Two major classes of retrotransposons have invaded eukaryotic genomes: the LTR retrotransposons closely resembling the proviral integrated form of infectious retroviruses, and the non-LTR retrotransposons including the widespread, autonomous LINE elements. Here, we review the modeling effects of the latter class of elements, which are the most active in humans, and whose enzymatic machinery is subverted to generate a large series of “secondary” retroelements. These include the processed pseudogenes, naturally present in all eukaryotic genomes possessing non-LTR retroelements, and the very successful SINE elements such as the human Alu sequences which have evolved refined parasitic strategies to efficiently bypass the original “protectionist” cis-preference of LINEs for their own retrotransposition.   

1.
Ashworth A, Skene B, Swift S, Lovell-Badge R: Zfa is an expressed retroposon derived from an alternative transcript of the Zfx transcript. EMBO J 9:1529–1534 (1990).
2.
Batzer MA, Deininger PL: Alu repeats and human genomic diversity. Nat Rev Genet 3:370–379 (2002).
3.
Baust C, Baillie GJ, Mager DL: Insertional polymorphisms of ETn retrotransposons include a disruption of the wiz gene in C57BL/6 mice. Mamm Genome 13:423–428 (2002).
4.
Bernstein E, Denli AM, Hannon GJ: The rest is silence. RNA 7:1509–1521 (2001).
5.
Boeke JD: LINEs and Alu-the polyA connection. Nat Genet 16:6–7 (1997).
6.
Boeke JD, Stoye JP: Retrotransposons, endogenous retroviruses, and the evolution of retroelements, in Coffin JM, Hughes SH, Varmus HE (eds): Retroviruses, pp 343–435 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor 1997).
7.
Boeke JD, Garfinkel DJ, Styles CA, Fink GR: Ty elements transpose through an RNA intermediate. Cell 40:491–500 (1985).
8.
Bovia F, Fornallaz M, Leffers H, Strub K: The SRP9/14 subunit of the signal recognition particle (SRP) is present in more than 20-fold excess over SRP in primate cells and exists primarily free but also in complex with small cytoplasmic Alu RNAs. Mol Biol Cell 6:471–484 (1995).
9.
Brosius J: RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 238:115–134 (1999).
10.
Brouha B, Schustak J, Badge RM, Lutz-Prigge S, Farley AH, Moran JV, Kazazian HH Jr: Hot L1s account for the bulk of retrotransposition in the human population. Proc Natl Acad Sci USA 100:5280–5285 (2003).
11.
Burke WD, Calalang CC, Eickbush TH: The site-specific ribosomal insertion element type II of Bombyx mori (R2Bm) contains the coding sequence for a reverse transcriptase-like enzyme. Mol Cell Biol 7:2221–2230 (1987).
12.
Buzdin A, Ustyugova S, Gogvadze E, Vinogradova T, Lebedev Y, Sverdlov E: A new family of chimeric retrotranscripts formed by a full copy of U6 small nuclear RNA fused to the 3′ terminus of l1. Genomics 80:402–406 (2002).
13.
Buzdin A, Gogvadze E, Kovalskaya E, Volchkov P, Ustyugova S, Illarionova A, Fushan A, Vinogradova T, Sverdlov E: The human genome contains many types of chimeric retrogenes generated through in vivo RNA recombination. Nucleic Acids Res 31:4385–4390 (2003).
14.
Chang DY, Maraia RJ: A cellular protein binds B1 and Alu small cytoplasmic RNAs in vitro. J Biol Chem 268:6423–6428 (1993).
15.
Chang DY, Nelson B, Bilyeu T, Hsu K, Darlington GJ, Maraia RJ: A human Alu RNA-binding protein whose expression is associated with accumulation of small cytoplasmic Alu RNA. Mol Cell Biol 14:3949–3959 (1994).
16.
Chu WM, Ballard R, Carpick BW, Williams BR, Schmid CW: Potential Alu function: regulation of the activity of double-stranded RNA-activated kinase PKR. Mol Cell Biol 18:58–68 (1998).
