DNA bending creates favored sites for retroviral integration: an explanation for preferred insertion sites in nucleosomes

Crystal Structure of a CAP-DNA Complex: the DNA Is Bent by 90°

Schultz, S. C., Shields, G. C., & Steitz, T. A. (1991) · Science · doi:10.1126/science.1653449 · Cited by 1,116

Structure of the nucleosome core particle at 7 Å resolution

Richmond, T. J., Finch, J. T., Rushton, B., Rhodes, D., & Klug, A. (1984) · Nature · doi:10.1038/311532a0 · Cited by 1,061

Integration of murine leukemia virus DNA depends on mitosis.

Roe, T., Reynolds, T. C., Yu, G., & Brown, P. O. (1993) · The EMBO Journal · doi:10.1002/j.1460-2075.1993.tb05858.x · Cited by 921

HIV-1 DNA integration: Mechanism of viral DNA cleavage and DNA strand transfer

Engelman, A., Mizuuchi, K., & Craigie, R. (1991) · Cell · doi:10.1016/0092-8674(91)90297-c · Cited by 655

Bent helical structure in kinetoplast DNA

Marini, J. C., Levene, S. D., Crothers, D. M., & Englund, P. T. (1982) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.79.24.7664 · Cited by 596

Crystal structure of a MATα2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions

Wolberger, C., Vershon, A. K., Liu, B., Johnson, A. D., & Pabo, C. O. (1991) · Cell · doi:10.1016/0092-8674(91)90526-5 · Cited by 525

Structure of the DNA-Eco RI Endonuclease Recognition Complex at 3 Å Resolution

McClarin, J. A., Frederick, C., Wang, B., Greene, P. J., Boyer, H. W., Grable, J., & Rosenberg, J. M. (1986) · Science · doi:10.1126/science.3024321 · Cited by 487

Chromatin Structure and Function

(1999) · Cell · doi:10.1016/s0092-8674(00)81490-7 · Cited by 441

Intrinsically bent DNA.

Crothers, D. M., Haran, T. E., & Nadeau, J. G. (1990) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)39080-5 · Cited by 427

DNA LOOPING

Schleif, R. F. (1992) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.61.070192.001215 · Cited by 423

The IN protein of Moloney murine leukemia virus processes the viral DNA ends and accomplishes their integration in vitro

Craigie, R., Fujiwara, T., & Bushman, F. (1990) · Cell · doi:10.1016/0092-8674(90)90126-y · Cited by 409

Retroviral integration: structure of the initial covalent product and its precursor, and a role for the viral IN protein

Brown, P. O., Bowerman, B., Varmus, H. E., & Bishop, J. M. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.8.2525 · Cited by 399

Retroviral DNA integration: structure of an integration intermediate

Fujiwara, T., & Mizuuchi, K. (1988) · Cell · doi:10.1016/0092-8674(88)90071-2 · Cited by 385

A nucleoprotein complex mediates the integration of retroviral DNA.Preprint

Bowerman, B. A., Brown, P. O., Bishop, J. M., & Varmus, H. E. (1989) · Genes & Development · doi:10.1101/gad.3.4.469 · Cited by 378

lac repressor forms loops with linear DNA carrying two suitably spaced lac operators.

Krämer, H., Niemöller, M., Amouyal, M., Révet, B., von Wilcken‐Bergmann, B., & Müller‐Hill, B. (1987) · The EMBO Journal · doi:10.1002/j.1460-2075.1987.tb02390.x · Cited by 351

The avian retroviral IN protein is both necessary and sufficient for integrative recombination in vitro

Katz, R. A., Merkel, G., Kulkosky, J., Leis, J., & Skalka, A. M. (1990) · Cell · doi:10.1016/0092-8674(90)90290-u · Cited by 346

Retroviral DNA integration directed by HIV integration protein in vitro

Bushman, F. D., Fujiwara, T., & Craigie, R. (1990) · Science · doi:10.1126/science.2171144 · Cited by 338

Energetic coupling between DNA bending and base pair opening.

