Эволюция короткого ретропозона В1
Диссертация
Другой большой класс подвижных элементов — это ретротранспозоны, они не вырезаются из хромосомы, как это делают транспозоны (механизм «cut-and-paste»), а амплифицируются, то есть образование их новых копий в геноме не сопряжено с потерей уже существующих («copy-and-paste») (Рис. 1). Механизм такой амплификации основан на открытой в 1970 году Г. Теминым и Д. Балтимором реакции обратной… Читать ещё >
Список литературы
- Adkins, R.M., Gelke, E.L., Rowe, D., and Honeycutt, R.L. (2001). Molecular phylogeny and divergence time estimates for major rodent groups: evidence from multiple genes. Mol Biol Evol 18,777−791.
- Adkins, R.M., Walton, A.H., and Honeycutt, R.L. (2003). Higher-level systematics of rodents and divergence time estimates based on two congruent nuclear genes. Mol Phylogenet Evol 26,409−420.
- Aksoy, S., Williams, S., Chang, S., and Richards, F.F. (1990). SLACS retrotransposon from Trypanosoma brucei gambiense is similar to mammalian LINEs. Nucleic Acids Res 18, 785 792.
- Allen, T.A., Von Kaenel, S., Goodrich, J.A., and Kugel, J.F. (2004). The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nature structural & molecular biology 11,816−821.
- Arkhipova, I.R., Lyubomirskaya, N.V., and Ilyin, Y.V. (1995). Drosophila Retrotransposons (Austin, R.G. Landes Company).
- Arnaud, P., Yukawa, Y., Lavie, L., Pelissier, Т., Sugiura, M., and Deragon, J.M. (2001). Analysis of the SINE SI Pol III promoter from Brassica- impact of methylation and influence of external sequences. Plant J 26,295−305.
- Athanasiadis, A., Rich, A., and Maas, S. (2004). Widespread A-to-I RNA editing of AIu-containing mRNAs in the human transcriptome. PLoS biology 2, e391.
- Babich, V., Aksenov, N., Alexeenko, V., Oei, S.L., Buchlow, G., and Tomilin, N. (1999). Association of some potential hormone response elements in human genes with the Alu family repeats. Gene 239,341−349.
- Bachvarova, R. (1988). Small B2 RNAs in mouse oocytes, embryos, and somatic tissues. Dev Biol 130,513−523.
- Bains, W., and Temple-Smith, K. (1989). Similarity and divergence among rodent repetitive DNA sequences. J Mol Evol 28,191−199.
- Batzer, M.A., and Deininger, P.L. (2002). Alu repeats and human genomic diversity. Nature reviews 3,370−379.
- Batzer, M.A., Deininger, P.L., Hellmann-Blumberg, U., Jurka, J., Labuda, D., Rubin, C.M., Schmid, C.W., Zietkiewicz, E., and Zuckerkandl, E. (1996). Standardized nomenclature for Alu repeats. J Mol Evol 42,3−6.
- Batzer, M.A., Kilroy, G.E., Richard, P.E., Shaikh, Т.Н., 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.
- Bhattacharya, R., Perumal, K., Sinha, K., Maraia, R., and Reddy, R. (2002). Methylphosphate cap structure in small RNAs reduces the affinity of RNAs to La protein. Gene Expr 10, 243 253.
- Bird, A.P. (1980). DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res 8,1499−1504.
- Boeke, J.D. (1997). LINEs and Alus~the polyA connection. Nat Genet 16,6−7.
- Boeke, J.D., Eickbush, Т.Н., Sandmeyer, S.B., and Voytas, D.F. (2002). Pseudoviridae. In Virus Taxonomy: Eighth Report of International Committee on Taxonomy of Viruses. Edited by Fauquet C.M. New York: Academic Press.
- Boeke, J.D., Eickbush, Т.Н., Sandmeyer, S.B., and Voytas, D.F. (2004). Metaviridae. In Virus Taxonomy: Eighth Report of International Committee on Taxonomy of Viruses. Edited by Fauquet C.M. New York: Academic Press.
- Borchert, G.M., Lanier, W., and Davidson, B.L. (2006). RNA polymerase III transcribes human microRNAs. Nature structural & molecular biology 13,1097−1101.
- Borodulina, O.R., and Kramerov, D.A. (1999). Wide distribution of short interspersed elements among eukaryotic genomes. FEBS Lett 457,409−413.
- 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.
- Borodulina, O.R., and Kramerov, D.A. (2005). PCR-based approach to SINE isolation: Simple and complex SINEs. Gene 349,197−205.
- Bowen, N.J., and McDonald, J.F. (1999). Genomic analysis of Caenorhabditis elegans reveals ancient families of retroviral-like elements. Genome Res 9,924−935.
- Brini, A.T., Lee, G.M., and Kinet, J.P. (1993). Involvement of Alu sequences in the cell-specific regulation of transcription of the gamma chain of Fc and T cell receptors. J Biol Chem 268,1355−1361.
- Britten, R.J. (1994). Evidence that most human Alu sequences were inserted in a process that ceased about 30 million years ago. Proc Natl Acad Sci U S A 91,6148−6150.
- Brookfield, J.F. (2005). The ecology of the genome mobile DNA elements and their hosts. Nature reviews 6,128−136.
- Bureau, Т.Е., White, S.E., and Wessler, S.R. (1994). Transduction of a cellular gene by a plant retroelement. Cell 77,479−480.
- Burke, W.D., Calalang, C.C., and Eickbush, Т.Н. (1987). 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.
- Burke, W.D., Muller, F., and Eickbush, Т.Н. (1995). R4, a non-LTR retrotransposon specific to the large subunit rRNA genes of nematodes. Nucleic Acids Res 23,4628−4634.
- Butler, M., Goodwin, Т., Simpson, M" Singh, M., and Poulter, R. (2001). Vertebrate LTR retrotransposons of the Tfl/sushi group. J Mol Evol 52,260−274.
- Cambareri, E.B., Helber, J., and Kinsey, J.A. (1994). Tadl-1, an active LINE-like element of Neurospora crassa. Mol Gen Genet 242,658−665.
- Carter, A.B., Salem, A.H., Hedges, D.J., Keegan, C.N., Kimball, В., Walker, J.A., Watkins, W.S., Jorde, L.B., and Batzer, M.A. (2004). Genome-wide analysis of the human Alu Yb-lineage. Human genomics 1,167−178.