17.
Cost GJ, Boeke JD: Targeting of human retrotransposon integration is directed by the specificity of the L1 endonuclease for regions of unusual DNA structure. Biochem 37:18081–18093 (1998).
18.
Cost GJ, Feng Q, Jacquier A, Boeke JD: Human L1 element target-primed reverse transcription in vitro. EMBO J 21:5899–5910 (2002).
19.
Curcio MJ, Garfinkel DJ: Single-step selection for Ty1 element retrotransposition. Proc Natl Acad Sci USA 88:936–940 (1991).
20.
Dahl HH, Brown RM, Hutchinson WM, Maragos C, Brown GK: A testis-specific form of the human pyruvate dehydrogenase E1 alpha subunit is coded by an intronless gene on chromosome 4. Genomics 8:225–232 (1990).
21.
Deininger PL: SINEs: Short interspersed repeated DNA elements in higher eucaryotes, in Berg DE, Howe MM (eds): Mobile DNA, pp 619–636 (American Society for Microbiology, Washington DC 1989).
22.
Deininger PL, Batzer MA: Alu repeats and human disease. Mol Genet Metab 67:183–193 (1999).
23.
Deininger PL, Batzer MA: Mammalian retroelements. Genome Res 12:1455–1465 (2002).
24.
Demers GW, Matunis MJ, Hardison RC: The L1 family of long interspersed repetitive DNA in rabbits: sequence, copy number, conserved open reading frames, and similarity to keratin. J Mol Evol 29:3–19 (1989).
25.
Derr LK, Strathern JN, Garfinkel DJ: RNA-mediated recombination in S. cerevisiae. Cell 67:355–364 (1991).
26.
Dewannieux M, Esnault C, Heidmann T: LINE-mediated retrotransposition of marked Alu sequences. Nat Genet 35:41–48 (2003).
27.
Dewannieux M, Dupressoir A, Harper F, Pierron G, Heidmann T: Identification of autonomous IAP LTR retrotransposons mobile in mammalian cells. Nat Genet 36:534–539 (2004).
28.
Dhellin O, Maestre J, Heidmann T: Functional differences between the human LINE retrotransposon and retroviral reverse transcriptases for in vivo mRNA reverse transcription. EMBO J 16:6590–6602 (1997).
29.
Dombroski BA, Mathias SL, Nanthakumar E, Scott AF, Kazazian HH: Isolation of an active human transposable element. Science 254:1805–1808 (1991).
30.
Dombroski BA, Scott AF, Kazazian HH: Two additional potential retrotransposons isolated from a human L1 subfamily that contains an active retrotransposable element. Proc Natl Acad Sci USA 90:6513–6517 (1993).
31.
Dornburg R, Temin HM: Retroviral vector system for the study of cDNA gene formation. Mol Cell Biol 8:2328–2334 (1988).
32.
Dornburg R, Temin HM: cDNA genes formed after infection with retroviral vector particles lack the hallmarks of natural processed pseudogenes. Mol Cell Biol 10:68–74 (1990).
33.
Eickbush T: Exon shuffling in retrospect. Science 283:1465–1467 (1999).
34.
Esnault C, Maestre J, Heidmann T: Human LINE retrotransposons generate processed pseudogenes. Nat Genet 24:363–367 (2000).
35.
Esnault C, Casella JF, Heidmann T: A Tetrahymena thermophila ribozyme-based indicator gene to detect transposition of marked retroelements in mammalian cells. Nucleic Acids Res 30:e49 (2002).
36.
Fawcett DH, Lister CK, Kellet E, Finnegan DJ: Transposable elements controlling I-R hybrid dysgenesis in D. melanogaster are similar to mammalian LINEs. Cell 47:1007–1015 (1986).
37.
Feng Q, Moran JV, Kazazian HH, Boeke JD: Human L1 retrotransposon encodes a conserved endonuclease required for retrotranposition. Cell 87:905–916 (1996).
