SINEs and LINEs share common 3' sequences: A review

Gene

Volumn 205, Issue 1-2, 1997, Pages 229-243

  Okada, Norihiro ^a   Hamada, Mitsuhiro ^a   Ogiwara, Ikuo ^a   Ohshima, Kazuhiko ^a  

^a TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

LINE; Retroposon; Reverse transcriptase; SINE

Indexed keywords

REPETITIVE DNA;

CONFERENCE PAPER; CONSENSUS SEQUENCE; DNA SEQUENCE; FISH; MAMMAL; NONHUMAN; PLANT; PRIORITY JOURNAL; RETROPOSON; TURTLE;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; DNA, COMPLEMENTARY; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; RETROELEMENTS; SEQUENCE HOMOLOGY, AMINO ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID;

ARIA; MAMMALIA; TESTUDINES;

EID: 0031593205     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(97)00409-5     Document Type: Conference Paper

References (80)

1. Adams, D.S., Eickbush, T.H., Herrera, R.J., Lizardi, P.M., 1986. A highly reiterated family of transcribed oligo(A)-terminated, interspersed DNA elements in the genome of Bombyx mori. J. Mol. Biol. 187, 465-478.
2. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J., 1990. Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
3. Bogenhagen, D.F., Brown, D.D., 1981. Nucleotide sequences in Xenopus 5S DNA required for transcription termination. Cell 24, 261-270.
4. Britten, R.J., Baron, W.F., Stout, D.B., Davidson, E.H., 1988. Sources and evolution of human Alu repeated sequences. Proc. Natl. Acad. Sci. USA 85, 4770-4774.
5. Burch, J.B.E., Davis, D.L., Hass, N.B., 1993. Chicken repeat 1 elements contain a pol-like open reading frame and belong to the non-long terminal repeat class of retrotransposons. Proc. Natl. Acad. Sci. USA 90, 8199-8203.
6. Burke, W.D., Eickbush, D.G., Xiong, Y., Jakubczak, J., Eickbush, T.H., 1993. Sequence relationship of retrotransposable elements R1 and R2 within and between divergent insect species. Mol. Biol. Evol. 10, 163-185.
7. Cozzarelli, N.R., Gerrard, S.P., Schlissel, M., Brown, D.D., Bogenhagen, D.F., 1983. Purified RNA polymerase III accurately and efficiently terminates transcription of 5S RNA genes. Cell 34, 829-835.
8. Danilevskaya, O.N., Arkhipova, I.R., Traverse, K.L., Pardue, M.L., 1997. Promoting in tandem: the promoter for telomere transposon HeT-A and implications for the evolution of retroviral LTRs. Cell 88, 647-655.
9. Degen, S.J.F, Davie, E.W., 1987. Nucleotide sequence of the gene for human prothrombin. Biochemistry 26, 6165-6177.
10. Deininger, P.L., Batzer, M.A., Hutchison, III, C.A., Edgell, M.H., 1992. Master genes in mammalian repetitive DNA amplification. Trends Genet. 8, 307-311.
11. Doolittle, R.F., Feng, D.-F., Johnson, M.S., McClure, M.A., 1989. Origins and evolutionary relationships of retroviruses. Quart. Rev. Biol. 64, 1-30.
12. Duncan, C.H., 1987. Novel Alu-type repeat in artiodactyls. Nucleic Acids Res. 15, 1340
13. Eickbush, T.H., 1992. Transposing without ends: the non-LTR retrotransposable elements. New Biol. 4, 430-440.
14. Eickbush, T.H., 1994. Origin and evolutionary relationships of retroelements. In: S.S. Morse (Ed.), The Evolutionary Biology of Viruses. Raven Press, New York, pp. 121-157.
15. Endoh, H., Nagahashi, S., Okada, N., 1990. A highly repetitive and transcribable sequence in the tortoise genome is probably a retroposon. Eur. J. Biochem. 189, 25-31.
16. Endoh, H., Okada, N., 1986. Total DNA transcription in vitro: a procedure to detect highly repetitive and transcribable sequences with tRNA-like structures. Proc. Natl. Acad. Sci. USA 83, 251-255.
17. Fanning, T.G., Singer, M.F., 1987. LINE-1: a mammalian transposable element. Biochim. Biophys. Acta 910, 203-212.