- Chesnokov, I., and Schmid, C.W. (1996). Flanking sequences of an Alu source stimulate transcription in vitro by interacting with sequence-specific transcription factors. J Mol Evol 42,30−36.
- Chu, W.M., Ballard, R., Carpick, B.W., Williams, B.R., and Schmid, C.W. (1998). Potential Alu function: regulation of the activity of double-stranded RNA-activated kinase PKR. Mol Cell Biol 18,58−68.
- 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.
- Churakov, G., Smit, A.F., Brosius, J., and Schmitz, J. (2005). A Novel Abundant Family of Retroposed Elements (DAS-SINEs) in the Nine-Banded Armadillo (Dasypus novemcinctus). Mol Biol Evol 22,886−893.
- Claypool, J.A., Malik, H.S., Eickbush, Т.Н., and Sandmeyer, S.B. (2001). Ten-kilodalton domain in Ty3 Gag3-Pol3p between PR and RT is dispensable for Ty3 transposition. J Virol 75,1557−1560.
- Comeron, J.M. (2001). What controls the length of noncoding DNA? Curr Opin Genet Dev 11,652−659.
- Cordaux, R., Hedges, D.J., Herke, S.W., and Batzer, M.A. (2006). Estimating the retrotransposition rate of human Alu elements. Gene 373,134−137.
- Cost, G.J., Feng, Q., Jacquier, A., and Boeke, J.D. (2002). Human LI element target-primed reverse transcription in vitro. Embo J 21,5899−5910.
- Dagan, Т., Sorek, R., Sharon, E., Ast, G., and Graur, D. (2004). AluGene: a database of Alu elements incorporated within protein-coding genes. Nucleic Acids Res 32, D489−492.
- Daniels, G.R., and Deininger, P.L. (1983). A second major class of Alu family repeated DNA sequences in a primate genome. Nucleic Acids Res 11,7595−7610.
- Daniels, G.R., and Deininger, P.L. (1985). Repeat sequence families derived from mammalian tRNA genes. Nature 317, 819−822.
- Deininger, P.L., and Batzer, M.A. (1999). Alu repeats and human disease. Molecular genetics and metabolism 67, 183−193.
- Deininger, P.L., Batzer, M.A., Hutchison, C.A., 3rd, and Edgell, M.H. (1992). Master genes in mammalian repetitive DNA amplification. Trends Genet 8,307−311.
- Dewannieux, M., Esnault, C., and Heidmann, T. (2003). LINE-mediated retrotransposition of marked Alu sequences. Nat Genet 35,41−48.
- Dewannieux, M., and Heidmann, T. (2005a). LI-mediated retrotransposition of murine BI and B2 SINEs recapitulated in cultured cells. Journal of molecular biology 349,241−247.
- Dewannieux, M., and Heidmann, T. (2005b). LINEs, SINEs and processed pseudogenes: parasitic strategies for genome modeling. Cytogenetic and genome research 110,35−48.
- Dewannieux, M., and Heidmann, T. (2005c). Role of poly (A) tail length in Alu retrotransposition. Genomics 86,378−381.
- Dignam, J.D., Lebovitz, R.M., and Roeder, R.G. (1983). Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res 11,1475−1489.
- Doolittle, W.F., and Sapienza, C. (1980). Selfish genes, the phenotype paradigm and genome evolution. Nature 284,601−603.
- Duncan, C.H. (1987). Novel Alu-type repeat in artiodactyls. Nucleic Acids Res 15,1340.
- Elder, J.T., Pan, J., Duncan, C.H., and Weissman, S.M. (1981). Transcriptional analysis of interspersed repetitive polymerase III transcription units in human DNA. Nucleic Acids Res 9, 1171−1189.
- Englert, M., Felis, M., Junker, V., and Beier, H. (2004). Novel upstream and intragenic control elements for the RNA polymerase Ill-dependent transcription of human 7SL RNA genes. Biochimie 86,867−874.
- Esnault, C., Maestre, J., and Heidmann, T. (2000). Human LINE retrotransposons generate processed pseudogenes. Nat Genet 24,363−367.
- Espinoza, C.A., Allen, T.A., Hieb, A.R., Kugel, J.F., and Goodrich, J.A. (2004). B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. Nature structural & molecular biology 11,822−829.
- Felger, I., and Hunt, J.A. (1992). A non-LTR retrotransposon from the Hawaiian Drosophila: the LOA element. Genetica 85,119−130.
- Felsenstein, J. (1985). Phylogenies from Gene Frequencies: A Statistical Problem. Systematic Zoology 300−311.
- Felsenstein, J. (1989). PHYLIP Phylogeny Inference Package (Version 3.2). Cladistics 5, 164−166.
- Feng, Q., Moran, J.V., Kazazian, H.H., Jr., and Boeke, J.D. (1996). Human LI retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87, 905−916.
- Ferrigno, O., Virolle, Т., Djabari, Z., Ortonne, J.P., White, R.J., and Aberdam, D. (2001). Transposable B2 SINE elements can provide mobile RNA polymerase II promoters. Nat Genet 28, 77−81.
- Fornace, A.J., Jr., and Mitchell, J.B. (1986). Induction of B2 RNA polymerase III transcription by heat shock: enrichment for heat shock induced sequences in rodent cells by hybridization subtraction. Nucleic Acids Res 14,5793−5811.
- Fornasari, D., Battaglioli, E., Flora, A., Terzano, S., and Clementi, F. (1997). Structural and functional characterization of the human alpha3 nicotinic subunit gene promoter. Molecular pharmacology 51, 250−261.
- Frame, I.G., Cutfield, J.F., and Poulter, R.T. (2001). New BEL-like LTR-retrotransposons in Fugu rubripes, Caenorhabditis elegans, and Drosophila melanogaster. Gene 263,219−230.
- Friesen, N., Brandes, A., and Heslop-Harrison, J.S. (2001). Diversity, origin, and distribution of retrotransposons (gypsy and copia) in conifers. Mol Biol Evol 18,1176−1188.
- Fuhrman, S.A., Deininger, P.L., LaPorte, P., Friedmann, Т., and Geiduschek, E.P. (1981). Analysis of transcription of the human Alu family ubiquitous repeating element by eukaryotic RNA polymerase III. Nucleic Acids Res 9,6439−6456.
- Gabriel, A., Yen, T.J., Schwartz, D.C., Smith, C.L., Boeke, J.D., Sollner-Webb, В., and Cleveland, D.W. (1990). A rapidly rearranging retrotransposon within the miniexon gene locus of Crithidia fasciculata. Mol Cell Biol 10,615−624.
