Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al: Initial sequencing and analysis of the human genome. Nature. 2001, 409 (6822): 860-921. 10.1038/35057062.
Article
CAS
PubMed
Google Scholar
Singer MF: SINEs and LINEs: highly repeated short and long interspersed sequences in mammalian genomes. Cell. 1982, 28 (3): 433-434. 10.1016/0092-8674(82)90194-5.
Article
CAS
PubMed
Google Scholar
Rogers J: Origins of repeated DNA. Nature. 1985, 317 (6040): 765-766. 10.1038/317765a0.
Article
CAS
PubMed
Google Scholar
Weiner AM, Deininger PL, Efstratiadis A: Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annual review of biochemistry. 1986, 55: 631-661. 10.1146/annurev.bi.55.070186.003215.
Article
CAS
PubMed
Google Scholar
Brosius J: Retroposons – seeds of evolution. Science. 1991, 251 (4995): 753-10.1126/science.1990437.
Article
CAS
PubMed
Google Scholar
Nikaido M, Okada N: CetSINEs and AREs are not SINEs but are parts of cetartiodactyl L1. Mamm Genome. 2000, 11 (12): 1123-1126. 10.1007/s003350010221.
Article
CAS
PubMed
Google Scholar
Kramerov DA, Vassetzky NS: Short retroposons in eukaryotic genomes. Int Rev Cytol. 2005, 247: 165-221. 10.1016/S0074-7696(05)47004-7.
Article
CAS
PubMed
Google Scholar
Ray DA, Xing J, Salem AH, Batzer MA: SINEs of a nearly perfect character. Systematic biology. 2006, 55 (6): 928-935. 10.1080/10635150600865419.
Article
PubMed
Google Scholar
Shedlock AM, Okada N: SINE insertions: powerful tools for molecular systematics. Bioessays. 2000, 22 (2): 148-160. 10.1002/(SICI)1521-1878(200002)22:2<148::AID-BIES6>3.0.CO;2-Z.
Article
CAS
PubMed
Google Scholar
Sasaki T, Takahashi K, Nikaido M, Miura S, Yasukawa Y, Okada N: First application of the SINE (short interspersed repetitive element) method to infer phylogenetic relationships in reptiles: an example from the turtle superfamily Testudinoidea. Mol Biol Evol. 2004, 21 (4): 705-715. 10.1093/molbev/msh069.
Article
CAS
PubMed
Google Scholar
Stoneking M, Fontius JJ, Clifford SL, Soodyall H, Arcot SS, Saha N, Jenkins T, Tahir MA, Deininger PL, Batzer MA: Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa. Genome research. 1997, 7 (11): 1061-1071.
PubMed Central
CAS
PubMed
Google Scholar
Serdobova IM, Kramerov DA: Short retroposons of the B2 superfamily: evolution and application for the study of rodent phylogeny. Journal of molecular evolution. 1998, 46 (2): 202-214. 10.1007/PL00006295.
Article
CAS
PubMed
Google Scholar
Nikaido M, Nishihara H, Hukumoto Y, Okada N: Ancient SINEs from African endemic mammals. Mol Biol Evol. 2003, 20 (4): 522-527. 10.1093/molbev/msg052.
Article
CAS
PubMed
Google Scholar
Takahashi K, Terai Y, Nishida M, Okada N: A novel family of short interspersed repetitive elements (SINEs) from cichlids: the patterns of insertion of SINEs at orthologous loci support the proposed monophyly of four major groups of cichlid fishes in Lake Tanganyika. Mol Biol Evol. 1998, 15 (4): 391-407.
Article
CAS
PubMed
Google Scholar
Schmitz J, Ohme M, Suryobroto B, Zischler H: The colugo (Cynocephalus variegatus, Dermoptera): the primates' gliding sister?. Mol Biol Evol. 2002, 19 (12): 2308-2312.
Article
CAS
PubMed
Google Scholar
Sasaki T, Nishihara H, Hirakawa M, Fujimura K, Tanaka M, Kokubo N, Kimura-Yoshida C, Matsuo I, Sumiyama K, Saitou N, et al: Possible involvement of SINEs in mammalian-specific brain formation. Proc Natl Acad Sci USA. 2008, 105 (11): 4220-4225. 10.1073/pnas.0709398105.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tomilin NV: Regulation of mammalian gene expression by retroelements and non-coding tandem repeats. Bioessays. 2008, 30 (4): 338-348. 10.1002/bies.20741.
Article
CAS
PubMed
Google Scholar
Mariner PD, Walters RD, Espinoza CA, Drullinger LF, Wagner SD, Kugel JF, Goodrich JA: Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Molecular cell. 2008, 29 (4): 499-509. 10.1016/j.molcel.2007.12.013.
Article
CAS
PubMed
Google Scholar
Eickbush TH: Transposing without ends: the non-LTR retrotransposable elements. The New biologist. 1992, 4 (5): 430-440.
CAS
PubMed
Google Scholar
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. 1993, 72 (4): 595-605. 10.1016/0092-8674(93)90078-5.
