| [1] | Chalker DL, Sandmeyer SB (1992) Ty3 integrates within the region of RNA polymerase III transcription initiation. Genes Dev 6: 117–128.
|
| [2] | Li X, Krishnan L, Cherepanov P, Engelman A (2011) Structural biology of retroviral DNA integration. Virology 411: 194–205.
|
| [3] | Bushman F, Lewinski M, Ciuffi A, Barr S, Leipzig J, et al. (2005) Genome-wide analysis of retroviral DNA integration. Nat Rev Microbiol 3: 848–858.
|
| [4] | Engelman A, Mizuuchi K, Craigie R (1991) HIV-1 DNA integration: mechanism of viral DNA cleavage and DNA strand transfer. Cell 67: 1211–1221.
|
| [5] | Craigie R (2001) HIV integrase, a brief overview from chemistry to therapeutics. J Biol Chem 276: 23213–23216.
|
| [6] | Engelman A, Craigie R (1992) Identification of conserved amino acid residues critical for human immunodeficiency virus type 1 integrase function in vitro. J Virol 66: 6361–6369.
|
| [7] | Skalka AM (1993) Retroviral DNA integration: lessons for transposon shuffling. Gene 135: 175–182.
|
| [8] | Chow SA, Vincent KA, Ellison V, Brown PO (1992) Reversal of integration and DNA splicing mediated by integrase of human immunodeficiency virus. Science 255: 723–726.
|
| [9] | Bushman FD, Engelman A, Palmer I, Wingfield P, Craigie R (1993) Domains of the integrase protein of human immunodeficiency virus type 1 responsible for polynucleotidyl transfer and zinc binding. Proc Natl Acad Sci U S A 90: 3428–3432.
|
| [10] | Li M, Mizuuchi M, Burke TR Jr, Craigie R (2006) Retroviral DNA integration: reaction pathway and critical intermediates. EMBO J 25: 1295–1304.
|
| [11] | Valkov E, Gupta SS, Hare S, Helander A, Roversi P, et al. (2009) Functional and structural characterization of the integrase from the prototype foamy virus. Nucleic Acids Res 37: 243–255.
|
| [12] | Maertens GN, Hare S, Cherepanov P (2010) The mechanism of retroviral integration from X-ray structures of its key intermediates. Nature 468: 326–329.
|
| [13] | Hare S, Gupta SS, Valkov E, Engelman A, Cherepanov P (2010) Retroviral intasome assembly and inhibition of DNA strand transfer. Nature 464: 232–236.
|
| [14] | Dyda F, Hickman AB, Jenkins TM, Engelman A, Craigie R, et al. (1994) Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases. Science 266: 1981–1986.
|
| [15] | Krishnan L, Li X, Naraharisetty HL, Hare S, Cherepanov P, et al. (2010) Structure-based modeling of the functional HIV-1 intasome and its inhibition. Proc Natl Acad Sci U S A 107: 15910–15915.
|
| [16] | Lewinski MK, Bisgrove D, Shinn P, Chen H, Hoffmann C, et al. (2005) Genome-wide analysis of chromosomal features repressing human immunodeficiency virus transcription. J Virol 79: 6610–6619.
|
| [17] | Maertens G, Cherepanov P, Pluymers W, Busschots K, De Clercq E, et al. (2003) LEDGF/p75 is essential for nuclear and chromosomal targeting of HIV-1 integrase in human cells. J Biol Chem 278: 33528–33539.
|
| [18] | Cherepanov P, Ambrosio AL, Rahman S, Ellenberger T, Engelman A (2005) Structural basis for the recognition between HIV-1 integrase and transcriptional coactivator p75. Proc Natl Acad Sci U S A 102: 17308–17313.
|
| [19] | Vanegas M, Llano M, Delgado S, Thompson D, Peretz M, et al. (2005) Identification of the LEDGF/p75 HIV-1 integrase-interaction domain and NLS reveals NLS-independent chromatin tethering. J Cell Sci 118: 1733–1743.