- Gilbert, N., and Labuda, D. (1999). CORE-SINEs: eukaryotic short interspersed retroposing elements with common sequence motifs. Proc Natl Acad Sci USA 96,2869−2874.
- Gilbert, N., Lutz-Prigge, S., and Moran, J.V. (2002). Genomic deletions created upon LINE-1 retrotransposition. Cell 110,315−325.
- Gogolevskaya, I.K., Koval, A.P., and Kramerov, D.A. (2005). Evolutionary History of 4.5SH RNA. Mol Biol Evol.
- Gogolevskaya, I.K., and Kramerov, D.A. (2002). Evolutionary history of 4.5SI RNA and indication that it is functional. J Mol Evol 54,354−364.
- Gogolevsky, K.P., and Kramerov, D.A. (2006). Short interspersed elements (SINEs) of the Geomyoidea superfamily rodents. Gene 373,67−14.
- Goodier, J.L., and Maraia, R.J. (1998). Terminator-specific recycling of a Bl-Alu transcription complex by RNA polymerase III is mediated by the RNA terminus-binding protein La. J Biol Chem 273,26 110−26 116.
- Goodwin, T.J., and Poulter, R.T. (2002). A group of deuterostome ТуЗ/ gypsy-like retrotransposons with Tyl/ copia-like pol-domain orders. Mol Genet Genomics 267,481−491.
- Gorinsek, В., Gubensek, F., and Kordis, D. (2004). Evolutionary genomics of chromoviruses in eukaryotes. Mol Biol Evol 21,781−798.
- Hambor, J.E., Mennone, J., Coon, M.E., Hanke, J.H., and Kavathas, P. (1993). Identification and characterization of an Alu-containing, T-cell-specific enhancer located in the last intron of the human CD8 alpha gene. Mol Cell Biol 13, 7056−7070.
- Hamdi, H.K., Nishio, H., Tavis, J., Zielinski, R., and Dugaiczyk, A. (2000). Alu-mediated phylogenetic novelties in gene regulation and development. Journal of molecular biology 299, 931−939.
- Han, K., Xing, J., Wang, H., Hedges, D.J., Garber, R.K., Cordaux, R., and Batzer, M.A. (2005). Under the genomic radar: the stealth model of Alu amplification. Genome Res 15, 655−664.
- Hanke, J.H., Hambor, J.E., and Kavathas, P. (1995). Repetitive Alu elements form a cruciform structure that regulates the function of the human CD8 alpha T cell-specific enhancer. Journal of molecular biology 246,63−73.
- Hartner, J.C., Schmittwolf, C., Kispert, A., Muller, A.M., Higuchi, M., and Seeburg, P.H. (2004). Liver disintegration in the mouse embryo caused by deficiency in the RNA-editing enzyme ADAR1. J Biol Chem 279,4894−4902.
- Hasler, J., and Strub, K. (2006). Alu elements as regulators of gene expression. Nucleic Acids Res 34,5491−5497.
- Havecker, E.R., Gao, X., and Voytas, D.F. (2004). The diversity of LTR retrotransposons. Genome Biol 5,225.
- Haynes, S.R., and Jelinek, W.R. (1981). Low molecular weight RNAs transcribed in vitro by RNA polymerase III from Alu-type dispersed repeats in Chinese hamster DNA are also found in vivo. Proc Natl Acad Sci USA 78,6130−6134.
- Hellmann-Blumberg, U., Hintz, M.F., Gatewood, J.M., and Schmid, C.W. (1993). Developmental differences in methylation of human Alu repeats. Mol Cell Biol 13, 45 234 530.
- Herrera, R.J., Rojas, D.P., and Terreros, M.C. (2007). Polymorphic Alu insertions among Mayan populations. Journal of human genetics 52,129−142.
- Huchon, D., Chevret, P., Jordan, U., Kilpatrick, C.W., Ranwez, V., Jenkins, P.D., Brosius, J., and Schmitz, J. (2007). Multiple molecular evidences for a living mammalian fossil. Proc Natl Acad Sci U S A 104,7495−7499.
- Huchon, D., and Douzery, E.J. (2001). From the Old World to the New World: a molecular chronicle of the phylogeny and biogeography of hystricognath rodents. Mol Phylogenet Evol 20,238−251.
- Inoue, H., Nojima, H., and Okayama, H. (1990). High efficiency transformation of Escherichia coli with plasmids. Gene 96,23−28.
- Jagadeeswaran, P., Forget, B.G., and Weissman, S.M. (1981). Short interspersed repetitive DNA elements in eucaryotes: transposable DNA elements generated by reverse transcription of RNA pol III transcripts? Cell 26,141−142.
- Jin, Y.K., and Bennetzen, J.L. (1994). Integration and nonrandom mutation of a plasma membrane proton ATPase gene fragment within the Bsl retroelement of maize. Plant Cell 6, 1177−1186.
- Jobse, C., Buntjer, J.B., Haagsma, N., Breukelman, H.J., Beintema, J.J., and Lenstra, J.A. (1995). Evolution and recombination of bovine DNA repeats. J Mol Evol 41,277−283.
- Jordan, I.K., Matyunina, L.V., and McDonald, J.F. (1999). Evidence for the recent horizontal transfer of long terminal repeat retrotransposon. Proc Natl Acad Sci U S A 96,12 621−12 625.
- Jurka, J. (1997). Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc Natl Acad Sci USA 94,1872−1877.
- Jurka, J., and Milosavljevic, A. (1991). Reconstruction and analysis of human Alu genes. J Mol Evol 32,105−121.
- Jurka, J., and Zuckerkandl, E. (1991). Free left arms as precursor molecules in the evolution of Alu sequences. J Mol Evol 33,49−56.
- Kajikawa, M., and Okada, N. (2002). LINEs mobilize SINEs in the eel through a shared 3' sequence. Cell 111, 433−444.
- Kalendar, R., Vicient, C.M., Peleg, 0., Anamthawat-Jonsson, K., Bolshoy, A., and Schulman, A.H. (2004). Large retrotransposon derivatives: abundant, conserved but nonautonomous retroelements of barley and related genomes. Genetics 166,1437−1450.
- Kapitonov, V., and Jurka, J. (1996). The age of Alu subfamilies. J Mol Evol 42,59−65.
