, Atasoy S, Cavalleri GL, Lillie AS, Roseman CC, Lin AA, Prince K, Oefner PJ, Shen P, Semino O, Cavalli-Sforza LL, Underbill PA (2004) Excavating Y-chromosome haplotype strata in Anatolia. Hum Genet 114:127-48
11. Desmarais D, Zhong Y, Chakraborty R, Perreault C, Busque L (1998) Development of a highly polymorphic STR marker for identity testing purposes at the human androgen receptor gene (HUMARA). J Forensic Sci 43:1046-1049
12. Dunn CA, Medstrand P, Mager DL (2003) An endogenous retroviral long terminal repeat is the dominant promoter for human β1,3- galactosyltransferase 5 in the colon. Proc Natl Acad Sci USA 100:12841-12846
13. Felsenstein J (1989) PHYLIP: phylogeny interference package. Cladistics 5:164-166
14. Gregorius HR (1984) A unique genetic distance. Biometrics J 26:13-18
15. Hammer MF, Redd AJ, Wood ET, Bonner MR, Jarjanazi H, Karafet T, Santachiara-Benerecetti S, Oppenheim A, Jobling MA, Jenkins T, Ostrer H, Bonne-Tamir B (2000) Jewish and Middle Eastern non-Jewish populations share a common pool of Y-chromosome biallelic haplotypes. Proc Natl Acad Sci USA 97:6769-6774
16. Harpending HC, Ward RH (1982) Chemical systematics and human population. In: Nitecki M (ed) Biochemical aspects of evolutionary biology. University of Chicago Press, Chicago, pp 213-252
17. Hughes JF, Coffin JM (2004) Human endogenous retrovirus K solo-LTR formation and insertional polymorphisms: implications for human and viral evolution. Proc Natl Acad Sci USA 101:1668-1672
18. Johnson WE, Coffin JM (1999) Constructing primate phylogenies from ancient retroviral sequences. Proc Natl Acad Sci USA 96:10254-10260
19. Jordan K, McDonald JF (2002) A biologically active family of human endogenous retroviruses evolved from an ancient inactive lineage. Genome Lett 1:1-5
20. King R, Underbill PA (2002) Congruent distribution of Neolithic painted pottery and ceramic figurines with Y-chromosome lineages. Antiquity 76:707-714
21. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W et al (2001) International Human Genome Sequencing Consortium: Initial sequencing and analysis of the human genome. . Nature 409:860-921
22. Lavie L, Medstrand P, Schempp W, Meese E, Mayer J (2004) Human endogenous retrovirus family HERV-K (HML-5): status, evolution, and reconstruction of an ancient betaretrovirus in the human genome. J Virol 78:8788-8798
23. Leib-Mosch C, Seifarth W (1996) Evolution and biological significance of human retroelements. Virus Genes 11:133-145
24. Li CC (1976) First course in population genetics. Boxwood Press, Pacific Grove, CA
25. Löwer R, Löwer J, Kurth R (1996) The viruses in all of us: characteristics and biological significance of human endogenous retrovirus sequences. Proc Natl Acad Sci USA 93:5177-5184
26. Löwer R (1999) The pathogenic potential of endogenous retroviruses: facts and fantasies. Trends Microbiol 7:350-356
27. Macfarlane C, Simmonds P (2004) Allelic variation of HERV-K(HML-2) endogenous retroviral elements in human populations. J Mol Evol 59:642-56
28. Mamedov I, Lebedev Y, Hunsmann G, Khusnutdinova, Sverdlov E (2004) A rare event of insertion polymorphism of a HERV-K LTR in the human genome. Genomics 84:596-599
29. Mariani-Costantini R, Horn TM, Callahan R (1989) Ancestry of a human endogenous retrovirus family. J Virol 63:4982-4985
30. Mayer J, Stuhr T, Reus K, Maldener E, Kitova M, Asmus F, Meese E (2005) Haplotype analysis of the human endogenous retrovirus locus HERV-K(HML-2.HOM) and its evolutionary implications. J Mol Evol 61:706-715
31. McDonald J (1995) Transposable elements: possible catalysts of organismic evolution. Trends Ecol Evol 10:23-26
32. Medstrand P, Mager D (1998) Human-specific integrations of the HERV-K endogenous retrovirus family. J Virol 72:9782-9787
33. Nei M, Roychoudhury AK (1974) Genetic variation within and between the three major races of man, Caucasoids, Negroids, and Mongoloids. Am J Hum Genet 26:421-443
34. Novick GE, Novick CC, Yunis E, Yunis J, Antunez de Mayolo P, Scheer WD, Deininger PL, Stoneking M, Batzer MA, Herrera RJ (1998) On the oriental origin of Native American populations. Hum Biol 70:23-39
35. Ota T (1993) DISPAN genetic distance and phylogenetic analysis. Pennsylvania State University
36. Patience C, Wilkinson DA, Weiss RA (1997) Our retroviral heritage. Trends Genet 13:116-120
37. Reus K, Mayer J, Sauter M, Zischler H, Muller-Lantzsch N, Meese E (2001) HERV-K (OLD): ancestor sequences of the human endogenous retrovirus family HERV-K (HML-2). J Virol 75:8917-8926
38. Rohlf FJ (1993) NTSYS-pc. Numerical taxonomy and multivariate analysis system. Exeter Software, New York
39. Sambrook J, Fritsch E, Maniatis T (1989) Molecular cloning:a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
40. Semino O, Magri C, Benuzzi G, Lin AA, Al-Zahery N, Battaglia V, Maccioni L, Triantaphyllidis C, Shen P, Oefner PJ, Zhivotovsky LA, King R, Torroni A, Cavalli-Sforza LL, Underhill PA, Santachiara-Benerecetti AS (2004) Origin, diffusion, and differentiation of Y-chromosome haplogroups E and J:inferences on the neolithization of Europe and later migratory events in the Mediterranean area. Am J Hum Genet 74:1023-1034
41. Smit AFA (1996) The origin of interspersed repeats in the human genome. Curr Opin Genet Dev 6:743-748
42. Sverdlov ED (2000) Retroviruses and primate evolution. Bioessays 22:161-171
43. Tristem M (2000) Identification and characterization of novel human endogenous retrovirus families by phylogenetic screening of the human genome mapping project database. J Virol 74:3715-3730
44. Turner G, Barbulescu M, Su M, Seaman MI, Kidd KK, Lenz J (2001) Insertional polymorphisms of full-length endogenous retroviruses in humans. Curr Biol 11:1531-1535
45. Villareal LP (1997) On viruses, sex and motherhood. J Virol 71:859-865
46. Von Sternberg RM, Novick GE, Gao GP, Herrera RJ (1992) Genome canalization: the coevolution of transposable and interspersed repetitive elements with single copy DNA. Genetica 86:215-246
47. Wilkinson DA, Mager DL, Leong J-A (1994) Endogenous human retroviruses. In: Levy JA (ed) The Retroviridae, vol 3. Plenum, New York, pp 465-534