1.1 5508 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Godelieve Gheysen aut author ug_LA25 0000-0003-1929-5059 Marc Van Montagu aut author ug_WE09 Patricia Zambryski aut author ug_WE09 eng The transfer DNA (T-DNA) mobilized into plant cells by Agrobacterium tumefaciens seems to integrate rather randomly into the plant genome. We analyzed a target site in the genome of Nicotiana tabacum before and after integration of a T-DNA. Clones presenting right and left T-DNA/plant DNA junctions were used as probes to identify and isolate a unique 1.8-kilobase EcoRI fragment corresponding to the plant DNA target site for a T-DNA insertion event. Comparison of the nucleotide sequences of the plant DNA portions of the T-DNA junction clones with the original plant DNA target revealed that several types of rearrangements resulted from insertion of the T-DNA. The most dramatic alteration was a 158-base-pair direct repeat of target plant sequences at the left and right T-DNA junctions. In addition, there were deletion and insertion events at the ends of the right and left copies of the 158-base-pair repeat. The variety of target-site rearrangements suggests that T-DNA insertion is a multistep process of recombination accompanied by local replicative and repair activities mediated by host-cell enzymes. Biology and Life Sciences http://hdl.handle.net/1854/LU-1902434 10.1073/pnas.84.17.6169 A1987J864900036 0027-8424 1987 0027-8424 1987 84 17 6169 6173 1987 No license (in copyright) published https://biblio.ugent.be/publication/1902434/file/1902440 application/pdf restricted ug 1902434 2011-09-16T16:40:24Z 2026-03-31T07:38:51Z A1 VABB-1 1 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Pieter Windels aut author Sylvie De Buck aut author ug_GE35 ug_UZGent 0000-0001-8048-0582 Erik Van Bockstaele aut author ug_UGent Marc De Loose aut author ug_UGent Anna Depicker aut author ug_WE09 0000-0003-0105-7407 eng To investigate the relationship between T-DNA integration and double-stranded break (DSB) repair in Arabidopsis, we studied 67 T-DNA/plant DNA junctions and 13 T-DNA/T-DNA junctions derived from transgenic plants. Three different types of T-DNA-associated joining could be distinguished. A minority of T-DNA/plant DNA junctions were joined by a simple ligation-like mechanism, resulting in a junction without microhomology or filler DNA insertions. For about one-half of all analyzed junctions, joining of the two ends occurred without insertion of filler sequences. For these junctions, microhomology was strikingly combined with deletions of the T-DNA ends. For the remaining plant DNA/T-DNA junctions, up to 51-bp-long filler sequences were present between plant DNA and T-DNA contiguous sequences. These filler segments are built from several short sequence motifs, identical to sequence blocks that occur in the T-DNA ends and/or the plant DNA close to the integration site. Mutual microhomologies among the sequence motifs that constitute a filler segment were frequently observed. When T-DNA integration and DSB repair were compared, the most conspicuous difference was the frequency and the structural organization of the filler insertions. In Arabidopsis, no filler insertions were found at DSB repair junctions. In maize (Zea mays) and tobacco (Nicotiana tabacum), DSB repair-associated filler was normally composed of simple, uninterrupted sequence blocks. Thus, although DSB repair and T-DNA integration are probably closely related, both mechanisms have some exclusive and specific characteristics. Biology and Life Sciences NONHOMOLOGOUS RECOMBINATION STRAND BREAK REPAIR ILLEGITIMATE RECOMBINATION PLANT-CELLS AGROBACTERIUM-TUMEFACIENS GENOME EVOLUTION MAMMALIAN-CELLS LIGASE-IV THALIANA MAIZE http://hdl.handle.net/1854/LU-348784 10.1104/pp.103.027532 000187528700063 0032-0889 2003 0032-0889 2003 133 4 2061 2068 2003 No license (in copyright) published https://biblio.ugent.be/publication/348784/file/4144327 application/pdf restricted ug 348784 2004-05-10T18:14:00Z 2026-09-03T12:45:35Z A1 VABB-1 2 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Godelieve Gheysen aut author ug_LA25 0000-0003-1929-5059 Raimundo Villarroel-Mandiola aut author ug_UGent Marc Van Montagu aut author ug_WE09 eng Agrobacterium tumefaciens is a soil bacterium capable of transferring DNA (the T-DNA) to the genome of higher plants, where it is then stably integrated. Six T-DNA inserts and their corresponding preinsertion sites were cloned from Arabidopsis thaliana and analyzed. Two T-DNA integration events from Nicotiana tabacum were included in the analysis. Nucleotide sequence comparison of plant target