- Kapitonov, V.V., and Jurka, J. (2003). A Novel Class of SINE Elements Derived from 5S rRNA. Mol Biol Evol 20,694−702.
- Kazazian, H.H., Jr., Wong, C., Youssoufian, H., Scott, A.F., Phillips, D.G., and Antonarakis, S.E. (1988). Haemophilia A resulting from de novo insertion of LI sequences represents a novel mechanism for mutation in man. Nature 332,164−166.
- Khitrinskaia, I, Stepanov, V.A., and Puzyrev, V.P. (2003). Alu repeats in the human genome. Molekuliarnaia biologiia 37,382−391.
- Kim, D.D., Kim, T.T., Walsh, Т., Kobayashi, Y., Matise, T.C., Buyske, S., and Gabriel, A. (2004). Widespread RNA editing of embedded alu elements in the human transcriptome. Genome Res 14,1719−1725.
- Kim, J., Martignetti, J.A., Shen, M.R., Brosius, J., and Deininger, P. (1994). Rodent BC1 RNA gene as a master gene for ID element amplification. Proc Natl Acad Sci U S A 91,36 073 611.
- Kishore, S., and Stamm, S. (2006). The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science 311,230−232.
- Knebelmann, В., Forestier, L., Drouot, L., Quinones, S., Chuet, C., Benessy, F., Saus, J., and Antignac, C. (1995). Splice-mediated insertion of an Alu sequence in the COL4A3 mRNA causing autosomal recessive Alport syndrome. Hum Mol Genet 4,675−679.
- Kobayashi, S., and Anzai, K. (1998). An E-box sequence acts as a transcriptional activator for BC1 RNA expression by RNA polymerase III in the brain. Biochemical and biophysical research communications 245,59−63.
- Kolosha, V.O., and Martin, S.L. (2003). High-affinity, non-sequence-specific RNA binding by the open reading frame 1 (ORF1) protein from long interspersed nuclear element 1 (LINE-1). J Biol Chem 278,8112−8117.
- Kordis, D. (2005). A genomic perspective on the chromodomain-containing retrotransposons: Chromoviruses. Gene 347,161−173.
- Kordis, D., and Gubensek, F. (1997). Bov-B long interspersed repeated DNA (LINE) sequences are present in Vipera ammodytes phospholipase A2 genes and in genomes of Viperidae snakes. Eur J Biochem 246,772−779.
- Kramerov, D., Vassetzky, N., and Serdobova, I. (1999). The evolutionary position of dormice (Gliridae) in Rodentia determined by a novel short retroposon. Mol Biol Evol, 715−716.
- Kramerov, D.A., Lekakh, I.V., Samarina, O.P., and Ryskov, A.P. (1982). The sequences homologous to major interspersed repeats BI and B2 of mouse genome are present in mRNA and small cytoplasmic poly (A) + RNA. Nucleic Acids Res 10,7477−7491.
- Kramerov, D.A., Tillib, S.V., Lekakh, I.V., Ryskov, A.P., and Georgiev, G.P. (1985). Biosynthesis and cytoplasmic distribution of small poly (A)-containing B2 RNA. Biochim Biophys Acta 824,85−98.
- Kramerov, D.A., Tillib, S.V., Shumyatsky, G.P., and Georgiev, G.P. (1990). The most abundant nascent poly (A) + RNAs are transcribed by RNA polymerase III in murine tumor cells. Nucleic Acids Res 18,4499−4506.
- Kramerov, D.A., and Vassetzky, N.S. (2001). Structure and origin of a novel dimeric retroposon В 1-diD. J Mol Evol 52,137−143.
- Kramerov, D.A., and Vassetzky, N.S. (2005). Short retroposons in eukaryotic genomes. International review of cytology 247,165−221.
- Krayev, A.S., Markusheva, T.V., Kramerov, D.A., Ryskov, A.P., Skryabin, K.G., Bayev, A. A., and Georgiev, G.P. (1982). Ubiquitous transposon-like repeats BI and B2 of the mouse genome: B2 sequencing. Nucleic Acids Res 10,7461−7475.
- Kriegs, J.O., Churakov, G., Jurka, J., Brosius, J., and Schmitz, J. (2007). Evolutionary history of 7SL RNA-derived SINEs in Supraprimates. Trends Genet 23,158−161.
- Labuda, D., Sinnett, D., Richer, C., Deragon, J.M., and Striker, G. (1991). Evolution of mouse BI repeats: 7SL RNA folding pattern conserved. J Mol Evol 32,405−414.
- Labuda, D., and Striker, G. (1989). Sequence conservation in Alu evolution. Nucleic Acids Res 17,2477−2491.
- Lander, E.S., Linton, L.M., Birren, В., 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.
- Laperriere, D., Wang, T.T., White, J.H., and Mader, S. (2007). Widespread Alu repeat-driven expansion of consensus DR2 retinoic acid response elements during primate evolution. BMC genomics 8,23.
- Lawrence, C.B., McDonnell, D.P., and Ramsey, W.J. (1985). Analysis of repetitive sequence elements containing tRNA-Iike sequences. Nucleic Acids Res 13,4239−4252.
- Lee, S.Y., and Rasheed, S. (1990). A simple procedure for maximum yield of high-quality plasmid DNA. BioTechniques 9,676−679.
- Li, Т.Н., and Schmid, C.W. (2001). Differential stress induction of individual Alu loci: implications for transcription and retrotransposition. Gene 276,135−141.
- Lin, Z., Nomura, O., Hayashi, Т., Wada, Y., and Yasue, H. (2001). Characterization of a SINE species from vicuna and its distribution in animal species including the family Camelidae. Mamm Genome 12,305−308.
- Liu, W.M., Chu, W.M., Choudary, P.V., and Schmid, C.W. (1995). Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts. Nucleic Acids Res 23,1758−1765.
- Liu, W.M., Maraia, R.J., Rubin, C.M., and Schmid, C.W. (1994). Alu transcripts: cytoplasmic localisation and regulation by DNA methylation. Nucleic Acids Res 22,1087−1095.
- Luan, D.D., Korman, M.H., Jakubczak, J.L., and Eickbush, Т.Н. (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.
- Ludwig, A., Rozhdestvensky, T.S., Kuryshev, V.Y., Schmitz, J., and Brosius, J. (2005). An unusual primate locus that attracted two independent Alu insertions and facilitates their transcription. Journal of molecular biology 350,200−214.
- Lyon, M.F. (1998). X-chromosome inactivation: a repeat hypothesis. Cytogenet Cell Genet 80,133−137.
