The structural features of thousands of T-DNA insertion sites are consistent with a double-strand break repair based insertion mechanism

Kleinbölting N, Huep G, Appelhagen I, Viehöver P, Li Y, Weisshaar B (2015)
Molecular Plant 8(11): 1651-1664.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Abstract / Bemerkung
Transformation by Agrobacterium tumefaciens, an important tool in modern plant research, involves the integration of T-DNA initially present on a plasmid in agrobacteria into the genome of plant cells. The process of attachment of the agrobacteria to plant cells and the transport of T-DNA into the cell and further to the nucleus has been well described. However, the exact mechanism of integration into the host's DNA is still unclear, although several models have been proposed. During confirmation of T-DNA insertion alleles from the GABI-Kat collection of Arabidopsis thaliana mutants, we have generated about 34 000 sequences from the junctions between inserted T-DNA and adjacent genome regions. Here, we describe the evaluation of this dataset with regard to existing models for T-DNA integration. The results suggest that integration into the plant genome is mainly mediated by the endogenous plant DNA repair machinery. The observed integration events showed characteristics highly similar to those of repair sites of double-strand breaks with respect to microhomology and deletion sizes. In addition, we describe unexpected integration events, such as large deletions and inversions at the integration site that are relevant for correct interpretation of results from T-DNA insertion mutants in reverse genetics experiments.
Erscheinungsjahr
2015
Zeitschriftentitel
Molecular Plant
Band
8
Ausgabe
11
Seite(n)
1651-1664
ISSN
1674-2052
eISSN
1752-9867
Page URI
https://pub.uni-bielefeld.de/record/2770216

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Kleinbölting N, Huep G, Appelhagen I, Viehöver P, Li Y, Weisshaar B. The structural features of thousands of T-DNA insertion sites are consistent with a double-strand break repair based insertion mechanism. Molecular Plant. 2015;8(11):1651-1664.
Kleinbölting, N., Huep, G., Appelhagen, I., Viehöver, P., Li, Y., & Weisshaar, B. (2015). The structural features of thousands of T-DNA insertion sites are consistent with a double-strand break repair based insertion mechanism. Molecular Plant, 8(11), 1651-1664. doi:10.1016/j.molp.2015.08.011
Kleinbölting, Nils, Huep, Gunnar, Appelhagen, Ingo, Viehöver, Prisca, Li, Yong, and Weisshaar, Bernd. 2015. “The structural features of thousands of T-DNA insertion sites are consistent with a double-strand break repair based insertion mechanism”. Molecular Plant 8 (11): 1651-1664.
Kleinbölting, N., Huep, G., Appelhagen, I., Viehöver, P., Li, Y., and Weisshaar, B. (2015). The structural features of thousands of T-DNA insertion sites are consistent with a double-strand break repair based insertion mechanism. Molecular Plant 8, 1651-1664.
Kleinbölting, N., et al., 2015. The structural features of thousands of T-DNA insertion sites are consistent with a double-strand break repair based insertion mechanism. Molecular Plant, 8(11), p 1651-1664.
N. Kleinbölting, et al., “The structural features of thousands of T-DNA insertion sites are consistent with a double-strand break repair based insertion mechanism”, Molecular Plant, vol. 8, 2015, pp. 1651-1664.
Kleinbölting, N., Huep, G., Appelhagen, I., Viehöver, P., Li, Y., Weisshaar, B.: The structural features of thousands of T-DNA insertion sites are consistent with a double-strand break repair based insertion mechanism. Molecular Plant. 8, 1651-1664 (2015).
Kleinbölting, Nils, Huep, Gunnar, Appelhagen, Ingo, Viehöver, Prisca, Li, Yong, and Weisshaar, Bernd. “The structural features of thousands of T-DNA insertion sites are consistent with a double-strand break repair based insertion mechanism”. Molecular Plant 8.11 (2015): 1651-1664.

13 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

The complex architecture and epigenomic impact of plant T-DNA insertions.
Jupe F, Rivkin AC, Michael TP, Zander M, Motley ST, Sandoval JP, Slotkin RK, Chen H, Castanon R, Nery JR, Ecker JR., PLoS Genet 15(1), 2019
PMID: 30657772
Comprehensive characterization of T-DNA integration induced chromosomal rearrangement in a birch T-DNA mutant.
Gang H, Liu G, Zhang M, Zhao Y, Jiang J, Chen S., BMC Genomics 20(1), 2019
PMID: 31014254
A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set.
Pucker B, Holtgräwe D, Stadermann KB, Frey K, Huettel B, Reinhardt R, Weisshaar B., PLoS One 14(5), 2019
PMID: 31112551
TDNAscan: A Software to Identify Complete and Truncated T-DNA Insertions.
Sun L, Ge Y, Sparks JA, Robinson ZT, Cheng X, Wen J, Blancaflor EB., Front Genet 10(), 2019
PMID: 31428129
Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides.
Coradetti ST, Pinel D, Geiselman GM, Ito M, Mondo SJ, Reilly MC, Cheng YF, Bauer S, Grigoriev IV, Gladden JM, Simmons BA, Brem RB, Arkin AP, Skerker JM., Elife 7(), 2018
PMID: 29521624
Influence of Chromatin 3D Organization on Structural Variations of the Arabidopsis thaliana Genome.
Tao JF, Zhou JZ, Xie T, Wang XT, Yang QY, Zhang HY., Mol Plant 10(2), 2017
PMID: 27742489
T-DNA-genome junctions form early after infection and are influenced by the chromatin state of the host genome.
Shilo S, Tripathi P, Melamed-Bessudo C, Tzfadia O, Muth TR, Levy AA., PLoS Genet 13(7), 2017
PMID: 28742090
Integration of Agrobacterium T-DNA into the Plant Genome.
Gelvin SB., Annu Rev Genet 51(), 2017
PMID: 28853920
A De Novo Genome Sequence Assembly of the Arabidopsis thaliana Accession Niederzenz-1 Displays Presence/Absence Variation and Strong Synteny.
Pucker B, Holtgräwe D, Rosleff Sörensen T, Stracke R, Viehöver P, Weisshaar B., PLoS One 11(10), 2016
PMID: 27711162
Genomic Scars Generated by Polymerase Theta Reveal the Versatile Mechanism of Alternative End-Joining.
van Schendel R, van Heteren J, Welten R, Tijsterman M., PLoS Genet 12(10), 2016
PMID: 27755535
T-DNA integration in plants results from polymerase-θ-mediated DNA repair.
van Kregten M, de Pater S, Romeijn R, van Schendel R, Hooykaas PJ, Tijsterman M., Nat Plants 2(11), 2016
PMID: 27797358

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