Ramstein, J., & Lavery, R. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.19.7231 · Cited by 295

Structure refined to 2Å of a nicked DNA octanucleotide complex with DNase I

Suck, D., Lahm, A., & Oefner, C. (1988) · Nature · doi:10.1038/332464a0 · Cited by 294

Nucleosomes, DNA-binding proteins, and DNA sequence modulate retroviral integration target site selection

Pryciak, P. M., & Varmus, H. E. (1992) · Cell · doi:10.1016/0092-8674(92)90289-o · Cited by 273

Highly preferred targets for retrovirus integration

Shih, C.-C., Stoye, J. P., & Coffin, J. M. (1988) · Cell · doi:10.1016/0092-8674(88)90569-7 · Cited by 259

Retrovirus integration and chromatin structure: Moloney murine leukemia proviral integration sites map near DNase I-hypersensitive sites

Rohdewohld, H., Weiher, H., Reik, W., Jaenisch, R., & Breindl, M. (1987) · Journal of Virology · doi:10.1128/jvi.61.2.336-343.1987 · Cited by 243

Human immunodeficiency virus integrase directs integration to sites of severe DNA distortion within the nucleosome core.

Pruss, D., Bushman, F. D., & Wolffe, A. P. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.13.5913 · Cited by 236

Retroviral Reverse Transcription and Integration: Progress and Problems

Whitcomb, J. M., & Hughes, S. H. (1992) · Annual Review of Cell Biology · doi:10.1146/annurev.cb.08.110192.001423 · Cited by 217

Ty3 integrates within the region of RNA polymerase III transcription initiation.Preprint

Chalker, D. L., & Sandmeyer, S. B. (1992) · Genes & Development · doi:10.1101/gad.6.1.117 · Cited by 208

DNase I-induced DNA conformation

Lahm, A., & Suck, D. (1991) · Journal of Molecular Biology · doi:10.1016/0022-2836(91)90502-w · Cited by 193

Nucleosome displacement in transcription

Adams, C. C., & Workman, J. L. (1993) · Cell · doi:10.1016/0092-8674(93)90109-4 · Cited by 180

Detection of localized DNA flexibility

Kahn, J. D., Yun, E., & Crothers, D. M. (1994) · Nature · doi:10.1038/368163a0 · Cited by 168

Protein-induced bending and DNA cyclization.

Kahn, J. D., & Crothers, D. M. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.14.6343 · Cited by 161

INTEGRATION SPECIFICITY OF RETROTRANSPOSONS AND RETROVIRUSES

Sandmeyer, S. B., Hansen, L. J., & Chalker, D. L. (1990) · Annual Review of Genetics · doi:10.1146/annurev.ge.24.120190.002423 · Cited by 160

Polynucleotidyl transfer reactions in transpositional DNA recombination.

Mizuuchi, K. (1992) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)36600-1 · Cited by 155

Nucleoprotein structures initiating DNA replication, transcription, and site-specific recombination.

Echols, H. (1990) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)77163-9 · Cited by 139

Conic: A fast renderer for spacefilling molecules with shadows

Huang, C. C., Pettersen, E. F., Klein, T. E., Ferrin, T. E., & Langridge, R. (1991) · Journal of Molecular Graphics · doi:10.1016/0263-7855(91)80016-s · Cited by 138

Why bend DNA?

TRAVERS, A. A. (1990) · Cell · doi:10.1016/0092-8674(90)90729-x · Cited by 135

Site-specific hydrolysis and alcoholysis of human immunodeficiency virus DNa termini mediated by the viral integrase protein

Vink, C., Yeheskiely, E., van der MAREL, G. A., BOOM, J. H. V., & Plasterk, R. H. A. (1991) · Nucleic Acids Research · doi:10.1093/nar/19.24.6691 · Cited by 129

THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA SEGMENTS

Winkler, F. K., Banner, D. W., Oefner, C., Tsernoglou, D., Brown, R. S., Heathman, S. P., Bryan, R. K., Martin, P. D., Petratos, K., & Wilson, K. S. (1993) · Worldwide Protein Data Bank · doi:10.2210/pdb4rve/pdb · Cited by 125

On the action of the cyclic AMP‐cyclic AMP receptor protein complex at the Escherichia coli lactose and galactose promoter regions.