|
| [20] | Busschots K, Vercammen J, Emiliani S, Benarous R, Engelborghs Y, et al. (2005) The interaction of LEDGF/p75 with integrase is lentivirus-specific and promotes DNA binding. J Biol Chem 280: 17841–17847.
|
| [21] | Levin HL, Moran JV (2011) Dynamic interactions between transposable elements and their hosts. Nat Rev Genet 12: 615–627.
|
| [22] | Devine SE, Boeke JD (1996) Integration of the yeast retrotransposon Ty1 is targeted to regions upstream of genes transcribed by RNA polymerase III. Genes Dev 10: 620–633.
|
| [23] | Xie W, Gai X, Zhu Y, Zappulla DC, Sternglanz R, et al. (2001) Targeting of the yeast Ty5 retrotransposon to silent chromatin is mediated by interactions between integrase and Sir4p. Mol Cell Biol 21: 6606–6614.
|
| [24] | Malik HS, Eickbush TH (1999) Modular evolution of the integrase domain in the Ty3/Gypsy class of LTR retrotransposons. J Virol 73: 5186–5190.
|
| [25] | Gao X, Hou Y, Ebina H, Levin HL, Voytas DF (2008) Chromodomains direct integration of retrotransposons to heterochromatin. Genome Res 18: 359–369.
|
| [26] | Kordis D (2005) A genomic perspective on the chromodomain-containing retrotransposons: Chromoviruses. Gene 347: 161–173.
|
| [27] | Singleton TL, Levin HL (2002) A long terminal repeat retrotransposon of fission yeast has strong preferences for specific sites of insertion. Eukaryot Cell 1: 44–55.
|
| [28] | Behrens R, Hayles J, Nurse P (2000) Fission yeast retrotransposon Tf1 integration is targeted to 5′ ends of open reading frames. Nucleic Acids Res 28: 4709–4716.
|
| [29] | Qi X, Sandmeyer SB (2012) In vitro targeting of strand transfer by the Ty3 retroelement integrase. J Biol Chem 287: 18589–18595.
|
| [30] | Engelman A, Bushman FD, Craigie R (1993) Identification of discrete functional domains of HIV-1 integrase and their organization within an active multimeric complex. EMBO J 12: 3269–3275.
|
| [31] | Papadopoulos JS, Agarwala R (2007) COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics 23: 1073–1079.
|
| [32] | Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673–4680.
|
| [33] | Notredame C, Higgins DG, Heringa J (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 302: 205–217.
|
| [34] | Kelley LA, Sternberg MJ (2009) Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc 4: 363–371.
|
| [35] | Karplus K (2009) SAM-T08, HMM-based protein structure prediction. Nucleic Acids Res 37: W492–497.
|
| [36] | Ponting CP, Schultz J, Milpetz F, Bork P (1999) SMART: identification and annotation of domains from signalling and extracellular protein sequences. Nucleic Acids Res 27: 229–232.
|
| [37] | Cole C, Barber JD, Barton GJ (2008) The Jpred 3 secondary structure prediction server. Nucleic Acids Res 36: W197–201.
|
| [38] | McGuffin LJ, Bryson K, Jones DT (2000) The PSIPRED protein structure prediction server. Bioinformatics 16: 404–405.
|
| [39] | Zhou H, Pandit SB, Skolnick J (2009) Performance of the Pro-sp3-TASSER server in CASP8. Proteins 77 Suppl 9123–127.
|
| [40] | Ho SN, Hunt HD, Horton RM, Pullen JK, Pease LR (1989) Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77: 51–59.
|
| [41] | Horton RM, Hunt HD, Ho SN, Pullen JK, Pease LR (1989) Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension. Gene 77: 61–68.
|
| [42] | Aamodt K, Abelev B, Abrahantes Quintana A, Adamova D, Adare AM, et al. (2012) Particle-yield modification in jetlike azimuthal dihadron correlations in Pb-Pb collisions at radicals(NN) = 2.76 TeV. Phys Rev Lett 108: 092301.
