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Research Paper

Targeting novel sites

The amino-terminal DNA binding domain of non-LTR retrotransposons is an adaptable module that is implicated in changing site specificities.

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Pages 169-178 | Received 22 Sep 2011, Accepted 17 Oct 2011, Published online: 01 Oct 2011

References

  • Malik HS, Burke WD, Eickbush TH. The age and evolution of non-LTR retrotransposable elements. Mol Biol Evol 1999; 16:793 - 805; PMID: 10368957
  • 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; PMID: 11237011; http://dx.doi.org/10.1038/35057062
  • Han JS, Boeke JD. LINE-1 retrotransposons: modulators of quantity and quality of mammalian gene expression?. Bioessays 2005; 27:775 - 784; PMID: 16015595; http://dx.doi.org/10.1002/bies.20257
  • Ye J, Eickbush TH. Chromatin structure and transcription of the R1- and R2-inserted rRNA genes of Drosophila melanogaster. Mol Cell Biol 2006; 26:8781 - 8790; PMID: 17000772; http://dx.doi.org/10.1128/MCB.01409-06
  • 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; PMID: 20602998; http://dx.doi.org/10.1016/j.cell.2010.05.021
  • 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; PMID: 16024797; http://dx.doi.org/10.1128/MCB.25.15.6617-6628.2005
  • 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; PMID: 7679954; http://dx.doi.org/10.1016/0092-8674(93)90078-5
  • 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
  • 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
  • Eickbush TH, Jamburuthugoda VK. The diversity of retrotransposons and the properties of their reverse transcriptases. Virus Res 2008; 134:221 - 234; PMID: 18261821; http://dx.doi.org/10.1016/j.virusres.2007.12.010
  • 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; PMID: 10393910; http://dx.doi.org/10.1073/pnas.96.14.7847
  • 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; PMID: 10331276
  • Moran JV, Holmes SE, Naas TP, DeBerardinis RJ, Boeke JD, Kazazian HHJ. High frequency retrotransposition in cultured mammalian cells. Cell 1996; 87:917 - 927; PMID: 8945518; http://dx.doi.org/10.1016/S0092-8674(00)81998-4
  • Feng Q, Moran JV, Kazazian HHJ, Boeke JD. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 1996; 87:905 - 916; PMID: 8945517; http://dx.doi.org/10.1016/S0092-8674(00)81997-2
  • Christensen S, Pont-Kingdon G, Carroll D. Comparative studies of the endonucleases from two related Xenopus laevis retrotransposons, Tx1L and Tx2L: target site specificity and evolutionary implications. Genetica 2000; 110:245 - 256; PMID: 11766845; http://dx.doi.org/10.1023/A:1012704812424
  • 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; PMID: 14871947; http://dx.doi.org/10.1128/EC.3.1.170-179.2004
  • Thompson BK, Christensen SM. Independently derived targeting of 28S rDNA by A- and D-clade R2 retrotransposons: plasticity of integration mechanism. Mobile Genet Elements 2011; 1:29 - 37
  • 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; PMID: 16284201; http://dx.doi.org/10.1093/nar/gki957
  • 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; PMID: 15037067; http://dx.doi.org/10.1016/j.jmb.2003.12.077
  • 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; PMID: 11343131
  • Malik HS, Eickbush TH. NeSL-1, an ancient lineage of site-specific non-LTR retrotransposons from Caenorhabditis elegans. Genetics 2000; 154:193 - 203; PMID: 10628980
  • 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; PMID: 11961096
  • 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
  • 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; PMID: 12949131; http://dx.doi.org/10.1093/molbev/msg235
  • Kojima KK, Fujiwara H. Long-term inheritance of the 28S rDNA-specific retrotransposon R2. Mol Biol Evol 2005; 22:2157 - 2165; PMID: 16014872; http://dx.doi.org/10.1093/molbev/msi210
  • 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; PMID: 17105809; http://dx.doi.org/10.1073/pnas.0605476103
  • Kojima KK, Kuma K, Toh H, Fujiwara H. Identification of rDNA-specific non-LTR retrotransposons in Cnidaria. Mol Biol Evol 2006; 23:1984 - 1993; PMID: 16870681; http://dx.doi.org/10.1093/molbev/msl067
  • Gladyshev EA, Arkhipova IR. Rotifer rDNA-specific R9 retrotransposable elements generate an exceptionally long target site duplication upon insertion. Gene 2009; 448:145 - 150; PMID: 19744548; http://dx.doi.org/10.1016/j.gene.2009.08.016
  • 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:R49; PMID: 19416522; http://dx.doi.org/10.1186/gb-2009-10-5-r49
  • Hayes JJ, Tullius TD. The missing nucleoside experiment: a new technique to study recognition of DNA by protein. Biochemistry 1989; 28:9521 - 9527; PMID: 2611245; http://dx.doi.org/10.1021/bi00450a041
  • Abramoff MD, Magalhaes PJ. Image Processing with ImageJ. Biophotonics International 2004; 11:36 - 42
  • Brenowitz B, Senear DF, Kingston RE. Ausubel FM. DNase I Footprint Analysis of Protein-DNA Binding. Current Protocols in Molecular Biology 2003; Hoboken, NJ John Wiley and Sons, Inc 12.4 - 12.5
  • Burke WD, Muller F, Eickbush TH. R4, a non-LTR retrotransposon specific to the large subunit rRNA genes of nematodes. Nucleic Acids Res 1995; 23:4628 - 4634; PMID: 8524653; http://dx.doi.org/10.1093/nar/23.22.4628
  • Teng SC, Wang SX, Gabriel A. A new non-LTR retrotransposon provides evidence for multiple distinct site-specific elements in Crithidia fasciculata miniexon arrays. Nucleic Acids Res 1995; 23:2929 - 2936; PMID: 7659515; http://dx.doi.org/10.1093/nar/23.15.2929