18. Feng, Q., Moran, J.V., Kazazian Jr., H.H., Boeke, J.D., 1996. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87, 905-916.
19. Gaffney, E.S., Meylan, P.A., 1988. A phylogeny of turtles. In: M.J. Benton (Ed.), The Phylogeny and Classification of the Tetrapods. Clarendon Press, Oxford, Vol. 1, pp. 157-219.
20. Groenen, M.A.M., Dijkhof, R.J.M., Verstege, A.J.M., Van der Poel, J.J., 1993. The complete sequence of the gene encoding bovine α-2-casein. Gene 123, 187-193.
21. Hamada, M., Kido, Y., Himberg, M., Reist, J.D., Cao, Y., Hasegawa, M., Okada, N., 1997. A newly isolated family of short interspersed repetitive elements (SINEs) in coregonid fishes (whitefish) with sequences that are almost identical to those of the SmaI family of repeats: possible evidence for the horizontal transfer of SINEs. 1997. Genetics 146, 355-367.
22. Jurka, J., 1993. A new subfamily of recently transposed human Alu repeats. Nucleic Acids Res. 21, 2252
23. Jurka, J., 1997. Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc. Natl. Acad. Sci. USA 94, 1872-1877.
24. Jurka, J., Milosavljevic, A., 1991. Reconstruction and analysis of human Alu genes. J. Mol. Evol. 32, 105-121.
25. Jurka, J., Smith, T., 1988. A fundamental division in the Alu family of repeated sequences. Proc. Natl. Acad. Sci. USA 85, 4775-4778.
26. Jurka, J., Walichiewicz, J., Milosavljevic, A., 1992. Prototypic sequences for human repetitive DNA. J. Mol. Evol. 35, 286-291.
27. Jurka, J., Zietkiewicz, E., Labuda, D., 1995. Ubiquitous mammalianwide interspersed repeats (MIRs) are molecular fossils from the mesozoic era. Nucleic Acids Res. 23, 170-175.
28. Kachroo, P., Leong, S.A., Chattoo, B.B., 1995. Mg-SINE: a short interspersed nuclear element from the rice blast fungus Magnaporthe grisea. Proc. Natl. Acad. Sci. USA 92, 11125-11129.
29. Kajikawa, M., Ohshima, K., Okada, N., 1997. Determination of the entire sequence of turtle CR1: the first open reading frame of the turtle CR1 element encodes a protein with a novel zinc finger motif. Mol. Biol. Evol., in press.
30. Kido, Y., Aono, M., Yamaki, T., Matsumoto, K., Murata, S., Saneyoshi, M., Okada, N., 1991. Shaping and reshaping of salmonid genomes by amplification of tRNA-derived retroposons during evolution. Proc. Natl. Acad. Sci. USA 88, 2326-2330.
31. Kido, Y., Himberg, M., Takasaki, N., Okada, N., 1994. Amplification of distinct subfamilies of short interspersed elements during evolution of the Salmonidae. J. Mol. Biol. 241, 633-644.
32. Kido, Y., Saitoh, M., Murata, S., Okada, N., 1995. Evolution of the active sequences of the Hpa I short interspersed elements. J. Mol. Evol. 41, 986-995.
33. Kim, J., Martignetti, J.A., Shen, M.R., Brosius, J., Deininger, P., 1994. Rodent BC1 RNA gene as a master gene for ID element amplification. Proc. Natl. Acad. Sci. USA 91, 3607-3611.
34. Kurose, K., Hata, K., Hattori, M., Sakaki, Y., 1995. RNA polymerase III dependence of the human L1 promoter and possible participation of the RNA polymerase II factor YY1 in the RNA polymerase III transcription system. Nucleic Acids Res. 23, 3704-3709.
35. Leeflang, E.P., Liu, W.-M., Hashimoto, C., Choudary, P.V., Schmid, C.W., 1992. Phylogenetic evidence for multiple Alu source genes. J. Mol. Evol. 35, 7-16.
36. Lenstra, J.A., Boxtel, J.A.F., Zwaagstra, K.A., Schwerin, M., 1993. Short interspersed nuclear element (SINE) sequences of the Bovidae. Animal Genetics 24, 33-39.
37. Liu, W.-M., Schmid, C.W., 1993. Proposed roles for DNA methylation in Alu transcriptional repression and mutational inactivation. Nucleic Acids Res. 21, 1351-1359.
38. Luan, D.D., Eickbush, T.H., 1995. RNA template requirements for target DNA-primed reverse transcription by the R2 retrotransposable element. Mol. Cell. Biol. 15, 3882-3891.