Spassky, A., Busby, S. J. W., & BUC, H. C. (1984) · The EMBO Journal · doi:10.1002/j.1460-2075.1984.tb01759.x · Cited by 122

Retroviral integration sites in transgenic Mov mice frequently map in the vicinity of transcribed DNA regions

Mooslehner, K. A., Karls, U., & Harbers, K. (1990) · Journal of Virology · doi:10.1128/jvi.64.6.3056-3058.1990 · Cited by 113

The human immunodeficiency virus integrase protein

Vink, C., & Plasterk, R. H. A. (1993) · Trends in Genetics · doi:10.1016/0168-9525(93)90107-s · Cited by 101

Cyclic AMP receptor protein interacts with lactose operator DNA

Schmitz, A. (1981) · Nucleic Acids Research · doi:10.1093/nar/9.2.277 · Cited by 98

Hotspots and warm spots: integration specificity of retroelements

Craigie, R. (1992) · Trends in Genetics · doi:10.1016/0168-9525(92)90223-q · Cited by 97

Nonrandom integration of retroviral DNA in vitro: effect of CpG methylation.

Kitamura, Y., Lee, Y. M., & Coffin, J. M. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.12.5532 · Cited by 96

Simian virus 40 minichromosomes as targets for retroviral integration in vivo.

Pryciak, P. M., Müller, H. P., & Varmus, H. E. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.19.9237 · Cited by 71

Concerted integration of viral DNA termini by purified avian myeloblastosis virus integrase

Fitzgerald, M. L., Vora, A. C., Zeh, W. G., & Grandgenett, D. P. (1992) · Journal of Virology · doi:10.1128/jvi.66.11.6257-6263.1992 · Cited by 59

Association of a Host DNA Structure with Retrovital Integration Sites in Chromosomal DNA

Milot, É., Belmaaza, A., Rassart, É., & Chartrand, P. (1994) · Virology · doi:10.1006/viro.1994.1310 · Cited by 28

Retroviral Integration Machinery as a Probe for DNA Structure and Associated ProteinsPreprint

Muller, H.-P., Pryciak, P. M., & Varmus, H. E. (1993) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.1993.058.01.060 · Cited by 8

Dodging the genes

Bushman, F. D. (1993) · Current Biology · doi:10.1016/0960-9822(93)90050-x · Cited by 6

Insertion Sequences

Mahillon, J., & Chandler, M. (1998) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.62.3.725-774.1998 · Cited by 1,292

Crystal Structure of the Catalytic Domain of HIV-1 Integrase: Similarity to Other Polynucleotidyl Transferases

Dyda, F., Hickman, A. B., Jenkins, T. M., Engelman, A., Craigie, R., & Davies, D. R. (1994) · Science · doi:10.1126/science.7801124 · Cited by 810

The site of HIV-1 integration in the human genome determines basal transcriptional activity and response to Tat transactivation

Jordan, A., Defechereux, P., & Verdin, E. (2001) · The EMBO Journal · doi:10.1093/emboj/20.7.1726 · Cited by 467

Side effects of retroviral gene transfer into hematopoietic stem cells

Baum, C., Düllmann, J., Li, Z., Fehse, B., Meyer, J., Williams, D. A., & Kalle, C. V. (2003) · Blood · doi:10.1182/blood-2002-07-2314 · Cited by 431

Genome-wide analysis of retroviral DNA integration

Bushman, F. D., Lewinski, M. K., Ciuffi, A., Barr, S. D., Leipzig, J. N., Hannenhalli, S. S., & Hoffmann, C. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1263 · Cited by 437

Nucleosomes, DNA-binding proteins, and DNA sequence modulate retroviral integration target site selection

Pryciak, P. M., & Varmus, H. E. (1992) · Cell · doi:10.1016/0092-8674(92)90289-o · Cited by 273

Intasome architecture and chromatin density modulate retroviral integration into nucleosome

Benleulmi, M. S., Matysiak, J., Henriquez, D. R., Vaillant, C., Lesbats, P., Calmels, C., Naughtin, M., Leon, O., Skalka, A. M., Ruff, M., et al. (2015) · Retrovirology · doi:10.1186/s12977-015-0145-9 · Cited by 47

The influence of DNA and nucleosome structure on integration events directed by HIV integrase

Pruss, D., Reeves, R., Bushman, F. D., & Wolffe, A. P. (1994) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)31494-1 · Cited by 173

Retroviral integration into minichromosomes in vitro.

Pryciak, P. M., Sil, A., & VARMUS, H. E. (1992) · The EMBO Journal · doi:10.1002/j.1460-2075.1992.tb05052.x · Cited by 159

Key determinants of target DNA recognition by retroviral intasomes

Serrao, E., Ballandras-Colas, A., Cherepanov, P., Maertens, G. N., & Engelman, A. N. (2015) · Retrovirology · doi:10.1186/s12977-015-0167-3 · Cited by 62