Cited by 224Chromosomal and Genetic VariationsDNA Repair MechanismsCRISPR and Genetic Engineering

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Transposition of hAT elements links transposable elements and V(D)J recombination

Zhou, Liqin, Mitra, Rupak, Atkinson, Peter W., Burgess Hickman, Alison, Dyda, Fred, Craig, Nancy L.·2004·Nature

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Abstract

Transposons are DNA sequences that encode functions that promote their movement to new locations in the genome. If unregulated, such movement could potentially insert additional DNA into genes, thereby disrupting gene expression and compromising an organism's viability. Transposable elements are classified by their transposition mechanisms and by the transposases that mediate their movement. The mechanism of movement of the eukaryotic hAT superfamily elements was previously unknown, but the divergent sequence of hAT transposases from other elements suggested that these elements might use a distinct mechanism. Here we have analysed transposition of the insect hAT element Hermes in vitro. Like other transposons, Hermes excises from DNA via double-strand breaks between the donor-site DNA and the transposon ends, and the newly exposed transposon ends join to the target DNA. Interestingly, the ends of the donor double-strand breaks form hairpin intermediates, as observed during V(D)J recombination, the process which underlies the combinatorial formation of antigen receptor genes. Significant similarities exist in the catalytic amino acids of Hermes transposase, the V(D)J recombinase RAG, and retroviral integrase superfamily transposases, thereby linking the movement of transposable elements and V(D)J recombination.