39. Luan, D.D., Korman, M.H., Jakubczak, J.L., Eickbush, T.H., 1993. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell 72, 595-605.
40. Matera, A.G., Hellmann, U., Hintz, M.F., Schmid, C.W., 1990. Recently transposed Alu repeats result from multiple source genes. Nucleic Acids Res. 18, 6019-6023.
41. Moran, J.V., Holmes, S.E., Naas, T.P., DeBerardinis, R.J., Boeke, J.D., Kazazian Jr., H.H., 1996. High frequency retrotransposition in cultured mammalian cells. Cell 87, 917-927.
42. Murata, S., Takasaki, N., Saitoh, M., Okada, N., 1993. Determination of the phylogenetic relationships among Pacific salmonids by using short interspersed elements (SINEs) as temporal landmarks of evolution. Proc. Natl. Acad. Sci. USA 90, 6995-6999.
43. Murata, S., Takasaki, N., Saitoh, M., Tachida, H., Okada, N., Details of retropositional genome dynamics that provide a rationale for a genetic division: the distinct branching of all the Pacific salmon and trout (Oncorhynchus) from the Atlantic salmon and trout (Salmo). 1996. Genetics 142, 915-926.
44. Ohshima, K., Hamada, M., Terai, Y., Okada, N., 1996. The 3′ ends of tRNA-derived short interspersed repetitive elements are derived from the 3′ ends of long interspersed repetitive elements. Mol. Cell. Biol. 16, 3756-3764.
45. Ohshima, K., Koishi, R., Matsuo, M., Okada, N., Several short interspersed repetitive elements (SINEs) in distant species may have originated from a common ancestral retrovirus: characterization of a squid SINE and a possible mechanism for generation of tRNA-derived retroposons. 1993. Proc. Natl. Acad. Sci. USA 90, 6260-6264.
46. Okada, N., 1991a. SINEs. Curr. Opin. Genet. Develop. 1, 498-504.
47. Okada, N., 1991b. SINEs: short interspersed repeated elements of the eukaryotic genome. Trends. Ecol. Evol. 6, 358-361.
48. Okada, N., Hamada, M., 1997. The 3′ ends of tRNA-derived SINEs originated from the 3′ ends of LINEs: a new example from the bovine genome. J. Mol. Evol., in press.
49. Okada, N., Ohshima, K., 1995. Evolution of tRNA-derived SINEs. In: R.J. Maraia (Ed.), The Impact of Short Interspersed Elements (SINEs) on the Host Genome. R. G. Landes Company, Austin, pp. 61-79.
50. Quentin, Y., 1988. The Alu family developed through successive waves of fixation closely connected with primate lineage history. J. Mol. Evol. 27, 194-202.
51. Rogers, J.H., 1985. The structure and evolution of retroposons. Int. Rev. Cytol. 93, 231-279.
52. Rougier, G.W., de la Fuente, M.S., Arcucci, A.B., 1995. Late Triassic turtles from South America. Science 268, 855-858.
53. Sakamoto, K., Okada, N., 1985. Rodent type 2 Alu family, rat identifier sequence, rabbit C family, and bovine or goat 73-bp repeat may have evolved from tRNA genes. J. Mol. Evol. 22, 134-140.
54. Schmid, C.W., 1991. Human Alu subfamilies and their methylation revealed by blot hybridization. Nucleic Acids Res. 19, 5613-5617.
55. Schmid, C., Maraia, R., 1992. Transcriptional regulation and transpositional selection of active SINE sequence. Curr. Opin. Genet. Dev. 2, 874-882.
56. Shen, M.R., Batzer, M.A., Deininger, P.L., 1991. Evolution of the master Alu gene(s). J. Mol. Evol. 33, 311-320.
57. Singer, M.F., 1982. SINEs and LINEs: highly repeated short and long interspersed sequences in mammalian genomes. Cell 28, 433-434.
58. Singer, M., Berg, P., 1991. Genes and Genomes. University Science Books, Mill Valley, CA.
59. Sinnett, D., Richer, C., Deragon, J.-M., Labuda, D., 1992. Alu RNA transcripts in human embryonal carcinoma cells: Model of post-transcriptional selection of master sequences. J. Mol. Biol. 226, 689-706.
60. Slagel, V., Flemington, E., Traina-Dorge, V., Bradshaw, H., Deininger, P., 1987. Clustering and subfamily relationships of the Alu family in the human genome. Mol. Biol. Evol. 4, 19-29.
