Analysis of T-DNA insertion site distribution patterns in Arabidopsis thaliana reveals special features of genes without insertions

Li Y, Rosso MG, Uelker B, Weisshaar B (2006)
Genomics 87(5): 645-652.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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DOI
Autor*in
Li, Yong; Rosso, Mario G.; Uelker, Bekir; Weisshaar, BerndUniBi
Einrichtung
Fakultät für Biologie > Genetik und Genomik der Pflanzen
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Centrum für Biotechnologie > Arbeitsgruppe B. Weisshaar
Stichworte
Arabidopsis thaliana; integration; T-DNA; restriction sites; insertional mutagenesis; gene expression
Erscheinungsjahr
2006
Zeitschriftentitel
Genomics
Band
87
Ausgabe
5
Seite(n)
645-652
ISSN
0888-7543
Page URI
https://pub.uni-bielefeld.de/record/1599329

Zitieren

Li Y, Rosso MG, Uelker B, Weisshaar B. Analysis of T-DNA insertion site distribution patterns in Arabidopsis thaliana reveals special features of genes without insertions. Genomics. 2006;87(5):645-652.
Li, Y., Rosso, M. G., Uelker, B., & Weisshaar, B. (2006). Analysis of T-DNA insertion site distribution patterns in Arabidopsis thaliana reveals special features of genes without insertions. Genomics, 87(5), 645-652. https://doi.org/10.1016/j.ygeno.2005.12.010
Li, Yong, Rosso, Mario G., Uelker, Bekir, and Weisshaar, Bernd. 2006. “Analysis of T-DNA insertion site distribution patterns in Arabidopsis thaliana reveals special features of genes without insertions”. Genomics 87 (5): 645-652.
Li, Y., Rosso, M. G., Uelker, B., and Weisshaar, B. (2006). Analysis of T-DNA insertion site distribution patterns in Arabidopsis thaliana reveals special features of genes without insertions. Genomics 87, 645-652.
Li, Y., et al., 2006. Analysis of T-DNA insertion site distribution patterns in Arabidopsis thaliana reveals special features of genes without insertions. Genomics, 87(5), p 645-652.
Y. Li, et al., “Analysis of T-DNA insertion site distribution patterns in Arabidopsis thaliana reveals special features of genes without insertions”, Genomics, vol. 87, 2006, pp. 645-652.
Li, Y., Rosso, M.G., Uelker, B., Weisshaar, B.: Analysis of T-DNA insertion site distribution patterns in Arabidopsis thaliana reveals special features of genes without insertions. Genomics. 87, 645-652 (2006).
Li, Yong, Rosso, Mario G., Uelker, Bekir, and Weisshaar, Bernd. “Analysis of T-DNA insertion site distribution patterns in Arabidopsis thaliana reveals special features of genes without insertions”. Genomics 87.5 (2006): 645-652.

