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Research Paper

Independently derived targeting of 28S rDNA by A- and D-clade R2 retrotransposons

Plasticity of integration mechanism

Pages 29-37 | Received 21 Apr 2011, Accepted 16 May 2011, Published online: 01 May 2011

References

  • Christensen SM, Eickbush TH. R2 target-primed reverse transcription: ordered cleavage and polymerization steps by protein subunits asymmetrically bound to the target DNA. Mol Cell Biol 2005; 25:6617 - 6628
  • Burke WD, Malik HS, Rich SM, Eickbush TH. Ancient lineages of non-LTR retrotransposons in the primitive eukaryote, Giardia lamblia. Mol Biol Evol 2002; 19:619 - 630
  • Malik HS, Eickbush TH. NeSL-1, an ancient lineage of site-specific non-LTR retrotransposons from Caenorhabditis elegans. Genetics 2000; 154:193 - 203
  • Burke WD, Malik HS, Jones JP, Eickbush TH. The domain structure and retrotransposition mechanism of R2 elements are conserved throughout arthropods. Mol Biol Evol 1999; 16:502 - 511
  • Kojima KK, Fujiwara H. Long-term inheritance of the 28S rDNA-specific retrotransposon R2. Mol Biol Evol 2005; 22:2157 - 2165
  • Kojima KK, Fujiwara H. Cross-genome screening of novel sequence-specific non-LTR retrotransposons: various multicopy RNA genes and microsatellites are selected as targets. Mol Biol Evol 2004; 21:207 - 217
  • Moran JV, Gilbert N. Craig NL, Craigie R, Gellert M, Lambowitz AM. Mammalian LINE-1 Retrotransposons and Related Elements. Mobile DNA II 2002; Washington, DC ASM Press 836 - 869
  • Feng Q, Moran JV, Kazazian HHJ, Boeke JD. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 1996; 87:905 - 916
  • Cost GJ, Feng Q, Jacquier A, Boeke JD. Human L1 element target-primed reverse transcription in vitro. EMBO J 2002; 21:5899 - 5910
  • Konkel MK, Batzer MA. A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome. Semin Cancer Biol 2010;
  • Deininger PL, Batzer MA. Mammalian retroelements. Genome Res 2002; 12:1455 - 1465
  • Moran JV, Holmes SE, Naas TP, DeBerardinis RJ, Boeke JD, Kazazian HHJ. High frequency retrotransposition in cultured mammalian cells. Cell 1996; 87:917 - 927
  • Takahashi H, Fujiwara H. Transplantation of target site specificity by swapping the endonuclease domains of two LINEs. EMBO J 2002; 21:408 - 417
  • Zingler N, Weichenrieder O, Schumann GG. APE-type non-LTR retrotransposons: determinants involved in target site recognition. Cytogenet Genome Res 2005; 110:250 - 268
  • Seleme MC, Disson O, Robin S, Brun C, Teninges D, Bucheton A. In vivo RNA localization of I factor, a non-LTR retrotransposon, requires a cis-acting signal in ORF2 and ORF1 protein. Nucleic Acids Res 2005; 33:776 - 785
  • Maita N, Aoyagi H, Osanai M, Shirakawa M, Fujiwara H. Characterization of the sequence specificity of the R1Bm endonuclease domain by structural and biochemical studies. Nucleic Acids Res 2007; 35:3918 - 3927
  • Gasior SL, Roy-Engel AM, Deininger PL. ERCC1/XPF limits L1 retrotransposition. DNA Repair (Amst) 2008; 7:983 - 989
  • Khazina E, Weichenrieder O. Non-LTR retrotransposons encode noncanonical RRM domains in their first open reading frame. Proc Natl Acad Sci USA 2009; 106:731 - 736
  • Yoshitake K, Aoyagi H, Fujiwara H. Creation of a novel telomere-cutting endonuclease based on the EN domain of telomere-specific non-long terminal repeat retrotransposon, TRAS1. Mob DNA 2010; 1:13
  • Beck CR, Collier P, Macfarlane C, Malig M, Kidd JM, Eichler EE, et al. LINE-1 retrotransposition activity in human genomes. Cell 2010; 141:1159 - 1170
  • Martin SL. Nucleic acid chaperone properties of ORF1p from the non-LTR retrotransposon, LINE-1. RNA Biol 2010; 7:67 - 72
  • Doucet AJ, Hulme AE, Sahinovic E, Kulpa DA, Moldovan JB, Kopera HC, et al. Characterization of LINE-1 ribonucleoprotein particles. PLoS Genet 2010; 6:e10001150
  • 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; 72:595 - 605
  • 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 1999; 96:7847 - 7852
  • Christensen SM, Bibillo A, Eickbush TH. Role of the Bombyx mori R2 element N-terminal domain in the target-primed reverse transcription (TPRT) reaction. Nucleic Acids Res 2005; 33:6461 - 6468