61. Smit, A.F.A., 1996. The origin of interspersed repeats in the human genome. Curr. Opin. Genet. Dev. 6, 743-748.
62. Smit, A.F.A., Riggs, A.D., 1995. MIRs are classic, tRNA-derived SINEs that amplified before the mammalian radiation. Nucleic Acids Res. 23, 98-102.
63. Smit, A.F.A., Toth, G., Riggs, A.D., Jurka, J., 1995. Ancestral mammalian-wide subfamilies of LINE-1 repetitive sequences. J. Mol. Biol. 246, 401-417.
64. Spence, S.E., Young, R.M., Garner, K.J., Lingrel, J.B., 1985. Localization and characterization of members of a family of repetitive sequences in the goat β globin locus. Nucleic Acids Res. 13, 2171-2186.
65. Stumph, W.E., Kristo, P., Tsai, M.-J., O'Malley, B.W., 1981. A chicken middle-repetitive DNA sequence which shares homology with mammalian ubiquitous repeats. Nucleic Acids Res. 9, 5383-5397.
66. Szemraj, J., Plucienniczak, G., Jaworski, J., Plucienniczak, A., 1995. Bovine Alu-like sequences mediate transposition of a new site-specific retroelement. Gene 152, 261-264.
67. Takasaki, N., Murata, S., Saitoh, M., Kobayashi, T., Park, L., Okada, N., 1994. Species-specific amplification of tRNA-derived short interspersed repetitive elements (SINEs) by retroposition: a process of parasitization of entire genomes during the evolution of salmonids. Proc. Natl. Acad. Sci. USA 91, 10153-10157.
68. Takasaki, N., Park, L., Kaeriyama, M., Gharrett, A.J., Okada, N., Characterization of species-specifically amplified SINEs in three salmonid species - chum salmon, pink salmon, and kokanee: the local environment of the genome may be important for the generation of a dominant source gene at a newly retroposed locus. 1996. J. Mol. Evol. 42, 103-116.
69. Tiedge, H., Drager, U.C., Brosius, J., 1992. Murine BC1 RNA in dendritic fields of the retinal inner plexiform layer. Neurosci. Lett. 141, 136-138.
70. Tiedge, H., Fremeau Jr., R.T., Weinstock, P.H., Arancio, O., Brosius, J., 1991. Dendritic location of neural BC1 RNA. Proc. Natl. Acad. Sci. USA 88, 2093-2097.
71. Ullu, E., Tschudi, C., 1984. Alu sequences are processed 7SL RNA genes. Nature 312, 171-172.
72. Vandergon, T.L., Reitman, M., 1994. Evolution of chicken repeat 1 (CR1) elements: evidence for ancient subfamilies and multiple progenitors. Mol. Biol. Evol. 11, 886-898.
73. Weiner, A.M., 1980. An abundant cytoplasmic 7S RNA is complementary to the dominant interspersed middle repetitive DNA sequence family in the human genome. Cell 22, 209-218.
74. Weiner, A.M., Deininger, P.L., Efstratiadis, A., 1986. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu. Rev. Biochem. 55, 631-661.
75. Willard, C., Nguyen, H.T., Schmid, C.W., 1987. Existence of at least three distinct Alu subfamilies. J. Mol. Evol. 26, 180-186.
76. Winkfein, R.J., Moir, R.D., Krawetz, S.A., Blanco, J., States, J.C., Dixon, G.H., 1988. A new family of repetitive, retroposon-like sequences in the genome of the rainbow trout. Eur. J. Biochem. 176, 255-264.
77. Xiong, Y., Eickbush, T.H., 1990. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9, 3353-3362.
78. Yoshioka, Y., Matsumoto, S., Kojima, S., Ohshima, K., Okada, N., Machida, Y., 1993. Molecular characterization of a short interspersed repetitive element from tobacco that exhibits sequence homology to specific tRNAs. Proc. Natl. Acad. Sci. USA 90, 6562-6566.
79. Zelnick, C.R., Burks, D.J., Duncan, C.H., 1987. A composite transposon 3′ to the cow fetal globin gene binds a sequence specific factor. Nucleic Acids Res. 15, 10437-10453.
80. Zimmerly, S., Guo, H., Perlman, P.S., Lambowitz, A.M., 1995. Group II intron mobility occurs by target DNA-primed reverse transcription. Cell 82, 545-554.