19 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Enhancing the GABI-Kat Arabidopsis thaliana T-DNA Insertion Mutant Database by Incorporating Araport11 Annotation.
Kleinboelting N, Huep G, Weisshaar B., Plant Cell Physiol 58(1), 2017
PMID: 28013277
A landscape of hairy and twisted: hunting for new trichome mutants in the Saskatoon Arabidopsis T-DNA population.
Taheri A, Gao P, Yu M, Cui D, Regan S, Parkin I, Gruber M., Plant Biol (Stuttg) 17(2), 2015
PMID: 25348773
Agrobacterium T-DNA integration into the plant genome can occur without the activity of key non-homologous end-joining proteins.
Park SY, Vaghchhipawala Z, Vasudevan B, Lee LY, Shen Y, Singer K, Waterworth WM, Zhang ZJ, West CE, Mysore KS, Gelvin SB., Plant J 81(6), 2015
PMID: 25641249
An efficient reverse genetics platform in the model legume Medicago truncatula.
Cheng X, Wang M, Lee HK, Tadege M, Ratet P, Udvardi M, Mysore KS, Wen J., New Phytol 201(3), 2014
PMID: 24206427
Genetic screens for floral mutants in Arabidopsis thaliana: enhancers and suppressors.
Dinh TT, Luscher E, Li S, Liu X, Won SY, Chen X., Methods Mol Biol 1110(), 2014
PMID: 24395255
An easy-to-use primer design tool to address paralogous loci and T-DNA insertion sites in the genome of Arabidopsis thaliana.
Huep G, Kleinboelting N, Weisshaar B., Plant Methods 10(), 2014
PMID: 25324895
Consequences of normalizing transcriptomic and genomic libraries of plant genomes using a duplex-specific nuclease and tetramethylammonium chloride.
Matvienko M, Kozik A, Froenicke L, Lavelle D, Martineau B, Perroud B, Michelmore R., PLoS One 8(2), 2013
PMID: 23409088
Matrix proteins are inefficiently imported into Arabidopsis peroxisomes lacking the receptor-docking peroxin PEX14.
Monroe-Augustus M, Ramón NM, Ratzel SE, Lingard MJ, Christensen SE, Murali C, Bartel B., Plant Mol Biol 77(1-2), 2011
PMID: 21553312
Plant proteins involved in Agrobacterium-mediated genetic transformation.
Gelvin SB., Annu Rev Phytopathol 48(), 2010
PMID: 20337518
Linking genotype to phenotype using the Arabidopsis unimutant collection.
O'Malley RC, Ecker JR., Plant J 61(6), 2010
PMID: 20409268
SNP discovery and genetic mapping of T-DNA insertional mutants in Fragaria vesca L.
Ruiz-Rojas JJ, Sargent DJ, Shulaev V, Dickerman AW, Pattison J, Holt SH, Ciordia A, Veilleux RE., Theor Appl Genet 121(3), 2010
PMID: 20349033
Genetic technologies for the identification of plant genes controlling environmental stress responses
Papdi Csaba, Joseph MaryPrathiba, Salamó ImmaPérez, Vidal Sabina, Szabados László., Funct Plant Biol 36(8), 2009
PMID: IND44235750
An archived activation tagged population of Arabidopsis thaliana to facilitate forward genetics approaches.
Robinson SJ, Tang LH, Mooney BA, McKay SJ, Clarke WE, Links MG, Karcz S, Regan S, Wu YY, Gruber MY, Cui D, Yu M, Parkin IA., BMC Plant Biol 9(), 2009
PMID: 19646253
Reverse genetics through random mutagenesis in Histoplasma capsulatum.
Youseff BH, Dougherty JA, Rappleye CA., BMC Microbiol 9(), 2009
PMID: 19919692
Dissection of genetic effects of quantitative trait loci (QTL) in transgenic cotton
Zhang Yongshan, Yu Shuxun, Guo Xiangmo, Wang Zhiwei, Wang Qinglian, Chu Li., Euphytica 159(1-2), 2008
PMID: IND43984942
Getting the most out of publicly available T-DNA insertion lines.
Ulker B, Peiter E, Dixon DP, Moffat C, Capper R, Bouché N, Edwards R, Sanders D, Knight H, Knight MR., Plant J 56(4), 2008
PMID: 18644000
Identifying essential genes in Arabidopsis thaliana.
Meinke D, Muralla R, Sweeney C, Dickerman A., Trends Plant Sci 13(9), 2008
PMID: 18684657
Non-random distribution of T-DNA insertions at various levels of the genome hierarchy as revealed by analyzing 13 804 T-DNA flanking sequences from an enhancer-trap mutant library.
Zhang J, Guo D, Chang Y, You C, Li X, Dai X, Weng Q, Zhang J, Chen G, Li X, Liu H, Han B, Zhang Q, Wu C., Plant J 49(5), 2007
PMID: 17253985
DNA microarray analyses in higher plants.
Galbraith DW., OMICS 10(4), 2006
PMID: 17233557

35 References

Daten bereitgestellt von Europe PubMed Central.

