Active Alu element "A-tails": Size does matter

Genome Research

Volumn 12, Issue 9, 2002, Pages 1333-1344

  Roy Engel, Astrid M ^a   Salem, Abdel Halim ^b,c   Oyeniran, Oluwatosin O ^a   Deininger, Lisa ^a   Hedges, Dale J ^b   Kilroy, Gail E ^b   Batzer, Mark A ^b   Deininger, Prescott L ^a,d  

^a TULANE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b LOUISIANA STATE UNIVERSITY   (United States)

^c Suez Canal University Faculty of Medicine   (Egypt)

^d OCHSNER MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE;

ALU SEQUENCE; CONTROLLED STUDY; GENE ACTIVITY; GENE AMPLIFICATION; GENE FUNCTION; GENE INSERTION SEQUENCE; GENE LOCUS; GENETIC ANALYSIS; GENETIC MODEL; GENETIC VARIABILITY; GENOME SIZE; HUMAN; HUMAN GENOME; LONG INTERSPERSED REPEAT; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; POISSON DISTRIBUTION; PRIORITY JOURNAL; RETROPOSON; REVIEW; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SHORT INTERSPERSED REPEAT;

3' FLANKING REGION; ALU ELEMENTS; BASE COMPOSITION; BASE SEQUENCE; DATABASES, GENETIC; DNA; GENE EXPRESSION REGULATION; GENES, NEUROFIBROMATOSIS 1; GENETIC MARKERS; GENETICS, POPULATION; GENOME, HUMAN; HUMANS; LONG INTERSPERSED NUCLEOTIDE ELEMENTS; MALE; MOLECULAR SEQUENCE DATA; POLY A; TERMINAL REPEAT SEQUENCES; VARIATION (GENETICS);

INSERTION SEQUENCES; UNIDENTIFIED INSERTION SEQUENCE;

EID: 0036737222     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.384802     Document Type: Review

References (77)