sites before and after T-DNA integration showed that the T-DNA usually causes only a small (13-28 bp) deletion in the plant DNA but larger target rearrangements can occur. Short homologies between the T-DNA ends and the target sites, as well as the presence of filler sequences at the junctions, indicate that T-DNA integration is mediated by illegitimate recombination and that these processes in plants are very analogous to events in mammalian cells. We propose a model for T-DNA integration on the basis of limited base-pairing for initial synapsis, followed by DNA repair at the junctions. Variations of the model can explain the formation of filler DNA at the junctions by polymerase slipping and template switching during DNA repair synthesis and the presence of larger plant target DNA rearrangements. Biology and Life Sciences CROWN GALL TUMOR AGROBACTERIUM-TUMEFACIENS BINDING-PROTEIN NONHOMOLOGOUS RECOMBINATION ESCHERICHIA-COLI MAMMALIAN-CELLS VIRD2 PROTEIN SEQUENCES MECHANISMS PLASMID AGROBACTERIUM-TUMEFACIENS REARRANGEMENT RECOMBINATION TARGET T-DNA TRANSGENIC PLANTS http://hdl.handle.net/1854/LU-8514406 10.1101/gad.5.2.287 A1991EX51800013 0890-9369 1991 0890-9369 1991 5 2 287 297 1991 No license (in copyright) published https://biblio.ugent.be/publication/8514406/file/8514407 application/unknown restricted ug 8514406 2017-03-15T12:25:49Z 2026-03-31T14:30:20Z A1 VABB-1 3 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Lieselot Hemeryck aut author ug_DI04 0000-0002-2451-3375 Anneleen Decloedt aut author ug_UGent Julie Vanden Bussche aut author ug_UGent Karen Geboes aut author ug_GE35 ug_UZGent Lynn Vanhaecke aut author ug_DI04 0000-0003-0400-2188 eng Exposure of DNA to endo- and exogenous DNA binding chemicals can result in the formation of DNA adducts and is believed to be the first step in chemically induced carcinogenesis. DNA adductomics is a relatively new field of research which studies the formation of known and unknown DNA adducts in DNA due to exposure to genotoxic chemicals. In this study, a new UHPLC-HRMS(/MS)-based DNA adduct detection method was developed and validated. Four targeted DNA adducts, which all have been linked to dietary genotoxicity, were included in the described method; O-6-methylguanine (O-6-MeG), O-6-carboxymethylguanine (O-6-CMG), pyrimidopurinone (M1G) and methylhydroxypropanoguanine (CroG). As a supplementary tool for DNA adductomics, a DNA adduct database, which currently contains 123 different diet-related DNA adducts, was constructed. By means of the newly developed method and database, all 4 targeted DNA adducts and 32 untargeted DNA adducts could be detected in different DNA samples. The obtained results clearly demonstrate the merit of the described method for both targeted and untargeted DNA adduct detection in vitro and in vivo, whilst the diet-related DNA adduct database can distinctly facilitate data interpretation. (C) 2015 Elsevier B.V. All rights reserved. Veterinary Sciences Medicine and Health Sciences Colorectal cancer Deoxyribonucleic acid adduct database Dietary chemicals High resolution mass spectrometry Quadrupole-Orbitrap DNA-DAMAGE LIPID-PEROXIDATION COLORECTAL-CANCER ENVIRONMENTAL-POLLUTANTS OXIDATIVE STRESS HUMAN LIVER IN-VITRO RED MEAT IDENTIFICATION RISK http://hdl.handle.net/1854/LU-6991587 10.1016/j.aca.2015.08.019 000361646900012 0003-2670 1873-4324 2015 0003-2670 1873-4324 2015 892 123 131 2015 No license (in copyright) published https://biblio.ugent.be/publication/6991587/file/6991595 application/pdf ug 6991587 2015-11-25T15:23:44Z 2026-09-03T07:02:43Z A1 VABB-1 4 info:srw/schema/1/mods-v3.3xml journalArticle Review A1 Nicolas Gryson aut author ug_UGent eng The applicability of a DNA-based method for GMO detection and quantification depends on the quality and quantity of the DNA. Important food-processing conditions, for example temperature and pH, may lead to degradation of the DNA, rendering PCR analysis impossible or GMO quantification unreliable. This review discusses the effect of several food processes on DNA degradation and subsequent GMO detection and quantification. The data show that, although many of these processes do indeed lead to the fragmentation of DNA, amplification of the DNA may still be possible. Length and composition of the amplicon may, however, affect the result, as also may the method of extraction used. Also, many techniques are used to describe the behaviour of DNA in food processing, which occasionally makes it difficult to compare research results. Further research should be aimed at defining ingredients in terms of their DNA quality and PCR amplification