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
Arabidopsis Genome Initiative., Nature 408(6814), 2000
PMID: 11130711
T-DNA as an insertional mutagen in Arabidopsis.
Krysan PJ, Young JC, Sussman MR., Plant Cell 11(12), 1999
PMID: 10590158
FLAGdb/FST: a database of mapped flanking insertion sites (FSTs) of Arabidopsis thaliana T-DNA transformants.
Samson F, Brunaud V, Balzergue S, Dubreucq B, Lepiniec L, Pelletier G, Caboche M, Lecharny A., Nucleic Acids Res. 30(1), 2002
PMID: 11752264
A high-throughput Arabidopsis reverse genetics system.
Sessions A, Burke E, Presting G, Aux G, McElver J, Patton D, Dietrich B, Ho P, Bacwaden J, Ko C, Clarke JD, Cotton D, Bullis D, Snell J, Miguel T, Hutchison D, Kimmerly B, Mitzel T, Katagiri F, Glazebrook J, Law M, Goff SA., Plant Cell 14(12), 2002
PMID: 12468722
Genome-wide insertional mutagenesis of Arabidopsis thaliana.
Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen H, Shinn P, Stevenson DK, Zimmerman J, Barajas P, Cheuk R, Gadrinab C, Heller C, Jeske A, Koesema E, Meyers CC, Parker H, Prednis L, Ansari Y, Choy N, Deen H, Geralt M, Hazari N, Hom E, Karnes M, Mulholland C, Ndubaku R, Schmidt I, Guzman P, Aguilar-Henonin L, Schmid M, Weigel D, Carter DE, Marchand T, Risseeuw E, Brogden D, Zeko A, Crosby WL, Berry CC, Ecker JR., Science 301(5633), 2003
PMID: 12893945
GABI-Kat SimpleSearch: a flanking sequence tag (FST) database for the identification of T-DNA insertion mutants in Arabidopsis thaliana.
Li Y, Rosso MG, Strizhov N, Viehoever P, Weisshaar B., Bioinformatics 19(11), 2003
PMID: 12874060
A sequence-based map of Arabidopsis genes with mutant phenotypes.
Meinke DW, Meinke LK, Showalter TC, Schissel AM, Mueller LA, Tzafrir I., Plant Physiol. 131(2), 2003
PMID: 12586866
The integration of T-DNA into plant genomes
Tinland, Trends Plant Sci. 1(), 1996
Agrobacterium T-DNA integration: molecules and models.
Tzfira T, Li J, Lacroix B, Citovsky V., Trends Genet. 20(8), 2004
PMID: 15262410
Characterization of T-DNA insertion sites in Arabidopsis thaliana and the implications for saturation mutagenesis.
Krysan PJ, Young JC, Jester PJ, Monson S, Copenhaver G, Preuss D, Sussman MR., OMICS 6(2), 2002
PMID: 12143962
An Arabidopsis thaliana T-DNA mutagenized population (GABI-Kat) for flanking sequence tag-based reverse genetics.
Rosso MG, Li Y, Strizhov N, Reiss B, Dekker K, Weisshaar B., Plant Mol. Biol. 53(1-2), 2003
PMID: 14756321
Site preferences of insertional mutagenesis agents in Arabidopsis.
Pan X, Li Y, Stein L., Plant Physiol. 137(1), 2004
PMID: 15618417
Distribution of 1000 sequenced T-DNA tags in the Arabidopsis genome.
Szabados L, Kovacs I, Oberschall A, Abraham E, Kerekes I, Zsigmond L, Nagy R, Alvarado M, Krasovskaja I, Gal M, Berente A, Redei GP, Haim AB, Koncz C., Plant J. 32(2), 2002
PMID: 12383088
T-DNA integration into the Arabidopsis genome depends on sequences of pre-insertion sites.
Brunaud V, Balzergue S, Dubreucq B, Aubourg S, Samson F, Chauvin S, Bechtold N, Cruaud C, DeRose R, Pelletier G, Lepiniec L, Caboche M, Lecharny A., EMBO Rep. 3(12), 2002
PMID: 12446565
T-DNA insertional mutagenesis in Arabidopsis.
Koncz C, Nemeth K, Redei GP, Schell J., Plant Mol. Biol. 20(5), 1992
PMID: 1463832
Tagging genomic sequences that direct transgene expression by activation of a promoter trap in plants.
Lindsey K, Wei W, Clarke MC, McArdle HF, Rooke LM, Topping JF., Transgenic Res. 2(1), 1993
PMID: 8513337
Generation and analysis of end sequence database for T-DNA tagging lines in rice.
An S, Park S, Jeong DH, Lee DY, Kang HG, Yu JH, Hur J, Kim SR, Kim YH, Lee M, Han S, Kim SJ, Yang J, Kim E, Wi SJ, Chung HS, Hong JP, Choe V, Lee HK, Choi JH, Nam J, Kim SR, Park PB, Park KY, Kim WT, Choe S, Lee CB, An G., Plant Physiol. 133(4), 2003
PMID: 14630961