1. Abdelhak, S., Kalatzis, V., Heilig, R., Compain, S., Samson, D., Vincent, C., Levi-Acobas, F., Cruaud, C., Le Merrer, M., Mathieu, M., et al. 1997. Clustering of mutations responsible for branchio-oto-renal (BOR) syndrome in the eyes absent homologous region (eyaHR) of EYA1. Hum. Mol. Genet. 6: 2247-2255.
2. Alemán, C., Roy-Engel, A.M., Shaikh, T.H., and Deininger, P.L. 2000. Cis-acting influences on Alu RNA levels. Nucleic Acids Res. 28: 4755-4761.
3. Arcot, S.S., Wang, Z., Weber, J.L., Deininger, P.L., and Batzer, M.A. 1995. Alu repeats: A source for the genesis of primate microsatellites. Genomics 29: 136-144.
4. Batzer, M.A. and Deininger, P.L. 1991. A human-specific subfamily of Alu sequences. Genomics 9: 481-487.
5. Batzer, M.A. and Deininger, P.L. 2002. Alu repeats and human genomic diversity. Nat. Rev. Genet. 3: 370-379.
6. Batzer, M.A., Kilroy, G.E., Richard, P.E., Shaikh, T.H., Desselle, T.D., Hoppens, C.L., and Deininger, P.L. 1990. Structure and variability of recently inserted Alu family members. Nucleic Acids Res. 18: 6793-6798.
7. Batzer, M.A., Bazan, H.A., Kim, J., Morrow, S.L., Shaikh, T.H., Arcot, S.S., and Deininger, P.L. 1992. Large-scale subcloning of bacteriophage λ ZAP clones. Biotechniques 12: 370-371.
8. Boeke, J.D. 1997. LINEs and Alus - The polyA connection. Nat. Genet. 16: 6-7.
9. Boissinot, S., Chevret, P., and Furano, A.V. 2000. L1 (LINE-1) retrotransposon evolution and amplification in recent human history. Mol. Biol. Evol. 17: 915-928.
10. Borodulina, O.R., and Kramerov, D.A. 2001. Short interspersed elements (SINEs) from insectivores. Two classes of mammalian SINEs distinguished by A-rich tail structure. Mamm. Genome 12: 779-786.
11. Bovia, F. and Strub, K. 1996. The signal recognition particle and related small cytoplasmic ribonucleoprotein particles. J. Cell Sci. (Pt 11) 109: 2601-2608.
12. Calabrese, P.P., Durrett, R.T., and Aquadro, C.F. 2001. Dynamics of microsatellite divergence under stepwise mutation and proportional slippage/point mutation models. Genetics 159: 839-852.
13. Cambien, F., Poirier, O., Lecerf, L., Evans, A., Cambou, J.P., Arveiler, D., Luc, G., Bard, J.M., Bara, L., Ricard, S., et al. 1992. Deletion polymorphism in the gene for angiotensin-converting enzyme is a potent risk factor for myocardial infarction. Nature 359: 641-644.
14. 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., et al. 2001. Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity. J. Mol. Biol. 311: 17-40.
15. Chang, D.Y., Hsu, K., and Maraia, R.J. 1996. Monomeric scAlu and nascent dimeric Alu RNAs induced by adenovirus are assembled into SRP9/14-containing RNPs in HeLa cells. Nucleic Acids Res. 24: 4165-4170.
16. Chen, Y., Sinha, K., Perumal, K., Gu, J., and Reddy, R. 1998. Accurate 3′ end processing and adenylation of human signal recognition particle RNA and alu RNA in vitro. J. Biol. Chem. 273: 35023-35031.
17. Chu, W.M., Liu, W.M., and Schmid, C.W. 1995. RNA polymerase III promoter and terminator elements affect Alu RNA expression. Nucleic Acids Res. 23: 1750-1757.
18. Cubero, E., Luque, F.J., and Orozco, M. 2001. Theoretical studies of d(A:T)-based parallel-stranded DNA duplexes. J. Am. Chem. Soc. 123: 12018-12025.
19. Deininger, P.L. and Batzer, M.A. 1995. SINE master genes and population biology. In The impact of short, interspersed elements (SINEs) on the host genome (ed. R. Maraia), pp. 43-60. R.G. Landes, Georgetown, TX.
20. Deininger, P.L. and Batzer, M.A. 1999. Alu repeats and human disease. Mol. Genet. Metab. 67: 183-193.
21. Deininger, P.L. and Daniels, G. 1986. The recent evolution of mammalian repetitive DNA elements. Trends Genet. 2: 76-80.