38.
Feng Q, Schumann G, Boeke JD: Retrotransposon R1Bm endonuclease cleaves the target sequence. Proc Natl Acad Sci USA 95:2083–2088 (1998).
39.
Fennelly J, Harper K, Laval S, Wright E, Plumb M: Co-amplification to tail-to-tail copies of MuRVY and IAPE retroviral genomes on the Mus musculus Y chromosome. Mamm Genome 7:31–36 (1996).
40.
Flint J, Rochette J, Craddock CF, Dode C, Vignes B, Horsley SW, Kearney L, Buckle VJ, Ayyub H, Higgs DR: Chromosomal stabilisation by a subtelomeric rearrangement involving two closely related Alu elements. Hum Mol Genet 5:1163–1169 (1996).
41.
Gilbert N, Lutz-Prigge S, Moran JV: Genomic deletions created upon LINE-1 retrotransposition. Cell 110:315–325 (2002).
42.
Goodier JL, Ostertag EM, Engleka KA, Seleme MC, Kazazian HH Jr: A potential role for the nucleolus in L1 retrotransposition. Hum Mol Genet 17:17 (2004).
43.
Hagan CR, Sheffield RF, Rudin CM: Human Alu element retrotransposition induced by genotoxic stress. Nat Genet 35:219–220 (2003).
44.
Han JS, Szak ST, Boeke JD: Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature 429:268–274 (2004).
45.
Harteveld KL, Losekoot M, Fodde R, Giordano PC, Bernini LF: The involvement of Alu repeats in recombination events at the alpha-globin gene cluster: characterization of two alphazero-thalassaemia deletion breakpoints. Hum Genet 99:528–534 (1997).
46.
Heidmann O, Heidmann T: Retrotransposition of a mouse IAP sequence tagged with an indicator gene. Cell 64:159–170 (1991).
47.
Heidmann T, Heidmann O, Nicolas JF: An indicator gene to demonstrate intracellular transposition of defective retroviruses. Proc Natl Acad Sci USA 85:2219–2223 (1988).
48.
Hohjoh H, Singer M: Cytoplasmic ribonucleoprotein complexes containing human LINE-1 protein and RNA. EMBO J 15:630–639 (1996).
49.
Holmes SE, Dombroski BA, Krebs CM, Boehm CD, Kazazian Jr HH: A new retrotransposable human L1 element from the LRE2 locus on chromosome 1q produces a chimaeric insertion. Nat Genet 7:143–148 (1994).
50.
Hutchinson CA III, Hardies SC, Loeb DD, Shehee WR, Edgell MH: LINEs and related retroposons: long interspersed repeated sequences in the eucaryotic genome, in Berg DE, Howe MM (eds): Mobile DNA, pp 593–617 (American Society for Microbiology, Washington DC 1989).
51.
International Human Genome Sequencing Consortium: Initial sequencing and analysis of the human genome. Nature 409:860–921 (2001).
52.
Jakubczak JL, Burke WD, Eickbush TH: Retrotransposable elements R1 and R2 interrupt the rRNA genes of most insects. Proc Natl Acad Sci USA 88:3295–3299 (1991).
53.
Jensen S, Heidmann T: An indicator gene for detection of germline retrotransposition in transgenic Drosophila demonstrates RNA-mediated transposition of the LINE I element. EMBO J 10:1927–1937 (1991).
54.
Jensen S, Gassama M-P, Heidmann T: Taming of transposable elements by homology-dependent gene silencing. Nat Genet 21:209–212 (1999).
55.
Jurka J: Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc Natl Acad Sci USA 94:1872–1877 (1997).
56.
Jurka J, Klonowski P: Integration of retroposable elements in mammals: selection of target sites. J Mol Evol 43:685–689 (1996).
57.
Kajikawa M, Okada N: LINEs mobilize SINEs in the eel through a shared 3′ sequence. Cell 111:433–444 (2002).