ability, and elaboration of matrix-specific certified reference materials. Agriculture and Food Sciences PCR analysis DNA quantification GMO detection DNA degradation Food processing GENETICALLY-MODIFIED ORGANISMS POLYMERASE-CHAIN-REACTION REAL-TIME PCR QUANTITATIVE COMPETITIVE PCR DIFFERENT EXTRACTION METHODS MODIFIED SOY BEANS MODIFIED BT MAIZE ZEA-MAYS L. MODIFIED SOYBEANS RECOMBINANT-DNA http://hdl.handle.net/1854/LU-812815 10.1007/s00216-009-3343-2 000275454900007 1618-2642 2010 1618-2642 2010 396 6 2003 2022 2010 No license (in copyright) published https://biblio.ugent.be/publication/812815/file/6824118 application/pdf restricted ug 812815 2009-12-16T13:37:59Z 2026-09-03T08:03:55Z A1 VABB-1 5 info:srw/schema/1/mods-v3.3xml journalArticle Review A1 José Antonio Pedroza-Garcia aut author ug_UGent Lieven De Veylder aut author ug_WE09 0000-0003-1150-4426 Cécile Raynaud aut author eng Maintenance of genome integrity is a key process in all organisms. DNA polymerases (Pols) are central players in this process as they are in charge of the faithful reproduction of the genetic information, as well as of DNA repair. Interestingly, all eukaryotes possess a large repertoire of polymerases. Three protein complexes, DNA Pol α, δ, and ε, are in charge of nuclear DNA replication. These enzymes have the fidelity and processivity required to replicate long DNA sequences, but DNA lesions can block their progression. Consequently, eukaryotic genomes also encode a variable number of specialized polymerases (between five and 16 depending on the organism) that are involved in the replication of damaged DNA, DNA repair, and organellar DNA replication. This diversity of enzymes likely stems from their ability to bypass specific types of lesions. In the past 10–15 years, our knowledge regarding plant DNA polymerases dramatically increased. In this review, we discuss these recent findings and compare acquired knowledge in plants to data obtained in other eukaryotes. We also discuss the emerging links between genome and epigenome replication. Biology and Life Sciences DNA replication DNA repair DOUBLE-STRAND BREAKS CELL-CYCLE REPLICATION STRESS ARABIDOPSIS-THALIANA CATALYTIC SUBUNIT GENOMIC STABILITY GENETIC-ANALYSIS DAMAGE RESPONSE ATPOL-LAMBDA POL-EPSILON http://hdl.handle.net/1854/LU-8632082 10.3390/ijms20194814 000494798300155 1422-0067 4814 25 p.

2019 1422-0067 2019 20 19 2019 Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) published https://biblio.ugent.be/publication/8632082/file/8632083 application/pdf ug 8632082 2019-10-17T08:35:07Z 2026-09-03T07:01:50Z A1 VABB-1 6 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Armin P Czernilofsky aut author Rüdiger Hain aut author Luis Herrera-Estrella aut author Horst Lörz aut author Elisabeth Goyvaerts aut author Barbara J Baker aut author Jeff Schell aut author eng To compare the effects of different transformation methods on the integration behavior and structural stability of integrated foreign genes in plant cells, tobacco protoplasts were transformed with Escherichia coli plasmid pLGV2103neo DNA using the Ca phosphate DNA coprecipitation technique. Parallel transformations were done by cocultivation with Agrobacterium tumefaciens harboring the Ti plasmid derivatives pGV3850::2103neo or pGV3850::1103neo. A comparison of the fine structure of the integrated donor DNA obtained by direct gene transfer and by cocultivation indicates that the donor DNA in cells transformed by the former technique undergoes structural changes and concatemerizations, while the DNA integrated by the latter procedure is often unaltered. The cotransformed nopaline synthase gene, which is present in the donor Ti plasmid DNA, was inactivated in two out of nine cases. Once integrated, the arrays of selectable marker DNA appear to be structurally stable under different cell culture and selection conditions, as well as after genetic transmission. Biology and Life Sciences http://hdl.handle.net/1854/LU-1903293 10.1089/dna.1986.5.101 A1986D177200002 0198-0238 1986 0198-0238 1986 5 2 101 113 1986 No license (in copyright) published https://biblio.ugent.be/publication/1903293/file/1903304 application/pdf restricted ug 1903293 2011-09-19T10:59:25Z 2026-03-31T13:24:49Z A1 VABB-1 7 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Sylvie De Buck aut author ug_GE35 ug_UZGent 0000-0001-8048-0582 Anni Jacobs aut author ug_WE09 Marc Van Montagu aut author ug_WE09 Anna Depicker aut author ug_WE09 0000-0003-0105-7407 eng After Agrobacterium-mediated plant transformation, multiple T-DNAs frequently integrate at the same position in the plant genome, resulting