22. Deininger, P.L., Jolly, D., Rubin, C., Friedmann, T., and Schmid, C.W. 1981. Base sequence studies of 300 nucleotide renatured repeated human DNA clones. J. Mol. Biol. 151: 17-33.
23. Deininger, P.L., Batzer, M.A., Hutchison, C.A., and Edgell, M.H. 1992. Master genes in mammalian repetitive DNA amplification. Trends Genet. 8: 307-311.
24. Deininger, P.L., Tiedge, H., Kim, J., and Brosius, J. 1996. Evolution, expression, and possible function of a master gene for amplification of an interspersed repeated DNA family in rodents. In Progress in nucleic acid research and molecular biology (eds. W.E. Cohn and K. Moldave), pp. 67-88. Academic Press, San Diego.
25. Divoky, V., Indrak, K., Mrug, M., Brabec, V., Huisman, T.H.J., and Prchal, J.T. 1996. A novel mechanism of β-thalassemia. The insertion of L1 retrotransposable element in β globin IVSII. Blood 88: 148a.
26. Economou, E.P., Bergen, A.W., Warren, A.C., and Antonarakis, S.E. 1990. The polydeoxyadenylate tract of Alu repetitive elements is polymorphic in the human genome. Proc. Natl. Acad. Sci. 87: 2951-2954.
27. Economou-Pachnis, A. and Tsichlis, P.N. 1985. Insertion of an Alu SINE in the human homologue of the Mlvi-2 locus. Nucleic Acids Res. 13: 8379-8387.
28. Englander, E.W., Wolffe, A.P., and Howard, B.H. 1993. Nucleosome interactions with a human Alu element. Transcriptional repression and effects of template methylation. J. Biol. Chem. 268: 19565-19573.
29. Feng, Q., Moran, J.V., Kazazian, Jr., H.H., and Boeke, J.D. 1996. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87: 905-916.
30. Gingras, A.C., Raught, B., and Sonenberg, N. 1999. eIF4 initiation factors: Effectors of mRNA recruitment to ribosomes and regulators of translation. Annu. Rev. Biochem. 68: 913-963.
31. Goncalves, I., Duret, L., and Mouchiroud, D. 2000. Nature and structure of human genes that generate retropseudogenes. Genome Res. 10: 672-678.
32. Harrison, P.M., Hegyi, H., Balasubramanian, S., Luscombe, N.M., Bertone, P., Echols, N., Johnson, T., and Gerstein, M. 2002. Molecular fossils in the human genome: Identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res. 12: 272-280.
33. Hizver, J., Rozenberg, H., Frolow, F., Rabinovich, D., and Shakked, Z. 2001. DNA bending by an adenine-thymine tract and its role in gene regulation. Proc. Natl. Acad. Sci. 98: 8490-8495.
34. Hsu, K., Chang, D.Y., and Maraia, R.J. (1995). Human signal recognition particle (SRP) Alu-associated protein also binds Alu interspersed repeat sequence RNAs. Characterization of human SRP9. J. Biol. Chem. 270: 10179-10186.
35. Jagadeeswaran, P., Forget, B.G., and Weissman, S.M. 1981. Short, interspersed repetitive DNA elements in eukaryotes: Transposable DNA elements generated by reverse transcription of RNA pol III transcripts? Cell 26: 141-142.
36. Jurka, J. and Pethiyagoda, C. 1995. Simple repetitive DNA sequences from primates: Compilation and analysis. J. Mol. Evol. 40: 120-126.
37. Kass, D.H., Kim, J., and Deininger, P.L. 1996. Sporadic amplification of ID elements in rodents. J. Mol. Evol. 42: 7-14.
38. Kim, J., Martignetti, J.A., Shen, M.R., Brosius, J., and Deininger, P.L. 1994. The rodent BC1 RNA gene is a master gene for ID element amplification. Proc. Natl. Acad. Sci. 91: 3607-3611.
39. Labuda, D. and Zietkiewicz, E. 1994. Evolution of secondary structure in the family of 7SL-like RNAs. J. Mol. Evol. 39: 506-518.
40. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
41. Lester, T., McMahon, C., VanRegemorter, N., Jones, A., and Genet, S. 1997. X-linked immunodeficiency caused by insertion of Alu repeat sequences. J. Med. Gen. Suppl. 34: S81.