- Majewska, K., Szemraj, J., Plucienniczak, G., Jaworski, J., and Plucienniczak, A. (1988). A new family of dispersed, highly repetitive sequences in bovine genome. Biochim Biophys Acta 949,119−124.
- Makalowski, W., Mitchell, G.A., and Labuda, D. (1994). Alu sequences in the coding regions of mRNA: a source of protein variability. Trends Genet 10,188−193.
- Maksakova, I.A., Romanish, M.T., Gagnier, L., Dunn, C.A., van de Lagemaat, L.N., and Mager, D.L. (2006). Retroviral elements and their hosts: insertional mutagenesis in the mouse germ line. PLoS Genet 2, e2.
- Malik, H.S., Burke, W.D., and Eickbush, Т.Н. (1999). The age and evolution of non-LTR retrotransposable elements. Mol Biol Evol 16,793−805.
- Malik, H.S., and Eickbush, Т.Н. (1999). Modular evolution of the integrase domain in the Ty3/Gypsy class of LTR retrotransposons. J Virol 73,5186−5190.
- Malik, H.S., Henikoff, S., and Eickbush, Т.Н. (2000). Poised for contagion: evolutionary origins of the infectious abilities of invertebrate retroviruses. Genome Res 10,1307−1318.
- Maraia, R.J. (1991). The subset of mouse BI (Alu-equivalent) sequences expressed as small processed cytoplasmic transcripts. Nucleic Acids Res 19,5695−5702.
- Maraia, R.J. (2001). La protein and the trafficking of nascent RNA polymerase iii transcripts. The Journal of cell biology 153, F13−18.
- Maraia, R.J., Chang, D.Y., Wolffe, A.P., Vorce, R.L., and Hsu, K. (1992). The RNA polymerase III terminator used by a Bl-Alu element can modulate 3' processing of the intermediate RNA product. Mol Cell Biol 12,1500−1506.
- Marin, I., and Llorens, C. (2000). Ty3/Gypsy retrotransposons: description of new Arabidopsis thaliana elements and evolutionary perspectives derived from comparative genomic data. Mol Biol Evol 17,1040−1049.
- Martignetti, J.A., and Brosius, J. (1995). BC1 RNA: transcriptional analysis of a neural cell-specific RNA polymerase III transcript. Mol Cell Biol 15,1642−1650.
- Martin, S.L. (1991). Ribonucleoprotein particles with LINE-1 RNA in mouse embryonal carcinoma cells. Mol Cell Biol //, 4804−4807.
- Martin, S.L., and Bushman, F.D. (2001). Nucleic acid chaperone activity of the ORF1 protein from the mouse LINE-1 retrotransposon. Mol Cell Biol 21,467−475.
- Martinez-Izquierdo, J.A., Garcia-Martinez, J., and Vicient, C.M. (1997). What makes Grande 1 retrotransposon different? Genetica 100,15−28.
- Mathias, S.L., Scott, A.F., Kazazian, H.H., Jr., Boeke, J.D., and Gabriel, A. (1991). Reverse transcriptase encoded by a human transposable element. Science 254,1808−1810.
- Medstrand, P., van de Lagemaat, L.N., and Mager, D.L. (2002). Retroelement distributions in the human genome: variations associated with age and proximity to genes. Genome Res 12, 1483−1495.
- Meischl, C., Boer, M., Ahlin, A., and Roos, D. (2000). A new exon created by intronic insertion of a rearranged LINE-1 element as the cause of chronic granulomatous disease. Eur J Hum Genet 8,697−703.
- Modi, W.S., Gallagher, D.S., and Womack, J.E. (1996). Evolutionary histories of highly repeated DNA families among the Artiodactyla (Mammalia). J Mol Evol 42,337−349.
- Modrek, В., and Lee, C. (2002). A genomic view of alternative splicing. Nat Genet 30,13−19.
- Moran, J.V., DeBerardinis, R.J., and Kazazian, H.H., Jr. (1999). Exon shuffling by LI retrotransposition. Science 283,1530−1534.
- Munclinger, P., Boursot, P., and Dod, B. (2003). Bl insertions as easy markers for mouse population studies. Mamm Genome 14,359−366.
- Murphy, W.J., Pringle, Т.Н., Crider, T.A., Springer, M.S., and Miller, W. (2007). Using genomic data to unravel the root of the placental mammal phylogeny. Genome Res /7, 413 421.
- Muslimov, I.A., Santi, E" Homel, P., Perini, S., Higgins, D., and Tiedge, H. (1997). RNA transport in dendrites: a cis-acting targeting element is contained within neuronal BC1 RNA. J Neurosci 17,4722−4733.
- Nekrutenko, A., and Li, W.H. (2001). Transposable elements are found in a large number of human protein-coding genes. Trends Genet 17,619−621.
- Neuveglise, C., Feldmann, H., Bon, E., Gaillardin, C., and Casaregola, S. (2002). Genomic evolution of the long terminal repeat retrotransposons in hemiascomycetous yeasts. Genome Res 12,930−943.
- Nikaido, M., Nishihara, H., Hukumoto, Y., and Okada, N. (2003). Ancient SINEs from African endemic mammals. Mol Biol Evol 20,522−527.
- Nikaido, M., Piskurek, O., and Okada, N. (2006). Toothed whale monophyly reassessed by SINE insertion analysis: The absence of lineage sorting effects suggests a small population of a common ancestral species. Mol Phylogenet Evol.
- Nishihara, H., Smit, A.F., and Okada, N. (2006). Functional noncoding sequences derived from SINEs in the mammalian genome. Genome Res 16,864−874.
- Nishihara, H., Terai, Y., and Okada, N. (2002). Characterization of Novel Alu- and tRNA-Related SINEs from the Tree Shrew and Evolutionary Implications of Their Origins. Mol Biol Evol 19,1964−1972.
- Novoa, I., and Carrasco, L. (1999). Cleavage of eukaryotic translation initiation factor 4G by exogenously added hybrid proteins containing poliovirus 2Apro in HeLa cells: effects on gene expression. Mol Cell Biol 19,2445−2454.
- Ogiwara, I., Miya, M" Ohshima, K., and Okada, N. (2002). V-SINEs: a new superfamily of vertebrate SINEs that are widespread in vertebrate genomes and retain a strongly conserved segment within each repetitive unit. Genome Res 12,316−324.
- Ohshima, К., Hamada, M., Terai, Y., and 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.