  • Volff JN, Korting C, Froschauer A, Sweeney K, Schartl M. Non-LTR retrotransposons encoding a restriction enzyme-like endonuclease in vertebrates. J Mol Evol 2001; 52:351 - 360
  • 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 2004; 3:170 - 179
  • Eickbush TH, Malik HS. Craig NL, Craigie R, Gellert M, Lambowitz AM. Origins and Evolution of Retrotransposons. Mobile DNA II 2002; Washington, DC ASM Press 1111 - 1146
  • Malik HS, Burke WD, Eickbush TH. The age and evolution of non-LTR retrotransposable elements. Mol Biol Evol 1999; 16:793 - 805
  • Ban N, Nissen P, Hansen J, Moore PB, Steitz TA. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 2000; 289:905 - 920
  • Stage DE, Eickbush TH. Origin of nascent lineages and the mechanisms used to prime second-strand DNA synthesis in the R1 and R2 retrotransposons of Drosophila. Genome Biol 2009; 10:49
  • Eickbush TH. Craig NL, Craigie R, Gellert M, Lambowitz AM. R2 and Related Site-Specific Non-Long Terminal Repeat Retrotransposons. Mobile DNA II 2002; Washington, DC ASM Press 813 - 835
  • Burke WD, Malik HS, Lathe WCr, Eickbush TH. Are retrotransposons long-term hitchhikers?. Nature 1998; 392:141 - 142
  • Zhang X, Zhou J, Eickbush TH. Rapid R2 retrotransposition leads to the loss of previously inserted copies via large deletions of the rDNA locus. Mol Biol Evol 2008; 25:229 - 237
  • Averbeck KT, Eickbush TH. Monitoring the mode and tempo of concerted evolution in the Drosophila melanogaster rDNA locus. Genetics 2005; 171:1837 - 1846
  • Eickbush TH, Eickbush DG. Finely orchestrated movements: evolution of the ribosomal RNA genes. Genetics 2007; 175:477 - 485
  • Perez-Gonzalez CE, Eickbush TH. Rates of R1 and R2 retrotransposition and elimination from the rDNA locus of Drosophila melanogaster. Genetics 2002; 162:799 - 811
  • Zhang X, Eickbush TH. Characterization of active R2 retrotransposition in the rDNA locus of Drosophila simulans. Genetics 2005; 170:195 - 205
  • Jakubczak JL, Burke WD, Eickbush TH. Retrotransposable elements R1 and R2 interrupt the rRNA genes of most insects. Proc Natl Acad Sci USA 1991; 88:3295 - 3299
  • Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. Initial sequencing and analysis of the human genome. Nature 2001; 409:860 - 921
  • Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 2002; 297:1301 - 1310
  • Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, et al. Initial sequencing and comparative analysis of the mouse genome. Nature 2002; 420:520 - 562
  • 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 1987; 7:2221 - 2230
  • Stage DE, Eickbush TH. Maintenance of multiple lineages of R1 and R2 retrotransposable elements in the ribosomal RNA gene loci of Nasonia. Insect Mol Biol 2010; 19:37 - 48
  • Kurzynska-Kokorniak A, Jamburuthugoda VK, Bibillo A, Eickbush TH. DNA-directed DNA polymerase and strand displacement activity of the reverse transcriptase encoded by the R2 retrotransposon. J Mol Biol 2007; 374:322 - 333
  • Christensen SM, Ye J, Eickbush TH. RNA from the 5′ end of the R2 retrotransposon controls R2 protein binding to and cleavage of its DNA target site. Proc Natl Acad Sci USA 2006; 103:17602 - 17607
  • Bibillo A, Eickbush TH. End-to-end template jumping by the reverse transcriptase encoded by the R2 retrotransposon. J Biol Chem 2004; 279:14945 - 14953
  • MD A, PJ M, SJ R. Image Processing with ImageJ. Biophotonics International 2004; 11:36 - 42
  • Hayes JJ, Tullius TD. The missing nucleoside experiment: a new technique to study recognition of DNA by protein. Biochemistry 1989; 28:9521 - 9527
  • Christensen S, Eickbush TH. Footprint of the retrotransposon R2Bm protein on its target site before and after cleavage. J Mol Biol 2004; 336:1035 - 1045
  • Brenowitz B, Senear DF, Kingston RE. Ausubel FM. DNase I Footprint Analysis of Protein-DNA Binding. Current Protocols in Molecular Biology 2003; 12:Hoboken, NJ John Wiley and Sons, Inc. 4 - 5
  • Kojima KK, Kuma K, Toh H, Fujiwara H. Identification of rDNA-specific non-LTR retrotransposons in Cnidaria. Mol Biol Evol 2006; 23:1984 - 1993
  • Gladyshev EA, Arkhipova IR. Rotifer rDNA-specific R9 retrotransposable elements generate an exceptionally long target site duplication upon insertion. Gene 2009; 448:145 - 150