Batzer and Deininger 2002 Nature Reviews Genetics

Genetica 107 149161 1999 46 roy engel a m et al alu

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Unformatted text preview: A. & Deininger, P. L. cDNAs derived from primary and small cytoplasmic Alu (scAlu) transcripts. J. Mol. Biol. 271, 222–234 (1997). Carroll, M. L. 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). 45. Roy, A. M. et al. Recently integrated human Alu repeats: finding needles in the haystack. Genetica 107, 149–161 (1999). 46. Roy-Engel, A. M. et al. Alu insertion polymorphisms for the study of human genomic diversity. Genetics 159, 279–290 (2001). 47. Shen, M. R., Batzer, M. A. & Deininger, P. L. Evolution of the master Alu gene(s). J. Mol. Evol. 33, 311–320 (1991). 48. Deininger, P. L. & Batzer, M. A. Alu repeats and human disease. Mol. Genet. Metab. 67, 183–193 (1999). This article provides an overview of the data that show a role for Alu elements in human genetic instability and disease. 49. Misra, S. & Rio, D. C. Cytotype control of Drosophila P element transposition: the 66 kd protein is a repressor of transposase activity. Cell 62, 269–284 (1990). 50. Deininger, P. L. & Slagel, V. K. Recently amplified Alu family members share a common parental Alu sequence. Mol. Cell. Biol. 8, 4566–4569 (1988). 51. Batzer, M. A. & Deininger, P. L. A human-specific subfamily of Alu sequences. Genomics 9, 481–487 (1991). 52. Matera, A. G., Hellmann, U. & Schmid, C. W. A transpositionally and transcriptionally competent Alu subfamily. Mol. Cell. Biol. 10, 5424–5432 (1990). 53. Batzer, M. A. et al. Amplification dynamics of human-specific (HS) Alu family members. Nucleic Acids Res. 19, 3619–3623 (1991). 54. Batzer, M. A. et al. Dispersion and insertion polymorphism in two small subfamilies of recently amplified human Alu repeats. J. Mol. Biol. 247, 418–427 (1995). 55. Jurka, J. A new subfamily of recently retroposed human Alu repeats. Nucleic Acids Res. 21, 2252 (1993). 56. Leeflang, E. P., Chesnokov, I. N. & Schmid, C. W. Mobility of short interspersed repeats within the chimpanzee lineage. J. Mol. Evol. 37, 566–572 (1993). 57. Leeflang, E. P., Liu, W. M., Chesnokov, I. N. & Schmid, C. W. Phylogenetic isolation of a human Alu founder gene: drift to new subfamily identity. J. Mol. Evol. 37, 559–565 (1993). 58. Leeflang, E. P., Liu, W. M., Hashimoto, C., Choudary, P. V. & Schmid, C. W. Phylogenetic evidence for multiple Alu source genes. J. Mol. Evol. 35, 7–16 (1992). 59. Batzer, M. A. et al. African origin of human-specific polymorphic Alu insertions. Proc. Natl Acad. Sci. USA 91, 12288–12292 (1994). This paper shows the use of Alu elements for the study of human population genetics and includes the first comprehensive survey of Alu-insertionpolymorphism-related human variation. 60. Perna, N. T., Batzer, M. A., Deininger, P. L. & Stoneking, M. Alu insertion polymorphism: a new type of marker for human population studies. Hum. Biol. 64, 641–648 (1992). 61. Arcot, S. S. et al. Alu fossil relics — distribution and insertion polymorphism. Genome Res. 6, 1084–1092 (1996). 62. Bamshad, M. et al. Genetic evidence on the origins of Indian caste populations. Genome Res. 11, 994–1004 (2001). 63. Batzer, M. A. et al. Genetic variation of recent Alu insertions in human populations. J. Mol. Evol. 42, 22–29 (1996). 64. Comas, D. et al. Alu insertion polymorphisms in NW Africa and the Iberian Peninsula: evidence for a strong genetic boundary through the Gibraltar Straits. Hum. Genet. 107, 312–319 (2000). 65. Jorde, L. B. et al. The distribution of human genetic diversity: a comparison of mitochondrial, autosomal, and Ychromosome data. Am. J. Hum. Genet. 66, 979–988 (2000). 66. Nasidze, I. et al. Alu insertion polymorphisms and the genetic structure of human populations from the Caucasus. Eur. J. Hum. Genet. 9, 267–272 (2001). 67. Novick, G. E. et al. Polymorphic Alu insertions and the Asian origin of Native American populations. Hum. Biol. 70, 23–39 (1998). 68. Sherry, S. T., Harpending, H. C., Batzer, M. A. & Stoneking, M. Alu evolution in human populations: using the coalescent 378 | M AY 2002 | VOLUME 3 © 2002 Nature Publishing Group REVIEWS to estimate effective population size. Genetics 147, 1977–1982 (1997). Stoneking, M. et al. Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa. Genome Res. 7, 1061–1071 (1997). Watkins, W. S. et al. Patterns of ancestral human diversity: an analysis of Alu-insertion and restriction-site polymorphisms. Am. J. Hum. Genet. 68, 738–752 (2001). 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, 749–761 (1994). Shimamura, M. et al. Molecular evidence from retroposons that whales form a clade within even-toed ungulates. Nature 388, 666–670 (1997). In this manuscript, the authors use SINE insertions to study the phylogenetic origin of whales. Nikaido, M., Rooney, A. P. & Okada, N...
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