58.
Kapitonov VV, Jurka J: A novel class of SINE elements derived from 5S rRNA. Mol Biol Evol 20:694–702 (2003).
59.
Kazazian HH Jr: An estimated frequency of endogenous insertional mutations in human. Nat Genet 22:130 (1999).
60.
Kazazian HH, Wong C, Youssoufian M, Scott AF, Phillips DG, Antonarakis SE: Haemophilia A resulting from de novo insertions of L1 sequences represent a novel mechanism for mutation in man. Nature 322:164–166 (1988).
61.
Kimberland ML, Divoky V, Prchal J, Schwahn U, Berger W, Kazazian HH Jr: Full-length human L1 insertions retain the capacity for high frequency retrotransposition in cultured cells. Hum Mol Genet 8:1557–1560 (1999).
62.
Ko TM, Tseng LH, Kao CH, Lin YW, Hwa HL, Hsu PM, Li SF, Chuang SM: Molecular characterization and PCR diagnosis of Thailand deletion of alpha-globin gene cluster. Am J Hematol 57:124–130 (1998).
63.
Kolosha VO, Martin SL: In vitro properties of the first ORF protein from mouse LINE-1 support its role in ribonucleoprotein particle formation during retroposition. Proc Natl Acad Sci USA 94:10155–10160 (1997).
64.
Kuff EL: Intracisternal A particles in mouse neoplasia. Cancer Cells 2:398–400 (1990).
65.
Kuff EL, Lueders KK: The intracisternal A-particle gene family: structure and functional aspects. Adv Cancer Res 51:183–276 (1988).
66.
Lev-Maor G, Sorek R, Shomron N, Ast G: The birth of an alternatively spliced exon: 3′ splice-site selection in Alu exons. Science 300:1288–1291 (2003).
67.
Levine KL, Steiner B, Johnson K, Aronoff R, Quinton TJ, Linial ML: Unusual features of integrated cDNAs generated by infection with genome-free retroviruses. Mol Cell Biol 10:1891–1900 (1990).
68.
Li TH, Schmid CW: Differential stress induction of individual Alu loci: implications for transcription and retrotransposition. Gene 276:135–141 (2001).
69.
Li T, Spearow J, Rubin CM, Schmid CW: Physiological stresses increase mouse short interspersed element (SINE) RNA expression in vivo. Gene 239:367–372 (1999).
70.
Linial M: Creation of a processed pseudogene by retroviral infection. Cell 49:93–102 (1987).
71.
Liu WM, Maraia RJ, Rubin CM, Schmid CW: Alu transcripts: cytoplasmic localisation and regulation by DNA methylation. Nucleic Acids Res 22:1087–1095 (1994).
72.
Liu WM, Chu WM, Choudary PV, Schmid CW: Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts. Nucleic Acids Res 23:1758–1765 (1995).
73.
Loeb D, Padgett RW, Hardies SC, Shehee W, Comer MB, Edgell MH, Hutchinson CA III: The sequence of a large L1Md element reveals a tandemly repeated 5′ end and several features found in retrotransposons. Mol Cell Biol 6:168–182 (1986).
74.
Luan DD, Eickbush TH: RNA template requirements for target DNA-primed reverse transcription by the R2 retrotransposable element. Mol Cell Biol 15:3882–3891 (1995).
75.
Luan DD, Korman MH, Jakubczak JL, Eickbush TH: 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 (1993).
76.
Maestre J, Tchénio T, Dhellin O, Heidmann T: mRNA retroposition in human cells: processed pseudogene formation. EMBO J 14:6333–6338 (1995).
77.
Malik HS, Eickbush TH: Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses. Genome Res 11:1187–1197 (2001).
78.
Malik HS, Burke WD, Eickbush TH: The age and evolution of non-LTR retrotransposable elements. Mol Biol Evol 16:793–805 (1999).
79.