Annotation of the Arabidopsis genome.
Wortman JR, Haas BJ, Hannick LI, Smith RK Jr, Maiti R, Ronning CM, Chan AP, Yu C, Ayele M, Whitelaw CA, White OR, Town CD., Plant Physiol. 132(2), 2003
PMID: 12805579
GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes.
Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G., Bioinformatics 20(18), 2004
PMID: 15297299
Improved PCR-walking for large-scale isolation of plant T-DNA borders.
Balzergue S, Dubreucq B, Chauvin S, Le-Clainche I, Le Boulaire F, de Rose R, Samson F, Biaudet V, Lecharny A, Cruaud C, Weissenbach J, Caboche M, Lepiniec L., BioTechniques 30(3), 2001
PMID: 11252785
High-throughput generation of sequence indexes from T-DNA mutagenized Arabidopsis thaliana lines.
Strizhov N, Li Y, Rosso MG, Viehoever P, Dekker KA, Weisshaar B., BioTechniques 35(6), 2003
PMID: 14682050
The VirD2 pilot protein of Agrobacterium-transferred DNA interacts with the TATA box-binding protein and a nuclear protein kinase in plants.
Bako L, Umeda M, Tiburcio AF, Schell J, Koncz C., Proc. Natl. Acad. Sci. U.S.A. 100(17), 2003
PMID: 12900506
Transcription start regions in the human genome are favored targets for MLV integration.
Wu X, Li Y, Crise B, Burgess SM., Science 300(5626), 2003
PMID: 12805549
The maternal chromosome set is the target of the T-DNA in the in planta transformation of Arabidopsis thaliana.
Bechtold N, Jaudeau B, Jolivet S, Maba B, Vezon D, Voisin R, Pelletier G., Genetics 155(4), 2000
PMID: 10924482
Female reproductive tissues are the primary target of Agrobacterium-mediated transformation by the Arabidopsis floral-dip method.
Desfeux C, Clough SJ, Bent AF., Plant Physiol. 123(3), 2000
PMID: 10889238
The endosperm and the embryo of Arabidopsis thaliana are independently transformed through infiltration by Agrobacterium tumefaciens.
Bechtold N, Jolivet S, Voisin R, Pelletier G., Transgenic Res. 12(4), 2003
PMID: 12885171
Genetic and molecular identification of genes required for female gametophyte development and function in Arabidopsis.
Pagnussat GC, Yu HJ, Ngo QA, Rajani S, Mayalagu S, Johnson CS, Capron A, Xie LF, Ye D, Sundaresan V., Development 132(3), 2005
PMID: 15634699
Identification of Arabidopsis thaliana transformants without selection reveals a high occurrence of silenced T-DNA integrations.
Francis KE, Spiker S., Plant J. 41(3), 2005
PMID: 15659104
The Arabidopsis knockout facility at the University of Wisconsin-Madison.
Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S., Plant Physiol. 124(4), 2000
PMID: 11115860
Rapid identification of Arabidopsis insertion mutants by non-radioactive detection of T-DNA tagged genes.
Rios G, Lossow A, Hertel B, Breuer F, Schaefer S, Broich M, Kleinow T, Jasik J, Winter J, Ferrando A, Farras R, Panicot M, Henriques R, Mariaux JB, Oberschall A, Molnar G, Berendzen K, Shukla V, Lafos M, Koncz Z, Redei GP, Schell J, Koncz C., Plant J. 32(2), 2002
PMID: 12383089
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694
Generalized Venn diagrams: a new method of visualizing complex genetic set relations.
Kestler HA, Muller A, Gress TM, Buchholz M., Bioinformatics 21(8), 2004
PMID: 15572472
The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community.
Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, Miller N, Mueller LA, Mundodi S, Reiser L, Tacklind J, Weems DC, Wu Y, Xu I, Yoo D, Yoon J, Zhang P., Nucleic Acids Res. 31(1), 2003
PMID: 12519987
A gene expression map of Arabidopsis thaliana development.
Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU., Nat. Genet. 37(5), 2005
PMID: 15806101
Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis.
Duret L, Mouchiroud D., Proc. Natl. Acad. Sci. U.S.A. 96(8), 1999
PMID: 10200288
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