- Ohtsubo, H., Kumekawa, N., and Ohtsubo, E. (1999). RIRE2, a novel gypsy-type retrotransposon from rice. Genes Genet Syst 74,83−91.
- Okada, N., and 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 44,52−56.
- Okada, N., and Ohshima, K. (1995). Evolution of tRNA-derived SINEs. In The impact of short interspersed elements (SINEs) on the host genome, R.J. Maraia, ed. (Austin, R.G. Landes), p. 61.
- Opazo, J.C. (2005). A molecular timescale for caviomorph rodents (Mammalia, Hystricognathi). Mol Phylogenet Evol 37,932−937.
- Orgel, L.E., and Crick, F.H. (1980). Selfish DNA: the ultimate parasite. Nature 284,604−607.
- Paul, M.S., and Bass, B.L. (1998). Inosine exists in mRNA at tissue-specific levels and is most abundant in brain mRNA. Embo J 77,1120−1127.
- Paule, M.R., and White, R.J. (2000). Survey and summary: transcription by RNA polymerases I and III. Nucleic Acids Res 28,1283−1298.
- Pecon-Slattery, J., Pearks Wilkerson, A.J., Murphy, W.J., and O’Brien, S.J. (2004). Phylogenetic assessment of introns and SINEs within the Y chromosome using the cat family felidae as a species tree. Mol Biol Evol 21,2299−2309.
- Pelissier, Т., Bousquet-Antonelli, C., Lavie, L., and Deragon, J.M. (2004). Synthesis and processing of tRNA-related SINE transcripts in Arabidopsis thaliana. Nucleic Acids Res 32, 3957−3966.
- Perepelitsa-Belancio, V., and Deininger, P. (2003). RNA truncation by premature polyadenylation attenuates human mobile element activity. Nat Genet 35, 363−366.
- Perez-Stable, C., Ayres, T.M., and Shen, C.K. (1984). Distinctive sequence organization and functional programming of an Alu repeat promoter. Proc Natl Acad Sci USA 81,5291−5295.
- Piedrafita, F.J., Molander, R.B., Vansant, G., Orlova, E.A., Pfahl, M., and Reynolds, W.F. (1996). An Alu element in the myeloperoxidase promoter contains a composite SP1-thyroid hormone-retinoic acid response element. J Biol Chem 271,14 412−14 420.
- Priimagi, A.F., Mizrokhi, L.J., and Ilyin, Y.V. (1988). The Drosophila mobile element jockey belongs to LINEs and contains coding sequences homologous to some retroviral proteins. Gene 70,253−262.
- Quentin, Y. (1989). Successive waves of fixation of BI variants in rodent lineage history. J Mol Evol 28,299−305.
- Quentin, Y. (1992). Origin of the Alu family: a family of Alu-like monomers gave birth to the left and the right arms of the Alu elements. Nucleic Acids Res 20,3397−3401.
- Quentin, Y. (1994a). Emergence of master sequences in families of retroposons derived from 7sl RNA. Genetica 93,203−215.
- Quentin, Y. (1994b). A master sequence related to a free left Alu monomer (FLAM) at the origin of the В1 family in rodent genomes. Nucleic Acids Res 22,2222−2227.
- Roos, C., Schmitz, J., and Zischler, H. (2004). Primate jumping genes elucidate strepsirrhine phylogeny. Proc Natl Acad Sci U S A101,10 650−10 654.
- Rothenburg, S., Eiben, M., Koch-Nolte, F., and Haag, F. (2002). Independent integration of rodent identifier (ID) elements into orthologous sites of some RT6 alleles of Rattus norvegicus and Rattus rattus. J Mol Evol 55,251−259.
- Roy-Engel, A.M., Carroll, M.L., El-Sawy, M., Salem, A.H., Garber, R.K., Nguyen, S.V., Deininger, P.L., and Batzer, M.A. (2002). Non-traditional Alu evolution and primate genomic diversity. Journal of molecular biology 316,1033−1040.
- 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.
- Roy-Engel, A.M., El-Sawy, M., Farooq, L., Odom, G.L., Perepelitsa-Belancio, V., Bruch, H., Oyeniran, O.O., and Deininger, P.L. (2005). Human retroelements may introduce intragenic polyadenylation signals. Cytogenetic and genome research 110,365−371.
- 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.
- Rozhdestvensky, T.S., Kopylov, A.M., Brosius, J., and Huttenhofer, A. (2001). Neuronal BC1 RNA structure: evolutionary conversion of a tRNA (Ala) domain into an extended stem-loop structure. RNA (New York, NY 7,722−730.
- Rubin, C.M., Kimura, R.H., and Schmid, C.W. (2002). Selective stimulation of translational expression by Alu RNA. Nucleic Acids Res 30,3253−3261.
- Ryskov, A.P., Ivanov, P.L., Kramerov, D.A., and Georgiev, G.P. (1983). Mouse ubiquitous B2 repeat in polysomal and cytoplasmic poly (A)+RNAs: uniderectional orientation and 3'-end localization. Nucleic Acids Res 11,6541−6558.
- Sabot, F., Sourdille, P., Chantret, N., and Bernard, M. (2006). Morgane, a new LTR retrotransposon group, and its subfamilies in wheats. Genetica 128,439−447.
- Sakamoto, K., and Okada, N. (1985). Rodent type 2 Alu family, rat identifier sequence, rabbit С family, and bovine or goat 73-bp repeat may have evolved from tRNA genes. J Mol Evol 22,134−140.
- Salem, A.H., Ray, D.A., Hedges, D.J., Jurka, J., and Batzer, M.A. (2005). Analysis of the human Alu Ye lineage. BMC evolutionary biology 5,18.
- Schoeniger, L.O., and Jelinek, W.R. (1986). 4.5S RNA is encoded by hundreds of tandemly linked genes, has a short half-life, and is hydrogen bonded in vivo to poly (A)-terminated RNAs in the cytoplasm of cultured mouse cells. Mol Cell Biol 6,1508−1519.
- Schramm, L., and Hernandez, N. (2002). Recruitment of RNA polymerase III to its target promoters. Genes Dev 16,2593−2620.
- Schwahn, U., Lenzner, S., Dong, J., Feil, S., Hinzmann, В., van Duijnhoven, G., Kirschner, R., Hemberger, M., Bergen, A.A., Rosenberg, Т., et al. (1998). Positional cloning of the gene for X-linked retinitis pigmentosa 2. Nat Genet 19,327−332.