in the formation of inverted and direct repeats. Because these inverted repeats cannot be amplified and analyzed by PCR, Arabidopsis root cells were co-transformed with two different T-DNAs with distinct sequences adjacent to the T-DNA borders. Nine direct or inverted T-DNA border junctions were analyzed at the sequence level. Precise end-to-end fusions were found between two right border ends, whereas imprecise fusions and filler DNA were present in T-DNA linkages containing a left border end. The results suggest that end-to-end ligation of double-stranded T-DNAs occurs especially between right T-DNA ends and that illegitimate recombination on the basis of microhomology, deletions, repair activities and insertions of filler DNA is involved in the formation of left border T-DNA junctions. Therefore, a similar illegitimate recombination mechanism is proposed that is involved in the formation of complex T-DNA inserts as well as in the integration of the T-DNA in the plant genome. Biology and Life Sciences GENOME PROTEIN GENE STRANDED-DNA MEDIATED TRANSFORMATION ILLEGITIMATE RECOMBINATION PLANT-CELLS AGROBACTERIUM-TUMEFACIENS VIRD2 CONJUGATION ARABIDOPSIS http://hdl.handle.net/1854/LU-112589 10.1046/j.1365-313X.1999.00602.x 000084156700004 0960-7412 1999 0960-7412 1999 20 3 295 304 1999 No license (in copyright) published https://biblio.ugent.be/publication/112589/file/4161283 application/pdf restricted ug 112589 2004-01-14T13:35:00Z 2026-03-31T06:57:36Z A1 VABB-1 8 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Godelieve Gheysen aut author ug_LA25 0000-0003-1929-5059 Lieve Herman aut author ug_CA20 Peter Breyne aut author ug_WE09 Jan Gielen aut author ug_UGent Marc Van Montagu aut author ug_WE09 Anna Depicker aut author ug_WE09 0000-0003-0105-7407 eng Transgenic plants produced by Agrobacterium-mediated transformation usually have one or a few stable and intact T-DNA insertions. However, in a significant number of the transformants Southern blot analysis has revealed the occurrence of aberrant T-DNA insertions missing one or both ends. During the study of this phenomenon, we obtained KmRNicotiana tabacum clones after cocultivation with an Agrobacterium strain containing a promoterless nptII gene located internally in the T-DNA. Expression of this nptII gene requires a break in the T-DNA region upstream from the nptII-coding sequence and insertion of the truncated T-DNA in a transcriptionally active plant DNA region. The most conspicuous results from Southern analyses on four such KmR plant clones is that they contain several T-DNAs truncated at other positions besides the upstream region of the nptII sequence. Four truncated T-DNA insertions have been cloned. Two insertions contain the nptII gene fused to plant expression signals and are missing the right part of the T-DNA. Another is missing the left T-DNA part and the last T-DNA is lacking both ends. Sequence analysis of the T-DNA:: plant junctions has shown that the T-DNA breakpoints are randomly distributed and do not show obvious homologies to one another or to the border consensus sequence. S1-type mapping of the most strongly expressed plant genome::nptII fusion revealed a specific transcription start point and putative TATA and CAAT boxes in the upstream plant DNA region; the steady-state nptII mRNA in these plants is about 20 times more abundant than in transgenic Pnos-nptII plants. Biology and Life Sciences Aberrant T-DNAs Agrobacterium tumefaciens cosmid clones insertional activation plant promoter pseudoborder recombinant DNA http://hdl.handle.net/1854/LU-7244394 10.1016/0378-1119(90)90382-2 A1990EK10200002 0378-1119 1990 0378-1119 1990 94 2 155 163 1990 No license (in copyright) published https://biblio.ugent.be/publication/7244394/file/8516744 application/pdf restricted ug 7244394 2016-06-06T13:38:42Z 2026-03-31T14:25:47Z A1 VABB-1 9 info:srw/schema/1/mods-v3.3xml journalArticle Article A1 Philippe Blayo aut author Pierre Rouzé aut author ug_UGent Marie-France Sagot aut author eng Biology and Life Sciences gene finding orphan gene exon assembly DNA/DNA and DNA/protein comparison coding DNA comparison models dynamic programming ARABIDOPSIS-THALIANA PROTEIN ALIGNMENT DNA-SEQUENCES LINEAR-SPACE GENOMIC DNA CODING DNA PREDICTION ALGORITHM COMPUTER ERRORS http://hdl.handle.net/1854/LU-215318 10.1016/S0304-3975(02)00043-9 000179441900007 0304-3975 2003 0304-3975 2003 290 3 1407 1431 2003 No license (in copyright) published https://biblio.ugent.be/publication/215318/file/4144219 application/pdf restricted ug 215318 2004-05-10T17:59:00Z 2026-09-03T07:04:07Z A1 VABB-1 10 1.1dnasrw.ServerChoicescrdna