Mandal PK, Bagchi A, Bhattacharya A, Bhattacharya S: An Entamoeba histolytica LINE/SINE pair inserts at common target sites cleaved by the restriction enzyme-like LINE-encoded endonuclease. Eukaryot Cell 3:170–179 (2004).
80.
Marcus S, Hellgren D, Lambert B, Fallstrom SP, Wahlstrom J: Duplication in the hypoxanthine phosphoribosyl-transferase gene caused by Alu-Alu recombination in a patient with Lesch Nyhan syndrome. Hum Genet 90:477–482 (1993).
81.
Martin F, Maranon C, Olivares M, Alonso C, Lopez M: Characterization of a non-long terminal repeat retrotransposon cDNA (L1Tc) from Trypanosoma cruzi: homology of the first ORF with the APE family of DNA repair enzymes. J Mol Biol 247:49–59 (1995).
82.
Martin SL: Ribonucleoprotein particles with LINE-1 RNA in mouse embryonal carcinoma cells. Mol Cell Biol 11:4804–4807 (1991).
83.
Martin SL, Bushman FD: Nucleic acid chaperone activity of the ORF1 protein from the mouse LINE-1 retrotransposon. Mol Cell Biol 21:467–475 (2001).
84.
Martin SL, Branciforte D, Keller D, Bain DL: Trimeric structure for an essential protein in L1 retrotransposition. Proc Natl Acad Sci USA 100:13815–13820 (2003).
85.
Matsumoto T, Takahashi H, Fujiwara H: Targeted nuclear import of open reading frame 1 protein is required for in vivo retrotransposition of a telomere-specific non-long terminal repeat retrotransposon, SART1. Mol Cell Biol 24:105–122 (2004).
86.
McCarrey JR, Thomas K: Human testis-specific PGK gene lacks introns and possesses characteristics of a processed gene. Nature 326:501–505 (1987).
87.
Medstrand P, van de Lagemaat LN, Mager DL: Retroelement distributions in the human genome: variations associated with age and proximity to genes. Genome Res 12:1483–1495 (2002).
88.
Miki Y, Nishisho I, Horii A, Miyoshi Y, Utsunomiya J, Kinzler KW, Vogelstein B, Nakamura Y: Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer. Cancer Res 52:643–645 (1992).
89.
Mizrokhi LJ, Georgieva SG, Ilyin YV: Jockey, a mobile Drosophila element similar to mammalian LINEs, is transcribed from the internal promotor by RNA polymerase II. Cell 54:685–691 (1988).
90.
Moran JV, Holmes SE, Nass TP, DeBerardinis RJ, Boeke JD, Kazazian HH: High frequency retroposition in cultured mammalian cells. Cell 87:917–927 (1996).
91.
Moran JV, DeBerardinis RJ, Kazazian HH Jr: Exon shuffling by L1 retrotransposition. Science 283:1530–1534 (1999).
92.
Morrish TA, Gilbert N, Myers JS, Vincent BJ, Stamato TD, Taccioli GE, Batzer MA, Moran JV: DNA repair mediated by endonuclease-independent LINE-1 retrotransposition. Nat Genet 31:159–165 (2002).
93.
Morse B, Rotherg PG, South VJ, Spandorfer JM, Astrin SM: Insertional mutagenesis of the myc locus by a LINE-1 sequence in a human breast carcinoma. Nature 333:87–90 (1988).
94.
Mouse Genome Sequencing Consortium: Initial sequencing and comparative analysis of the mouse genome. Nature 420:520–562 (2002).
95.
Muddashetty R, Khanam T, Kondrashov A, Bundman M, Iacoangeli A, Kremerskothen J, Duning K, Barnekow A, Huttenhofer A, Tiedge H, Brosius J: Poly(A)-binding protein is associated with neuronal BC1 and BC200 ribonucleoprotein particles. J Mol Biol 321:433–445 (2002).
96.