- Serdobova, I.M., and Kramerov, D.A. (1998). Short retroposons of the B2 superfamily: evolution and application for the study of rodent phylogeny. J Mol Evol 46,202−214.
- Shaikh, Т.Н., and Deininger, P.L. (1996). The role and amplification of the HS Alu subfamily founder gene. J Mol Evol 42,15−21.
- Shaikh, Т.Н., Roy, A.M., Kim, J., Batzer, M.A., and Deininger, P.L. (1997). eDNAs derived from primary and small cytoplasmic Alu (scAlu) transcripts. Journal of molecular biology 271,222−234.
- Sharan, C., Hamilton, N.M., Pari, A.K., Singh, P.K., and Chaudhuri, G. (1999). Identification and characterization of a transcriptional silencer upstream of the human BRCA2 gene. Biochemical and biophysical research communications 265,285−290.
- Shedlock, A.M., and Okada, N. (2000). SINE insertions: powerful tools for molecular systematics. Bioessays 22,148−160.
- Shimamura, M., Nikaido, M., Ohshima, K., and Okada, N. (1998). A SINE that acquired a role in signal transduction during evolution. Mol Biol Evol 15,923−925.
- Shimamura, M., Yasue, H., Ohshima, K., Abe, H., Kato, H" Kishiro, Т., Goto, M., Munechika, I., and Okada, N. (1997). Molecular evidence from retroposons that whales form a clade within even-toed ungulates. Nature 388,666−670.
- Shimba, S., Buckley, В., Reddy, R., Kiss, Т., and Filipowicz, W. (1992). Cap structure of U3 small nucleolar RNA in animal and plant cells is different. gamma-Monomethyl phosphate cap structure in plant RNA. J Biol Chem 267,13 772−13 777.
- Shumyatsky, G., Wright, D., and Reddy, R. (1993). Methylphosphate cap structure increases the stability of 7SK, B2 and U6 small RNAs in Xenopus oocytes. Nucleic Acids Res 21, 4756−4761.
- Shumyatsky, G.P., Tillib, S.V., and Kramerov, D.A. (1990). B2 RNA and 7SK RNA, RNA polymerase III transcripts, have a cap-like structure at their 5' end. Nucleic Acids Res 18, 6347−6351.
- Silva, R., and Burch, J.B. (1989). Evidence that chicken CR1 elements represent a novel family of retroposons. Mol Cell Biol 9,3563−3566.
- Singh, R., and Reddy, R. (1989). Gamma-monomethyl phosphate: a cap structure in spliceosomal U6 small nuclear RNA. Proc Natl Acad Sci USA 86, 8280−8283.
- Smit, A.F. (1996). The origin of interspersed repeats in the human genome. Curr Opin Genet Dev 6,743−748.
- Sorek, R., Ast, G., and Graur, D. (2002). Alu-containing exons are alternatively spliced. Genome Res 12,1060−1067.
- Steppan, S., Adkins, R., and Anderson, J. (2004). Phylogeny and divergence-date estimates of rapid radiations in muroid rodents based on multiple nuclear genes. Syst Biol 53, 533−553.
- Sun, F.J., Fleurdepine, S., Bousquet-Antonelli, C., Caetano-Anolles, G., and Deragon, J.M. (2007). Common evolutionary trends for SINE RNA structures. Trends Genet 23,26−33.
- Suoniemi, A., Tanskanen, J., and Schulman, A.H. (1998). Gypsy-like retrotransposons are widespread in the plant kingdom. Plant J13,699−705.
- Sutcliffe, J.G., Milner, R.J., Bloom, F.E., and Lerner, R.A. (1982). Common 82-nucleotide sequence unique to brain RNA. Proc Natl Acad Sci USA 79,4942−4946.
- Symer, D.E., Connelly, C., Szak, S.T., Caputo, E.M., Cost, G.J., Parmigiani, G., and Boeke, J.D. (2002). Human 11 retrotransposition is associated with genetic instability in vivo. Cell 110,327−338.
- Terai, Y., Takahashi, K., Nishida, M., Sato, Т., and Okada, N. (2003). Using SINEs to probe ancient explosive speciation: «hidden» radiation of African cichlids? Mol Biol Evol 20, 924 930.
- Thanaraj, T.A., Clark, F., and Muilu, J. (2003). Conservation of human alternative splice events in mouse. Nucleic Acids Res 31,2544−2552.
- Tiedge, H., Chen, W., and Brosius, J. (1993), Primary structure, neural-specific expression, and dendritic location of human BC200 RNA. J Neurosci 13,2382−2390.
- Tomilin, N.V. (1999). Control of genes by mammalian retroposons. International review of cytology 186,1−48.
- Toyoda, N., Zavacki, A.M., Maia, A.L., Harney, J.W., and Larsen, P.R. (1995). A novel retinoid X receptor-independent thyroid hormone response element is present in the human type 1 deiodinase gene. Mol Cell Biol 15,5100−5112.
- Ullu, E., and Tschudi, C. (1984). Alu sequences are processed 7SL RNA genes. Nature 312, 171−172.
- Ullu, E., and Weiner, A.M. (1984). Human genes and pseudogenes for the 7SL RNA component of signal recognition particle. Embo J 3,3303−3310.
- Vansant, G., and Reynolds, W.F. (1995). The consensus sequence of a major Alu subfamily contains a functional retinoic acid response element. Proc Natl Acad Sci U S A 92, 82 298 233.
- Vassetzky, N.S., Ten, O.A., and Kramerov, D.A. (2003). BI and related SINEs in mammalian genomes. Gene 319,149−160.
- Vervoort, R., Gitzelmann, R., Lissens, W., and Liebaers, I. (1998). A mutation (IVS8+0.6kbdelTC) creating a new donor splice site activates a cryptic exon in an Alu-element in intron 8 of the human beta-glucuronidase gene. Human genetics 103,686−693.
- Vicient, C.M., Kalendar, R., and Schulman, A.H. (2001). Envelope-class retrovirus-like elements are widespread, transcribed and spliced, and insertionally polymorphic in plants. Genome Res 11, 2041−2049.
- Volff, J., Korting, C., and Schartl, M. (2001). Ty3/Gypsy retrotransposon fossils in mammalian genomes: did they evolve into new cellular functions? Mol Biol Evol 18, 266 270.
