Comprehensive analysis of Alu-associated diversity on the human sex chromosomes

Gene

Volumn 317, Issue 1-2, 2003, Pages 103-110

  Callinan, Pauline A ^a   Hedges, Dale J ^a   Salem, Abdel Halim ^a,b   Xing, Jinchuan ^a   Walker, Jerilyn A ^a   Garber, Randall K ^a   Watkins, W Scott ^c   Bamshad, Michael J ^c,d   Jorde, Lynn B ^c   Batzer, Mark A ^a  

^a LOUISIANA STATE UNIVERSITY   (United States)

^b Suez Canal University Faculty of Medicine   (Egypt)

^c UNIVERSITY OF UTAH HEALTH SCIENCES CENTER   (United States)

^d UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

Author keywords

Identical by descent; Insertion polymorphism; Retroposon

Indexed keywords

ALU SEQUENCE; ANALYTIC METHOD; ANIMAL CELL; CHROMOSOME ANALYSIS; CONFERENCE PAPER; CONTROLLED STUDY; EVOLUTION; FEMALE; GENE IDENTIFICATION; GENE INSERTION; GENETIC MARKER; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOME ANALYSIS; GENOMICS; HUMAN; HUMAN CELL; HUMAN CHROMOSOME; MALE; NONHUMAN; POLYMERASE CHAIN REACTION; POPULATION RESEARCH; PRIORITY JOURNAL; RECOMBINANT GENE; SEX CHROMOSOME; X CHROMOSOME; Y CHROMOSOME;

INSERTION SEQUENCES;

EID: 10744230253     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(03)00662-0     Document Type: Conference Paper

References (38)

1. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410.
2. Arcot S.S., Adamson A.W., Risch G.W., LaFleur J., Robichaux M.B., Lamerdin J.E., Carrano A.V., Batzer M.A. High-resolution cartography of recently integrated human chromosome 19-specific Alu fossils. J. Mol. Biol. 281:1998;843-856.
3. Bamshad M., Kivisild T., Watkins W.S., Dixon M.E., Ricker C.E., Rao B.B., Naidu J.M., Prasad B.V., Reddy P.G., Rasanayagam A., Papiha S.S., Villems R., Redd A.J., Hammer M.F., Nguyen S.V., Carroll M.L., Batzer M.A., Jorde L.B. Genetic evidence on the origins of Indian caste populations. Genome Res. 11:2001;994-1004.
4. Batzer M.A., Deininger P.L. Alu repeats and human genomic diversity. Nat. Rev. Genet. 3:2002;370-379.
5. Batzer M.A., Kilroy G.E., Richard P.E., Shaikh T.H., Desselle T.D., Hoppens C.L., Deininger P.L. Structure and variability of recently inserted Alu family members. Nucleic Acids Res. 18:1990;6793-6798.
6. Batzer M.A., Deininger P.L., Hellmann-Blumberg U., Jurka J., Labuda D., Rubin C.M., Schmid C.W., Zietkiewicz E., Zuckerkandl E. Standardized nomenclature for Alu repeats. J. Mol. Evol. 42:1996;3-6.
7. Begun D.J., Whitley P. Reduced X-linked nucleotide polymorphism in Drosophila simulans. Proc. Natl. Acad. Sci. U. S. A. 97:2000;5960-5965.
8. Bird A.P. DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res. 8:1980;1499-1504.
9. Boeke J.D. LINEs and Alus - the polyA connection. Nat. Genet. 16:1997;6-7.
10. Boissinot S., Entezam A., Furano A.V. Selection against deleterious LINE-1-containing loci in the human lineage. Mol. Biol. Evol. 18:2001;926-935.
11. Carroll M.L., Roy-Engel A.M., Nguyen S.V., Salem A.H., Vogel E., Vincent B., Myers J., Ahmad Z., Nguyen L., Sammarco M., Watkins W.S., Henke J., Makalowski W., Jorde L.B., Deininger P.L., Batzer M.A. Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity. J. Mol. Biol. 311:2001;17-40.
12. Charlesworth B., Sniegowski P., Stephan W. The evolutionary dynamics of repetitive DNA in eukaryotes. Nature. 371:1994;215-220.
13. Deininger P.L., Batzer M.A. Evolution of retroposons. Evol. Biol. 27:1993;157-196.
14. Deininger P.L., Batzer M.A., Hutchison C.A. III, Edgell M.H. Master genes in mammalian repetitive DNA amplification. Trends Genet. 8:1992;307-311.
15. Erlandsson R., Wilson J.F., Paabo S. Sex chromosomal transposable element accumulation and male-driven substitutional evolution in humans. Mol. Biol. Evol. 17:2000;804-812.
16. Feng Q., Moran J.V., Kazazian H.H. Jr., Boeke J.D. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell. 87:1996;905-916.
17. Hammer M.F. A recent insertion of an alu element on the Y chromosome is a useful marker for human population studies. Mol. Biol. Evol. 11:1994;749-761.
18. Huang W., Chang B.H., Gu X., Hewett-Emmett D., Li W. Sex differences in mutation rate in higher primates estimated from AMG intron sequences. J. Mol. Evol. 44:1997;463-465.
19. Jorde L.B., Watkins W.S., Bamshad M.J., Dixon M.E., Ricker C.E., Seielstad M.T., Batzer M.A. The distribution of human genetic diversity: a comparison of mitochondrial, autosomal, and Y-chromosome data. Am. J. Hum. Genet. 66:2000;979-988.
20. Jurka J. Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc. Natl. Acad. Sci. U. S. A. 94:1997;1872-1877.
21. Jurka J., Krnjaic M., Kapitonov V., Stenger J.E., Kokhanyy O. Active Alu elements are passed primarily through paternal germ lines. Theor. Popul. Biol. 2002.
22. Kazazian H.H. Jr., Moran J.V. The impact of L1 retrotransposons on the human genome. Nat. Genet. 19:1998;19-24.
23. Labuda D., Striker G. Sequence conservation in Alu evolution. Nucleic Acids Res. 17:1989;2477-2491.
24. Lander E.S.et al. Initial sequencing and analysis of the human genome. Nature. 409(6822):2001;860-921.
25. Luan D.D., Korman M.H., Jakubczak J.L., Eickbush T.H. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell. 72:1993;595-605.
26. Miyamoto M.M., Slightom J.L., Goodman M. Phylogenetic relations of humans and African apes from DNA sequences in the psi eta-globin region. Science. 238:1987;369-373.
27. Nachman M.W. Patterns of DNA variability at X-linked loci in Mus domesticus. Genetics. 147:1997;1303-1316.
28. Nikaido M., Rooney A.P., Okada N. Phylogenetic relationships among cetartiodactyls based on insertions of short and long interspersed elements: hippopotamuses are the closest extant relatives of whales. Proc. Natl. Acad. Sci. U. S. A. 96:1999;10261-10266.
29. Nikaido M., Matsuno F., Hamilton H., Brownell R.L. Jr., Cao Y., Ding W., Zuoyan Z., Shedlock A.M., Fordyce R.E., Hasegawa M., Okada N. Retroposon analysis of major cetacean lineages: the monophyly of toothed whales and the paraphyly of river dolphins. Proc. Natl. Acad. Sci. U. S. A. 98:2001;7384-7389.
30. Roy-Engel A.M., Carroll M.L., Vogel E., Garber R.K., Nguyen S.V., Salem A.H., Batzer M.A., Deininger P.L. Alu insertion polymorphisms for the study of human genomic diversity. Genetics. 159:2001;279-290.
31. Roy-Engel A.M., Carroll M.L., El-Sawy M., Salem A.H., Garber R.K., Nguyen S.V., Deininger P.L., Batzer M.A. Non-traditional Alu evolution and primate genomic diversity. J. Mol. Biol. 316:2002;1033-1040.
32. Schmid C.W. Alu: structure, origin, evolution, significance and function of one-tenth of human DNA. Prog. Nucleic Acid Res. Mol. Biol. 53:1996;283-319.
33. Shedlock A.M., Okada N. SINE insertions: powerful tools for molecular systematics. Bioessays. 22:2000;148-160.
34. Sinnett D., Richer C., Deragon J.M., Labuda D. Alu RNA transcripts in human embryonal carcinoma cells. Model of post-transcriptional selection of master sequences. J. Mol. Biol. 226:1992;689-706.
35. Smit A.F. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr. Opin. Genet. Dev. 9:1999;657-663.
36. Wichman H.A., Van den Bussche R.A., Hamilton M.J., Baker R.J. Transposable elements and the evolution of genome organization in mammals. Genetica. 86:1992;287-293.
37. Xing J., Salem A.-H., Hedges D.J., Kilroy G.E., Watkins W.S., Schienman J.E., Stewart C.-B., Jurka J., Jorde L.B., Batzer M.A. Comprehensive analysis of two Alu Yd subfamilies. J. Mol. Evol. 2003;. in press.
38. Yu N., Zhao Z., Fu Y.X., Sambuughin N., Ramsay M., Jenkins T., Leskinen E., Patthy L., Jorde L.B., Kuromori T., Li W.H. Global patterns of human DNA sequence variation in a 10-kb region on chromosome 1. Mol. Biol. Evol. 18:2001;214-222.