Naas TP, DeBerardinis RJ, Moran JV, Ostertag EM, Kingsmore SF, Seldin MF, Hayashizaki Y, Martin SL, Kazazian HH: An actively retrotransposing, novel subfamilly of mouse L1 elements. EMBO J 17:590–597 (1998).
97.
Narita N, Nishio H, Kitoh Y, Ishikawa Y, Minami R, Nakamura H, Matsuo M: Insertion of a 5′ truncated L1 element into the 3′ end of exon 44 of the dystrophin gene resulted in skipping of the exon during splicing in a case of Duchenne muscular dystrophy. J Clin Invest 91:1862–1867 (1993).
98.
Nicholls RD, Fiscel-Ghodsian N, Higgs DR: Recombination at the human α-globin gene cluster: Sequence features and topological constraints. Cell 49:369–378 (1987).
99.
Ohshima K, Okada N: Generality of the tRNA origin of short interspersed repetitive elements (SINEs). Characterization of three different tRNA-derived retroposons in the octopus. J Mol Biol 243:25–37 (1994).
100.
Ohshima K, Hamada M, Terai Y, Okada N: The 3′ ends of tRNA-derived short interspersed repetitive elements are derived from 3′ ends of long interspersed repetitive elements. Mol Cell Biol 16:3756–3764 (1996).
101.
Ohshima K, Hattori M, Yada T, Gojobori T, Sakaki Y, Okada N: Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates. Genome Biol 4:R74 (2003).
102.
Okada N, Hamada M: The 3′ ends of tRNA-derived SINEs originated from the 3′ ends of LINEs: a new example from the bovine genome. J Mol Evol 44:S52–56 (1997).
103.
Okada N, Hamada M, Ogiwara I, Ohshima K: SINEs and LINEs share common 3′ sequences: a review. Gene 205:229–243 (1997).
104.
Okazaki S, Ishikawa H, Fujiwara H: Structural analysis of TRAS1, a novel family of telomeric repeat-associated retrotransposons in the silkworm, Bombyx mori. Mol Cell Biol 15:4545–552 (1995).
105.
Onno M, Nakamura T, Hillova J, Hill M: Rearrangement of the human tre oncogene by homologous recombination between Alu repeats of nucleotide sequences from two different chromosomes. Oncogene 7:2519–1523 (1992).
106.
Ostertag EM, Kazazian HH Jr: Biology of mammalian L1 retrotransposons. Annu Rev Genet 35:501–538 (2001).
107.
Pardue ML, DeBaryshe PG: Retrotransposons provide an evolutionarily robust non-telomerase mechanism to maintain telomeres. Annu Rev Genet 37:485–511 (2003).
108.
Pavlicek A, Jabbari K, Paces J, Paces V, Hejnar JV, Bernardi G: Similar integration but different stability of Alus and LINEs in the human genome. Gene 276:39–45 (2001).
109.
Pelisson A, Finnegan DJ, Bucheton A: Evidence for retrotransposition of the I factor, a LINE element of Drosophila melanogaster. Proc Natl Acad Sci USA 88:4907–4910 (1991).
110.
Perepelitsa-Belancio V, Deininger P: RNA truncation by premature polyadenylation attenuates human mobile element activity. Nat Genet 35:363–366 (2003).
111.
Puget N, Sinilnikova OM, Stoppa-Lyonnet D, Audoynaud C, Pages S, Lynch HT, Goldgar D, Lenoir GM, Mazoyer S: An Alu-mediated 6-kb duplication in the BRCA1 gene: a new founder mutation? Am J Hum Genet 64:300–302 (1999).
112.
Rashkova S, Karam SE, Pardue ML: Element-specific localization of Drosophila retrotransposon Gag proteins occurs in both nucleus and cytoplasm. Proc Natl Acad Sci USA 99:3621–3626 (2002).
113.
Rashkova S, Athanasiadis A, Pardue ML: Intracellular targeting of Gag proteins of the Drosophila telomeric retrotransposons. J Virol 77:6376–6384 (2003).
114.