- Volff, J.N., Lehrach, H., Reinhardt, R., and Chourrout, D. (2004). Retroelement dynamics and a novel type of chordate retrovirus-like element in the miniature genome of the tunicate Oikopleura dioica. Mol Biol Evol 21,2022−2033.
- Wahle, E., and Ruegsegger, U. (1999). З'-End processing of pre-mRNA in eukaryotes. FEMS Microbiol Rev 23,277−295.
- Walter, P., and Blobel, G. (1983). Disassembly and reconstitution of signal recognition particle. Cell 34,525−533.
- Wang, H., Iacoangeli, A., Lin, D., Williams, K., Denman, R.B., Hellen, C.U., and Tiedge, H. (2005). Dendritic BC1 RNA in translational control mechanisms. The Journal of cell biology 777,811−821.
- Waterston, R.H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J.F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An, P., et al. (2002). Initial sequencing and comparative analysis of the mouse genome. Nature 420,520−562.
- 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 LI retrotransposition: cis preference versus trans complementation. Mol Cell Biol 21,1429−1439.
- Weil, P.A., Segall, J., Harris, В., Ng, S.Y., and Roeder, R.G. (1979). Faithful transcription of eukaryotic genes by RNA polymerase III in systems reconstituted with purified DNA templates. J Biol Chem 254,6163−6173.
- Weiner, A.M. (2002). SINEs and LINEs: the art of biting the hand that feeds you. Curr Opin Cell Biol 14,343−350.
- West, N. Roy-Engel, A.M., Imataka, H., Sonenberg, N., and Deininger, P. (2002). Shared protein components of SINE RNPs. Journal of molecular biology 321,423−432.
- Wilson, E.T., Condliffe, D.P., and Sprague, K.U. (1988). Transcriptional properties of BmX, a moderately repetitive silkworm gene that is an RNA polymerase III template. Mol Cell Biol 8, 624−631.
- Witte, C.P., Le, Q.H., Bureau, Т., and Kumar, A. (2001). Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes. Proc Natl Acad Sci U S A 98, 13 778−13 783.
- Wright, D.A., and Voytas, D.F. (2002). Athila4 of Arabidopsis and Calypso of soybean define a lineage of endogenous plant retroviruses. Genome Res 12,122−131.
- Wu, J., Grindlay, G.J., Bushel, P., Mendelsohn, L., and Allan, M. (1990). Negative regulation of the human epsilon-globin gene by transcriptional interference: role of an Alu repetitive element. Mol Cell Biol 10,1209−1216.
- Xiong, Y., and Eickbush, Т.Н. (1988). The site-specific ribosomal DNA insertion element RIBm belongs to a class of non-long-terminal-repeat retrotransposons. Mol Cell Biol 8, 114 123.
- Xu, C.F., Chambers, J.A., and Solomon, E. (1997). Complex regulation of the BRCA1 gene. J Biol Chem 272,20 994−20 997.
- Yang, J., Malik, H.S., and Eickbush, Т.Н. (1999). Identification of the endonuclease domain encoded by R2 and other site-specific, non-long terminal repeat retrotransposable elements. Proc Natl Acad Sci U S A 96,7847−7852.
- Youngman, S., van Luenen, H.G., and Plasterk, R.H. (1996). Rte-1, a retrotransposon-like element in Caenorhabditis elegans. FEBS Lett 380,1−7.
- Zhang, C.Y., Kim, S., Harney, J.W., and Larsen, P.R. (1998). Further characterization of thyroid hormone response elements in the human type 1 iodothyronine deiodinase gene. Endocrinology 139,1156−1163.
- Zhou, Y.H., Zheng, J.B., Gu, X., Saunders, G.F., and Yung, W.K. (2002). Novel PAX6 binding sites in the human genome and the role of repetitive elements in the evolution of gene regulation. Genome Res 12,1716−1722.
- Zietkiewicz, E., Richer, C., Sinnett, D., and Labuda, D. (1998). Monophyletic origin of Alu elements in primates. J Mol Evol 47,172−182.
- Павлинов, И. (2003). Систематика современных млекопитающих. (Москва, Издательство Московского Университета).
- Семин, Б.В., Ильин, Ю.В. (2005). Многообразие ДКП-ретротранспозонов и механизмы их участия в реорганизации генома. Генетика 41,542−548.
- XTTTTAfAT^CTTTCATAt^l^ri^yT—gS ----—т т с с т с, а т gg «vwy.^r----, ссдсэдДтДтаосталттссАт^Дт--ДД--------gGTGATTGGOgT^gCTT- -gfi
- ТЭ2ТСАССН<�ЗС2стадасщтЛССАТ—ДА tacgtgt? gtctc?ttcagg^*Itgcat—щ --------25jccttatgtggctggac2—аа-AgA^GSTGCAjjATTGTATGigA^AAG—ТА
- А52ааааааааааааллА'"А^^А: — ассааааааааааааалаааладдаЕv^pj^jaaaaaa^^assaa!
- Sral-I3c Sfti-l€b Seal-2 Ob S mi-2lbami-23b AJ71S794 SEHCRYAAl ЛГ438 211 ЛМ0399Э4 AJ715794a AF438220 AJ34B061 jJjS®11®1'
- Тар—04а Тар-04с Тар—05 Твр-08 Тар-09 Тер-16 Т"р-17 T*p-ls» Т"р-25 тер-33 Т"р—40 Тар-44 тар-51 Тар-541. Qncx---GAXTTCTtjaTCT
- FVGGCGGATC ТСГО TG^TTCAAI ag^cggatglgtgtgagttcaa a g g с? gat стщрз т g ас ттс аа1. ЗОЙАТСТЙТд1. ХЩАААгфЧС tcaaaaagacaaaaaaaaiJaJааааааа '*"*шvryw^AAA^
- AY247042 TCATAA^jGACTAGAATAC
- AY247041 ------—---------J
- AY24 7040 AATTAJ^AAATTAAAAT' AY247039 AAAATA^AAAATCATGA'
- AY247034 CATTAGGAAGCCTATTAA".
- BlJUw Лвр-01 Аяр-02 Аир-ОЭ А*р-06 А*р-08 А*р-091. А*р-101. Аяр-11*1. А"р-11Ь1. А*р-11с1. Аар-12″
- Аяр-12Ь А*р-13 А*р-14 А*р-151.GAG
- Выравнивание последовательностей В1-элементов шипохвостов (семейство Anomaluridae). Консенсус (В1Апо) дан сверху. Последовательности Asp-nn были клонированы из Anomcilurus sp. (шипохвост) в этой работе.