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CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.22.4673 · Cited by 64,617
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
The sequence of the human genome
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909
The PSIPRED protein structure prediction server
McGuffin, L. J., Bryson, K., & Jones, D. T. (2000) · Bioinformatics · doi:10.1093/bioinformatics/16.4.404 · Cited by 3,887
Mobile DNA II
(2007) · Wiley eBooks · doi:10.1128/9781555817954 · Cited by 1,311
Hairpin opening and overhang processing by an Artemis/DNA-dependent protein kinase complex in nonhomologous end joining and V(D)J recombination
Ma, Y., Pannicke, U., Schwarz, K., & Lieber, M. R. (2002) · Cell · doi:10.1016/s0092-8674(02)00671-2 · Cited by 1,166
Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system
Agrawal, A., Eastman, Q. M., & Schatz, D. G. (1998) · Nature · doi:10.1038/29457 · Cited by 811
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 · cited 1×
“Structural analysis of the HIV integrase and Mu and Tn5 transposases has previously demonstrated that the highly conserved catalytic DDE acidic amino acids lie on a common structure, that is, an RNaseH-like fold, and that they are closely juxtaposed, as appropriate for formation of a single active sit”
BackgroundSelf-citation
V(D)J Recombination: RAG Proteins, Repair Factors, and Regulation
Gellert, M. F. (2002) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.71.090501.150203 · Cited by 771
DNA Transposition by the RAG1 and RAG2 Proteins
Hiom, K., Melek, M., & Gellert, M. (1998) · Cell · doi:10.1016/s0092-8674(00)81587-1 · Cited by 534
V(D)J recombination: Broken DNA molecules with covalently sealed (hairpin) coding ends in scid mouse thymocytes
Roth, D. B., Menetski, J. P., Nakajima, P. B., Bosma, M. J., & Gellert, M. F. (1992) · Cell · doi:10.1016/0092-8674(92)90248-b · Cited by 440
Metal ion catalysis in the Tetrahymena ribozyme reaction
Piccirilli, J. A., Vyle, J. S., Caruthers, M. H., & Cech, T. R. (1993) · Nature · doi:10.1038/361085a0 · Cited by 386
Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes
Brautigam, C. A., & Steitz, T. A. (1998) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(98)80010-9 · Cited by 377
BASE FLIPPING
Roberts, R. J., & Cheng, X. (1998) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.67.1.181 · Cited by 315
Similarities Between Initiation of V(D)J Recombination and Retroviral Integration
van Gent, D. C., Mizuuchi, K., & Gellert, M. F. (1996) · Science · doi:10.1126/science.271.5255.1592 · Cited by 283
Transposable elements generate novel spatial patterns of gene expression in antirrhinum majus
Coen, E., Carpenter, R., & Martin, C. R. (1986) · Cell · doi:10.1016/0092-8674(86)90451-4 · Cited by 278
Evidence for a common evolutionary origin of inverted repeat transposons in Drosophila and plants: hobo, activator, and Tam3
Calvi, B. R., Hong, T. J., Findley, S. D., & Gelbart, W. M. (1991) · Cell · doi:10.1016/0092-8674(81)90010-6 · Cited by 271
Integrating DNA: Transposases and Retroviral Integrases
Haren, L., Ton‐Hoang, B., & Chandler, M. (1999) · Annual Review of Microbiology · doi:10.1146/annurev.micro.53.1.245 · Cited by 261
RAG Proteins Shepherd Double-Strand Breaks to a Specific Pathway, Suppressing Error-Prone Repair, but RAG Nicking Initiates Homologous Recombination
Lee, G. S., Neiditch, M. B., Salus, S. S., & Roth, D. B. (2004) · Cell · doi:10.1016/s0092-8674(04)00301-0 · Cited by 240
Mutational analysis of RAG1 and RAG2 identifies three catalytic amino acids in RAG1 critical for both cleavage steps of V(D)J recombination
Landree, M. A., Wibbenmeyer, J. A., & Roth, D. B. (1999) · Genes & Development · doi:10.1101/gad.13.23.3059 · Cited by 209
Mutations of acidic residues in RAG1 define the active site of the V(D)J recombinase
Kim, D. R., Dai, Y., Mundy, C. L., Yang, W., & Oettinger, M. A. (1999) · Genes & Development · doi:10.1101/gad.13.23.3070 · Cited by 199 · cited 1×
“The RAG1 subunit of the V(D)J recombinase also contains catalytic acidic amino acids that may also be organized in an RNaseH-like fol”
Background
Tn10 Transposition via a DNA Hairpin Intermediate
Kennedy, A. K., Guhathakurta, A., Kleckner, N. E., & Haniford, D. B. (1998) · Cell · doi:10.1016/s0092-8674(00)81788-2 · Cited by 199
Molecular evolutionary analysis of the widespread piggyBac transposon family and related "domesticated" sequences
Sarkar, A., Sim, C., Hong, Y. S., Hogan, J. R., Fraser, M. J., Robertson, H. M., & Collins, F. H. (2003) · Molecular Genetics and Genomics · doi:10.1007/s00438-003-0909-0 · Cited by 199
Comparative architecture of transposase and integrase complexes.
Rice, P. A., & Baker, T. A. (2001) · Nature Structural Biology · doi:10.1038/86166 · Cited by 192
TheHermestransposable element from the house fly,Musca domestica, is a short inverted repeat-type element of thehobo, Ac, andTam3(hAT) element family
Warren, W. D., Atkinson, P. W., & O’Brochta, D. A. (1994) · Genetics Research · doi:10.1017/s0016672300032699 · Cited by 169
Self-citation
Structure and Evolution of the hAT Transposon Superfamily
Rubin, E., Gila, L., & Levy, A. A. (2001) · Genetics · doi:10.1093/genetics/158.3.949 · Cited by 166
Inversion of the phosphate chirality at the target site of Mu DNA strand transfer: Evidence for a one-step transesterification mechanism
Mizuuchi, K., & Adzuma, K. (1991) · Cell · doi:10.1016/0092-8674(91)90145-o · Cited by 165
Identification of Two Catalytic Residues in RAG1 that Define a Single Active Site within the RAG1/RAG2 Protein Complex
Fugmann, S. D., Villey, I. J., Ptaszek, L. M., & Schatz, D. G. (2000) · Molecular Cell · doi:10.1016/s1097-2765(00)80406-2 · Cited by 165
The Tn7 transposase is a heteromeric complex in which DNA breakage and joining activities are distributed between different gene products.
Sarnovsky, R. J., May, E. W., & Craig, N. L. (1996) · The EMBO Journal · doi:10.1002/j.1460-2075.1996.tb01024.x · Cited by 160
Self-citation
Hairpin Formation in Tn5 Transposition