|
| [43] | Quan J, Tian J (2009) Circular polymerase extension cloning of complex gene libraries and pathways. PLoS One 4: e6441.
|
| [44] | Quan J, Tian J (2011) Circular polymerase extension cloning for high-throughput cloning of complex and combinatorial DNA libraries. Nat Protoc 6: 242–251.
|
| [45] | Yon J, Fried M (1989) Precise gene fusion by PCR. Nucleic Acids Res 17: 4895.
|
| [46] | Morita K, Tadano M, Nakaji S, Kosai K, Mathenge EG, et al. (2001) Locus of a virus neutralization epitope on the Japanese encephalitis virus envelope protein determined by use of long PCR-based region-specific random mutagenesis. Virology 287: 417–426.
|
| [47] | Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406–3415.
|
| [48] | Wassman CD, Tam PY, Lathrop RH, Weiss GA (2004) Predicting oligonucleotide-directed mutagenesis failures in protein engineering. Nucleic Acids Res 32: 6407–6413.
|
| [49] | Larsen LS, Wassman CD, Hatfield GW, Lathrop RH (2008) Computationally Optimised DNA Assembly of synthetic genes. Int J Bioinform Res Appl 4: 324–336.
|
| [50] | Sharp PM, Li WH (1987) The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias. Mol Biol Evol 4: 222–230.
|
| [51] | Kassavetis GA, Soragni E, Driscoll R, Geiduschek EP (2005) Reconfiguring the connectivity of a multiprotein complex: fusions of yeast TATA-binding protein with Brf1, and the function of transcription factor IIIB. Proc Natl Acad Sci U S A 102: 15406–15411.
|
| [52] | Yieh L, Kassavetis G, Geiduschek EP, Sandmeyer SB (2000) The Brf and TATA-binding protein subunits of the RNA polymerase III transcription factor IIIB mediate position-specific integration of the gypsy-like element, Ty3. J Biol Chem 275: 29800–29807.
|
| [53] | Hickman AB, Palmer I, Engelman A, Craigie R, Wingfield P (1994) Biophysical and enzymatic properties of the catalytic domain of HIV-1 integrase. J Biol Chem 269: 29279–29287.
|
| [54] | Baronio R, Danziger SA, Hall LV, Salmon K, Hatfield GW, et al. (2010) All-codon scanning identifies p53 cancer rescue mutations. Nucleic Acids Res 38: 7079–7088.
|
| [55] | Esposito D, Craigie R (1998) Sequence specificity of viral end DNA binding by HIV-1 integrase reveals critical regions for protein-DNA interaction. EMBO J 17: 5832–5843.
|
| [56] | Shibagaki Y, Chow SA (1997) Central core domain of retroviral integrase is responsible for target site selection. J Biol Chem 272: 8361–8369.
|
| [57] | Appa RS, Shin CG, Lee P, Chow SA (2001) Role of the nonspecific DNA-binding region and alpha helices within the core domain of retroviral integrase in selecting target DNA sites for integration. J Biol Chem 276: 45848–45855.
|
| [58] | Berger N, Heller AE, Stormann KD, Pfaff E (2001) Characterization of chimeric enzymes between caprine arthritis–encephalitis virus, maedi–visna virus and human immunodeficiency virus type 1 integrases expressed in Escherichia coli. J Gen Virol 82: 139–148.
|
| [59] | Katzman M, Sudol M, Pufnock JS, Zeto S, Skinner LM (2000) Mapping target site selection for the non-specific nuclease activities of retroviral integrase. Virus Res 66: 87–100.
|
| [60] | Lee HS, Kang SY, Shin CG (2005) Characterization of the functional domains of human foamy virus integrase using chimeric integrases. Mol Cells 19: 246–255.
|
| [61] | Katzman M, Sudol M (1995) Mapping domains of retroviral integrase responsible for viral DNA specificity and target site selection by analysis of chimeras between human immunodeficiency virus type 1 and visna virus integrases. J Virol 69: 5687–5696.
|