Article
CAS
PubMed
Google Scholar
Ohshima K, Hamada M, Terai Y, Okada N: The 3' ends of tRNA-derived short interspersed repetitive elements are derived from the 3' ends of long interspersed repetitive elements. Mol Cell Biol. 1996, 16 (7): 3756-3764.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ogiwara I, Miya M, Ohshima K, Okada N: Retropositional parasitism of SINEs on LINEs: identification of SINEs and LINEs in elasmobranchs. Mol Biol Evol. 1999, 16 (9): 1238-1250.
Article
CAS
PubMed
Google Scholar
Okada N, Hamada M, Ogiwara I, Ohshima K: SINEs and LINEs share common 3' sequences: a review. Gene. 1997, 205 (1–2): 229-243. 10.1016/S0378-1119(97)00409-5.
Article
CAS
PubMed
Google Scholar
Ohshima K, Okada N: SINEs and LINEs: symbionts of eukaryotic genomes with a common tail. Cytogenet Genome Res. 2005, 110 (1–4): 475-490. 10.1159/000084981.
Article
CAS
PubMed
Google Scholar
Kajikawa M, Okada N: LINEs mobilize SINEs in the eel through a shared 3' sequence. Cell. 2002, 111 (3): 433-444. 10.1016/S0092-8674(02)01041-3.
Article
CAS
PubMed
Google Scholar
Kajikawa M, Ichiyanagi K, Tanaka N, Okada N: Isolation and characterization of active LINE and SINEs from the eel. Mol Biol Evol. 2005, 22 (3): 673-682. 10.1093/molbev/msi054.
Article
CAS
PubMed
Google Scholar
Moran JV, Holmes SE, Naas TP, DeBerardinis RJ, Boeke JD, Kazazian HH: High frequency retrotransposition in cultured mammalian cells. Cell. 1996, 87 (5): 917-927. 10.1016/S0092-8674(00)81998-4.
Article
CAS
PubMed
Google Scholar
Dewannieux M, Esnault C, Heidmann T: LINE-mediated retrotransposition of marked Alu sequences. Nature genetics. 2003, 35 (1): 41-48. 10.1038/ng1223.
Article
CAS
PubMed
Google Scholar
Bibillo A, Eickbush TH: The reverse transcriptase of the R2 non-LTR retrotransposon: continuous synthesis of cDNA on non-continuous RNA templates. Journal of molecular biology. 2002, 316 (3): 459-473. 10.1006/jmbi.2001.5369.
Article
CAS
PubMed
Google Scholar
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. 2002, 80 (4): 402-406. 10.1006/geno.2002.6843.
Article
CAS
PubMed
Google Scholar
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 research. 2003, 31 (15): 4385-4390. 10.1093/nar/gkg496.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kido Y, Himberg M, Takasaki N, Okada N: Amplification of distinct subfamilies of short interspersed elements during evolution of the Salmonidae. J Mol Biol. 1994, 241 (5): 633-644. 10.1006/jmbi.1994.1540.
Article
CAS
PubMed
Google Scholar
Ogiwara I, Miya M, Ohshima K, Okada N: 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. 2002, 12 (2): 316-324. 10.1101/gr.212302.
Article
PubMed Central
CAS
PubMed
Google Scholar
Weiner AM: SINEs and LINEs: the art of biting the hand that feeds you. Current opinion in cell biology. 2002, 14 (3): 343-350. 10.1016/S0955-0674(02)00338-1.
Article
CAS
PubMed
Google Scholar
Wang X, Li J, He S: Molecular evidence for the monophyly of East Asian groups of Cyprinidae (Teleostei: Cypriniformes) derived from the nuclear recombination activating gene 2 sequences. Molecular phylogenetics and evolution. 2007, 42 (1): 157-170. 10.1016/j.ympev.2006.06.014.
Article
CAS
PubMed
Google Scholar
Maniatis T, Fritsch EF, Sambrook J: Molecular Cloning: A Laboratory Manual. 1982, NY: Cold Spring Harbor Laboratory Press, Cold Spring Harbor
Google Scholar
Borodulina OR, Kramerov DA: Wide distribution of short interspersed elements among eukaryotic genomes. FEBS Lett. 1999, 457 (3): 409-413. 10.1016/S0014-5793(99)01059-5.
Article
CAS
PubMed
Google Scholar
Ochman H, Gerber AS, Hartl DL: Genetic applications of an inverse polymerase chain reaction. Genetics. 1988, 120 (3): 621-623.
PubMed Central
CAS
PubMed
Google Scholar
Raba M, Limburg K, Burghagen M, Katze JR, Simsek M, Heckman JE, Rajbhandary UL, Gross HJ: Nucleotide sequence of three isoaccepting lysine tRNAs from rabbit liver and SV40-transformed mouse fibroblasts. European journal of biochemistry/FEBS. 1979, 97 (1): 305-318. 10.1111/j.1432-1033.1979.tb13115.x.