Bhasin, A., Goryshin, I. Y., & Reznikoff, W. S. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.52.37021 · Cited by 152
Hermes, a Functional Non-Drosophilid Insect Gene Vector From Musca domestica
O’Brochta, D. A., Warren, W. D., Saville, K., & Atkinson, P. W. (1996) · Genetics · doi:10.1093/genetics/142.3.907 · Cited by 115
Self-citation
ThehATand CACTA Superfamilies of Plant Transposons
Kunze, R., & Weil, C. F. (2007) · Wiley eBooks · doi:10.1128/9781555817954.ch24 · Cited by 110
Evolution of DNA Transposons in Eukaryotes
Robertson, H. M. (2007) · Wiley eBooks · doi:10.1128/9781555817954.ch48 · Cited by 106
Transposition of maize Ac/Ds transposable elements in the yeast Saccharomyces cerevisiae
Weil, C. F., & Kunze, R. (2000) · Nature Genetics · doi:10.1038/82827 · Cited by 105
Separation-of-Function Mutants Reveal Critical Roles for RAG2 in Both the Cleavage and Joining Steps of V(D)J Recombination
Qiu, J.-X., Kale, S. B., Schultz, H. Y., & Roth, D. B. (2001) · Molecular Cell · doi:10.1016/s1097-2765(01)00156-3 · Cited by 97
Single Active Site Catalysis of the Successive Phosphoryl Transfer Steps by DNA Transposases
Kennedy, A. K., Haniford, D. B., & Mizuuchi, K. (2000) · Cell · doi:10.1016/s0092-8674(00)80839-9 · Cited by 94
The Hermes element from Musca domestica can transpose in four families of cyclorrhaphan flies
Sarkar, A., Coates, C. J., Whyard, S., Willhoeft, U., Atkinson, P. W., & O’Brochta, D. A. (1997) · Genetica · doi:10.1007/bf02259495 · Cited by 82
Self-citation
The Three-dimensional Structure of a Tn5Transposase-related Protein Determined to 2.9-Å Resolution
Davies, D. R., Braam, L. A. M., Reznikoff, W. S., & Rayment, I. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.17.11904 · Cited by 76
The same two monomers within a MuA tetramer provide the DDE domains for the strand cleavage and strand transfer steps of transposition
Namgoong, S. Y., & Harshey, R. M. (1998) · The EMBO Journal · doi:10.1093/emboj/17.13.3775 · Cited by 70
Mutational Analysis of All Conserved Basic Amino Acids in RAG-1 Reveals Catalytic, Step Arrest, and Joining-Deficient Mutants in the V(D)J Recombinase
Huye, L. E., Purugganan, M. M., Jiang, M., & Roth, D. B. (2002) · Molecular and Cellular Biology · doi:10.1128/mcb.22.10.3460-3473.2002 · Cited by 69
The Origins of V(D)J Recombination
Lewis, S. M., & Wu, G. E. (1997) · Cell · doi:10.1016/s0092-8674(00)81833-4 · Cited by 68
Organization and dynamics of the Mu transpososome: recombination by communication between two active sitesPreprint
Williams, T., Jackson, E. L., Carritte, A., & Baker, T. A. (1999) · Genes & Development · doi:10.1101/gad.13.20.2725 · Cited by 67
Microhomology-Dependent End Joining and Repair of Transposon-Induced DNA Hairpins by Host Factors in Saccharomyces cerevisiae
Yu, J., Marshall, K., Yamaguchi, M., Haber, J. E., & Weil, C. F. (2004) · Molecular and Cellular Biology · doi:10.1128/mcb.24.3.1351-1364.2004 · Cited by 65
MuDR/MuTransposable Elements of Maize
Walbot, V., & Rudenko, G. N. (2007) · doi:10.1128/9781555817954.ch23 · Cited by 58
All three residues of the Tn 10 transposase DDE catalytic triad function in divalent metal ion binding 1 1Edited by M. Gottesman
Allingham, J. S., Pribil, P. A., & Haniford, D. B. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2837 · Cited by 54
Putting the pieces together: identification and characterization of structural domains in the V(D)J recombination protein RAG1
De, P., & Rodgers, K. K. (2004) · Immunological Reviews · doi:10.1111/j.0105-2896.2004.00154.x · Cited by 50
Tfo1: an Ac -like transposon from the plant pathogenic fungus Fusarium oxysporum
Okuda, M., Ikeda, K., Namiki, F., Nishi, K., & Tsuge, T. (1998) · Molecular and General Genetics MGG · doi:10.1007/s004380050773 · Cited by 49
Mixing active-site components: A recipe for the unique enzymatic activity of a telomere resolvase
Bankhead, T., & Chaconas, G. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0405762101 · Cited by 46
Mutational Analysis of the Base Flipping Event Found in Tn5 Transposition
Ason, B. L., & Reznikoff, W. S. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m111119200 · Cited by 40
The C-terminus of the Hermes transposase contains a protein multimerization domain
Michel, K., O’Brochta, D. A., & Atkinson, P. W. (2003) · Insect Biochemistry and Molecular Biology · doi:10.1016/s0965-1748(03)00102-4 · Cited by 27
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Authors: Zhou, L., Mitra, R., Atkinson, P. W., Burgess Hickman, A., Dyda, F., & Craig, N. L.
Affiliations: Howard Hughes Medical Institute (US)
University of California, Riverside (US)
National Institutes of Health (US)
Corresponding author: Craig, Nancy L.
ORCID: Zhou, Liqin
Atkinson, Peter W.
Dyda, Fred
Craig, Nancy L.
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2004-12
Volume: 432
Issue: 7020
Pages: 995-1001
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature03157
OpenAlex: W2071441005
Cited by: 224
References: 50
Citations by year: 2026: 2 · 2025: 5 · 2024: 2 · 2023: 1 · 2022: 3 · 2021: 4 · 2020: 4 · 2019: 6 · 2018: 6 · 2017: 7 · 2016: 6 · 2015: 23 · 2014: 15 · 2013: 11 · 2012: 19
FWCI: 20.37
Type: journal article
Language: en
Open access: closed
Licence: www.springer.com/tdm (tdm)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
RePEc: Research Papers in Economics (submittedVersion)
Funders: Howard Hughes Medical Institute
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
Keywords: hAT transposons, transposition mechanism, V(D)J recombination, DNA double-strand breaks, transposon excision
MeSH terms: Animals, Base Sequence, Binding Sites, DNA, DNA Transposable Elements, Drosophila melanogaster, Nucleic Acid Conformation, Recombination, Genetic, Substrate Specificity, Gene Rearrangement, B-Lymphocyte, Homeodomain Proteins, Transposases

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Transposition of hAT elements links transposable elements and V(D)J recombination

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