42. Li, X., Scaringe, W.A., Hill, K.A., Roberts, S., Mengos, A., Careri, D., Pinto, M.T., Kasper, C.K., and Sommer, S.S. 2001. Frequency of recent retrotransposition events in the human factor IX gene. Hum. Mutat. 17: 511-519.
43. Lisitsky, I., Rott, R., and Schuster, G. 2001. Insertion of polydeoxyadenosine-rich sequences into an intergenic region increases transcription in Chlamydomonas reinhardtii chloroplasts. Planta 212: 851-857.
44. Liu, W.M. and Schmid, C.W. 1993. Proposed roles for DNA methylation in Alu transcriptional repression and mutational inactivation. Nucleic Acids Res. 21: 1351-1359.
45. Matera, A.G., Hellmann, U., and Schmid, C.W. 1990. A transpositionally and transcriptionally competent Alu subfamily. Mol. Cell. Biol. 10: 5424-5432.
46. Mathias, S.L., Scott, A.F., Kazazian Jr., H.H., Boeke, J.D., and Gabriel, A. 1991. Reverse transcriptase encoded by a human transposable element. Science 254: 1808-1810.
47. McConnell, K.J. and Beveridge, D.L. 2001. Molecular dynamics simulations of B'-DNA: Sequence effects on A-tract-induced bending and flexibility. J. Mol. Biol. 314: 23-40.
48. Miki, Y., Nishisho, I., Horii, A., Miyoshi, Y., Utsunomiya, J., Kinzler, K.W., Vogelstein, B., and Nakamura, Y. 1992. Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer. Cancer Res. 52: 643-645.
49. Montermini, L., Andermann, E., Labuda, M., Richter, A., Pandolfo, M., Cavalcanti, F., Pianese, L., Iodice, L, Farina, G., Monticelli, A., et al. 1997. The Friedreich ataxia GAA triplet repeat: Premutation and normal alleles. Hum. Mol. Genet. 6; 1261-1266.
50. Moran, J.V., Holmes, S.E., Naas, T.P., DeBerardinis, R.J., Boeke, J.D., and Kazazian Jr., H.H. 1996. High frequency retrotransposition in cultured mammalian cells. Cell 87: 917-927.
51. Muddashetty, R.S., Khanam, T., Kondrashov, A., Bundman, M., Iacoangeli, A., Kremershothen, J., Cuning, K., Barnekow, A., Huttenhoffer, A., Tiedge, H., et al. 2002. Poly(A) binding protein is associated with neuronal BC1 and BC200 ribonucleoprotein particles. J. Mol. Biol. (in press).
52. Mustajoki, S., Ahola, H., Mustajoki, P., and Kauppinen, R. 1999. Insertion of Alu element responsible for acute intermittent porphyria. Hum. Mutat. 13: 431-438.
53. Naas, T.P., DeBerardinis, R.J., Moran, J.V., Ostertag, E.M., Kingsmore, S.F., Seldin, M.F., Hayashizaki, Y., Martin, S.L., and Kazazian, H.H. 1998. An actively retrotransposing, novel subfamily of mouse L1 elements. EMBO J. 17: 590-597.
54. Ovchinnikov, I., Troxel, A.B., and Swergold, G.D. 2001. Genomic characterization of recent human LINE-1 insertions: Evidence supporting random insertion. Genome Res. 11: 2050-2058.
55. Prak, E.T. and Kazazian Jr., H.H. 2000. Mobile elements and the human genome. Nat. Rev. Genet. 1: 134-144.
56. Rogers, J.H. and Willison, K.R. 1983. A major rearrangement in the H-2 complex of mouse t haplotypes. Nature 304: 549-552.
57. Rowe, S.M., Coughlan, S.J., McKenna, N.J., Garrett, E., Kieback, D.G., Carney, D.N., and Headon, D.R. 1995. Ovarian carcinoma-associated TaqI restriction fragment length polymorphism in intron G of the progesterone receptor gene is due to an Alu sequence insertion. Cancer Res. 55: 2743-2745.
58. Roy, A.M., Carroll, M.L., Nguyen, S.V., Salem, A.H., Oldridge, M., Wilkie, A.O., Batzer, M.A., and Deininger, P.L. 2000. Potential gene conversion and source genes for recently integrated Alu elements. Genome Res. 10: 1485-1495.
59. Roy-Engel, A.M., Carroll, M.L., Vogel, E., Garber, R.K., Nguyen, S.V., Salem, A.H., Batzer, M.A., and Deininger, P.L. 2001. Alu insertion polymorphisms for the study of human genomic diversity. Genetics 159: 279-290.