Article
CAS
PubMed
Google Scholar
Matsumoto K, Murakami K, Okada N: Gene for lysine tRNA1 may be a progenitor of the highly repetitive and transcribable sequences present in the salmon genome. Proc Natl Acad Sci USA. 1986, 83 (10): 3156-3160. 10.1073/pnas.83.10.3156.
Article
PubMed Central
CAS
PubMed
Google Scholar
Malik HS, Burke WD, Eickbush TH: The age and evolution of non-LTR retrotransposable elements. Mol Biol Evol. 1999, 16 (6): 793-805.
Article
CAS
PubMed
Google Scholar
Lovsin N, Gubensek F, Kordi D: Evolutionary dynamics in a novel L2 clade of non-LTR retrotransposons in Deuterostomia. Mol Biol Evol. 2001, 18 (12): 2213-2224.
Article
CAS
PubMed
Google Scholar
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J: Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005, 110 (1–4): 462-467. 10.1159/000084979.
Article
CAS
PubMed
Google Scholar
Tamura K, Dudley J, Nei M, Kumar S: MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 2007, 24 (8): 1596-1599. 10.1093/molbev/msm092.
Article
CAS
PubMed
Google Scholar
Terai Y, Takahashi K, Okada N: SINE cousins: the 3'-end tails of the two oldest and distantly related families of SINEs are descended from the 3' ends of LINEs with the same genealogical origin. Mol Biol Evol. 1998, 15 (11): 1460-1471.
Article
CAS
PubMed
Google Scholar
Baba S, Kajikawa M, Okada N, Kawai G: Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2. Rna. 2004, 10 (9): 1380-1387. 10.1261/rna.7460104.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kido Y, Aono M, Yamaki T, Matsumoto K, Murata S, Saneyoshi M, Okada N: Shaping and reshaping of salmonid genomes by amplification of tRNA-derived retroposons during evolution. Proc Natl Acad Sci USA. 1991, 88 (6): 2326-2330. 10.1073/pnas.88.6.2326.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hamada M, Takasaki N, Reist JD, DeCicco AL, Goto A, Okada N: Detection of the ongoing sorting of ancestrally polymorphic SINEs toward fixation or loss in populations of two species of charr during speciation. Genetics. 1998, 150 (1): 301-311.
PubMed Central
CAS
PubMed
Google Scholar
Takasaki N, Yamaki T, Hamada M, Park L, Okada N: The salmon SmaI family of short interspersed repetitive elements (SINEs): interspecific and intraspecific variation of the insertion of SINEs in the genomes of chum and pink salmon. Genetics. 1997, 146 (1): 369-380.
PubMed Central
CAS
PubMed
Google Scholar
Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic acids research. 1997, 25 (5): 955-964. 10.1093/nar/25.5.955.
Article
PubMed Central
CAS
PubMed
Google Scholar
Okada N: SINEs. Current opinion in genetics & development. 1991, 1 (4): 498-504. 10.1016/S0959-437X(05)80198-4.
Article
CAS
Google Scholar
Lund V, Schmid R, Rickwood D, Hornes E: Assessment of methods for covalent binding of nucleic acids to magnetic beads, Dynabeads, and the characteristics of the bound nucleic acids in hybridization reactions. Nucleic acids research. 1988, 16 (22): 10861-10880. 10.1093/nar/16.22.10861.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zammatteo N, Alexandre I, Ernest I, Le L, Brancart F, Remacle J: Comparison between microwell and bead supports for the detection of human cytomegalovirus amplicons by sandwich hybridization. Analytical biochemistry. 1997, 253 (2): 180-189. 10.1006/abio.1997.2352.
Article
CAS
PubMed
Google Scholar
Zane L, Bargelloni L, Patarnello T: Strategies for microsatellite isolation: a review. Molecular ecology. 2002, 11 (1): 1-16. 10.1046/j.0962-1083.2001.01418.x.
Article
CAS
PubMed
Google Scholar
Endoh H, Okada N: Total DNA transcription in vitro: a procedure to detect highly repetitive and transcribable sequences with tRNA-like structures. Proc Natl Acad Sci USA. 1986, 83 (2): 251-255. 10.1073/pnas.83.2.251.
Article
PubMed Central
CAS
PubMed
Google Scholar
Okada N, Shedlock AM, Nikaido M: Retroposon mapping in molecular systematics. Methods Mol Biol. 2004, 260: 189-226.
CAS
PubMed
Google Scholar
Borodulina OR, Kramerov DA: PCR-based approach to SINE isolation: simple and complex SINEs. Gene. 2005, 349: 197-205. 10.1016/j.gene.2004.12.035.
Article
CAS
PubMed
Google Scholar
Xu H, Zhang S, Liu D, Liang CC: End-labeling of long DNA fragments with biotin and detection of DNA immobilized on magnetic beads. Molecular biotechnology. 2001, 17 (2): 183-185. 10.1385/MB:17:2:183.
Article
CAS
PubMed
Google Scholar