Ribet D, Dewannieux M, Heidmann T: An active murine transposon family pair: retrotransposition of “master” MusD copies and ETn in trans-mobilization. Genome Res 14:2261–2267 (2004).
115.
Robinson MO, McCarrey JR, Simon MI: Transcriptional regulatory regions of testis-specific PGK2 defined in transgenic mice. Proc Natl Acad Sci USA 86:8437–8441 (1989).
116.
Rowold DJ, Herrera RJ: Alu elements and the human genome. Genetica 108:57–72 (2000).
117.
Rubin CM, Kimura RH, Schmid CW: Selective stimulation of translational expression by Alu RNA. Nucleic Acids Res 30:3253–3261 (2002).
118.
Sandmeyer S: Targeting transposition: at home in the genome. Genome Res 8:416–418 (1998).
119.
Sassaman D, Dombroski B, Moran J, Kimberland M, Naas T, DeBerardinis R, Gabriel A, Swergold G, Kazazian H: Many human L1 elements are capable of retrotransposition. Nat Genet 16:37–43 (1997).
120.
Schichman SA, Caligiuri MA, Strout MP, Carter SL, Gu Y, Canaani E, Bloomfield CD, Croce CM: ALL-1 tandem duplication in acute myeloid leukemia with a normal karyotype involves homologous recombination between Alu elements. Cancer Res 54:4277–4280 (1994).
121.
Schmid CW: Does SINE evolution preclude Alu function? Nucleic Acids Res 26:4541–4550 (1998).
122.
Schwahn U, Lenzner S, Dong J, Feil S, Hinzmann B, van Duijnhoven G, Kirschner R, Hemberger M, Bergen AA, Rosenberg T, Pinckers AJ, Fundele R, Rosenthal A, Cremers FP, Ropers HH, Berger W: Positional cloning of the gene for X-linked retinitis pigmentosa 2. Nat Genet 19:327–332 (1998).
123.
Shimada F, Taira M, Suzuki Y, Hashimoto N, Nozaki O, Tatibana M, Ebina Y, Tawata M, Onaya T, et al: Insulin-resistant diabetes associated with partial deletion of insulin-receptor gene. Lancet 335:1179–1181 (1990).
124.
Sinnett D, Richer C, Deragon JM, Labuda D: Alu RNA secondary structure consists of two independent 7 SL RNA-like folding units. J Biol Chem 266:8675–8678 (1991).
125.
Sisodia S, Sollner-Webb B, Cleveland D: Specificity of RNA maturation pathways: RNAs transcribed by RNA polymerase III are not substrates for splicing or polyadenylation. Mol Cell Biol 7:3602–3612 (1987).
126.
Skowronski J, Fanning TG, Singer MF: Unit-length Line-1 transcripts in human teratocarcinoma cells. Mol Cell Biol 8:1385–1397 (1988).
127.
Smit AFA: The origin of interspersed repeats in the human genome. Curr Opin Genet Dev 6:743–748 (1996).
128.
So CW, Ma ZG, Price CM, Dong S, Chen SJ, Gu LJ, So CK, Wiedemann LM, Chan LC: MLL self fusion mediated by Alu repeat homologous recombination and prognosis of AML-M4/M5 subtypes. Cancer Res 57:117–122 (1997).
129.
Sorek R, Ast G, Graur D: Alu-containing exons are alternatively spliced. Genome Res 12:1060–1067 (2002).
130.
Swensen J, Hoffman M, Skolnick MH, Neuhausen SL: Identification of a 14 kb deletion involving the promoter region of BRCA1 in a breast cancer family. Hum Mol Genet 6:1513–1517 (1997).
131.
Symer DE, Connelly C, Szak ST, Caputo EM, Cost GJ, Parmigiani G, Boeke JD: Human l1 retrotransposition is associated with genetic instability in vivo. Cell 110:327–338 (2002).
132.
Takahashi H, Okazaki S, Fujiwara H: A new family of site-specific retrotransposons, SART1, is inserted into telomeric repeats of the silkworm, Bombyx mori. Nucleic Acids Res 25:1578–1584 (1997).