60. Sapienza, C. and St Jacques, B. 1986. 'Brain-specific' transcription and evolution of the identifier sequence. Nature 319: 418-420.
61. Schmid, C.W., and Maraia, R. 1992. Transcriptional regulation and transpositional selection of active SINE sequences. Curr. Opin. Genet. Dev. 2: 874-882.
62. Schwahn, U., Lenzner, S., Dong, J., Feil, S., Hinzmann, B., van Duijnhoven, G., Kirschner, R., Hemberger, M., Bergen, A.A., Rosenberg, T., et al. 1998. Positional cloning of the gene for X-linked retinitis pigmentosa 2. Nat. Genet. 19: 327-332.
63. Shaikh, T.H. and Deininger, P.L. 1996. The role and amplification of the HS Alu subfamily founder gene. J. Mol. Evol. 42: 15-21.
64. Shaikh, T.H., Roy, A.M., Kim, J., Batzer, M.A., and Deininger, P.L. 1997. cDNAs derived from primary and small cytoplasmic Alu (scAlu) transcripts. J. Mol. Biol. 271: 222-234.
65. Sheen, F.M., Sherry, S.T., Risch, G.M., Robichaux, M., Nasidze, I., Stoneking, M., Batzer, M.A., and Swergold, G.D. 2000. Reading between the LINEs: Human genomic variation induced by LINE-1 retrotransposition. Genome Res. 10: 1496-1508.
66. Shen, M.R., Batzer, M.A., and Deininger, P.L. 1991. Evolution of the master Alu gene(s). J. Mol. Evol. 33: 311-320.
67. Smith, B.L., Gallie, D.R., Le, H., and Hansma, P.K. 1997. Visualization of poly(A)-binding protein complex formation with poly(A) RNA using atomic force microscopy. J. Struct. Biol. 119: 109-117.
68. Sukarova, E., Dimovski, A.J., Tchacarova, P., Petkov, G.H., and Efremov, G.D. 2001. An Alu insert as the cause of a severe form of hemophilia A. Acta Haematol. 106: 126-129.
69. Wallace, M.R., Andersen, L.B., Saulino, A.M., Gregory, P.E., Glover, T.W., and Collins, F.S. 1991. A de novo Alu insertion results in neurofibromatosis type 1. Nature 353: 864-866.
70. Walter, P. and Johnson, A.E. 1994. Signal sequence recognition and protein targeting to the endoplasmic reticulum membrane. Annu. Rev. Cell Biol. 10: 87-119.
71. Wang, T., Lerer, I., Gueta, Z., Sagi, M., Kadouri, L., Peretz, T., and Abeliovich, D. 2001. A deletion/insertion mutation in the BRCA2 gene in a breast cancer family: A possible role of the Alu-polyA tail in the evolution of the deletion. Genes Chromosomes Cancer 31: 91-95.
72. Wei, W., Gilbert, N., Ooi, S.L., Lawler, J.F., Ostertag, E.M., Kazazian, H.H., Boeke, J.D., and Moran, J.V. 2001. Human L1 retrotransposition: Cis preference versus trans complementation. Mol. Cell Biol. 21: 1429-1439.
73. Weiner, A., Deininger, P., and Efstradiatis, A. 1986. The reverse flow of genetic information: Pseudogenes and transposable elements derived from nonviral cellular RNA. Annu. Rev. Biochem. 55: 631-661.
74. West, N.C., Roy-Engel, A.M., Imataka, H., Sonenberg, N., and Deininger, P.L. 2002. Shared components of SINE RNPs. J. Mol. Biol. (in press).
75. Woods-Samuels, P., Wong, C., Mathias, S.L., Scott, A.F., Kazazian Jr., H.H., and Antonarakis, S.E. 1989. Characterization of a nondeleterious L1 insertion in an intron of the human factor VIII gene and further evidence of open reading frames in functional L1 elements. Genomics 4: 290-296.
76. Wulff, K., Gazda, H., Schroder, W., Robicka-Milewska, R., and Herrmann, F.H. 2000. Identification of a novel large F9 gene mutation - An insertion of an Alu repeated DNA element in exon e of the factor 9 gene. Hum. Mutat. 15: 299.
77. Yoshida, K., Nakamura, A., Yazaki, M., Ikeda, S., and Takeda, S. 1998. Insertional mutation by transposable element, L1, in the DMD gene results in X-linked dilated cardiomyopathy. Hum. Mol. Genet. 7: 1129-1132.