133.
Tchénio T, Heidmann T: Defective retroviruses can disperse in the human genome by intracellular transposition. J Virol 65:2113–2118 (1991).
134.
Tchénio T, Heidmann T: High-frequency intracellular transposition of a defective mammalian provirus detected by an in situ colorimetric assay. J Virol 66:1571–1578 (1992).
135.
Tchénio T, Ségal-Bendirdjian E, Heidmann T: Generation of processed pseudogenes in murine cells. EMBO J 12:1487–1497 (1993).
136.
Ullu E, Tschudi C: Alu sequences are processed 7SL RNA genes. Nature 312:171–172 (1984).
137.
Varon R, Gooding R, Steglich C, Marns L, Tang H, Angelicheva D, Yong KK, Ambrugger P, Reinhold A, Morar B, et al: Partial deficiency of the C-terminal-domain phosphatase of RNA polymerase II is associated with congenital cataracts, facial dysmorphism, neuropathy syndrome. Nat Genet 35:185–189 (2003).
138.
Wallace MR, Andersen LB, Saulino AM, Gregory PE, Glover TW, Collins FS: A de novo Alu insertion results in neurofibromatosis type 1. Nature 353:864–866 (1991).
139.
Wei W, Gilbert N, Ooi SL, Lawler JF, Ostertag EM, Kazazian HH, Boeke JD, Moran JV: Human L1 retrotransposition: cis preference versus trans complementation. Mol Cell Biol 21:1429–1439 (2001).
140.
Weiner A: An abundant cytoplasmic 7S RNA is complementary to the dominant interspersed middle repetitive DNA sequence family in the human genome. Cell 22:209–218 (1980).
141.
Weiner AM, Deininger PL, Efstratiadis A: Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu Rev Biochem 55:631–661 (1986).
142.
Welker R, Janetzko A, Kräusslich HG: Plasma membrane targeting of chimeric intracisternal A-type particle polyproteins leads to particle release and specific activation of the viral protein. J Virol 71:5209–5217 (1997).
143.
West N, Roy-Engel AM, Imataka H, Sonenberg N, Deininger P: Shared protein components of SINE RNPs. J Mol Biol 321:423–432 (2002).
144.
Whitman SP, Strout MP, Marcucci G, Freud AG, Culley LL, Zeleznik-Le NJ, Mrozek K, Theil KS, Kees UR, Bloomfield CD, Caligiuri MA: The partial nontandem duplication of the MLL (ALL1) gene is a novel rearrangement that generates three distinct fusion transcripts in B-cell acute lymphoblastic leukemia. Cancer Res 61:59–63 (2001).
145.
Willoughby DA, Vilalta A, Oshima RG: An Alu element from the K18 gene confers position-independent expression in transgenic mice. J Biol Chem 275:759–768 (2000).
146.
Xiong Y, Eickbush TH: Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J 9:3353–3362 (1990).
147.
Yang J, Malik HS, Eickbush TH: Identification of the endonuclease domain encoded by R2 and other site-specific, non-long terminal repeat retrotransposable elements. Proc Natl Acad Sci USA 96:7847–7852 (1999).
© 2005 S. Karger AG, Basel
2005
Copyright / Drug Dosage / Disclaimer
Copyright: All rights reserved. No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, microcopying, or by any information storage and retrieval system, without permission in writing from the publisher.
Drug Dosage: The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in government regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any changes in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug.
Disclaimer: The statements, opinions and data contained in this publication are solely those of the individual authors and contributors and not of the publishers and the editor(s). The appearance of advertisements or/and product references in the publication is not a warranty, endorsement, or approval of the products or services advertised or of their effectiveness, quality or safety. The publisher and the editor(s) disclaim responsibility for any injury to persons or property resulting from any ideas, methods, instructions or products referred to in the content or advertisements.
You do not currently have access to this content.