Site preferences of insertional mutagenesis agents in Arabidopsis

Pan X, Li Y, Stein L (2005)
Plant Physiology 137(1): 168-175.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
Pan, X.; Li, Yong; Stein, L.
Abstract / Bemerkung
We have performed a comparative analysis of the insertion sites of engineered Arabidopsis (Arabidopsis thaliana) insertional mutagenesis vectors that are based on the maize (Zea mays) transposable elements and Agrobacterium T-DNA. The transposon-based agents show marked preference for high GC content, whereas the T-DNA-based agents show preference for low GC content regions. The transposon-based agents show a bias toward insertions near the translation start codons of genes, while the T-DNAs show a predilection for the putative transcriptional regulatory regions of genes. The transposon-based agents also have higher insertion site densities in exons than do the T-DNA insertions. These observations show that the transposon-based and T-DNA-based mutagenesis techniques could complement one another well, and neither alone is sufficient to achieve the goal of saturation mutagenesis in Arabidopsis. These results also suggest that transposon-based mutagenesis techniques may prove the most effective for obtaining gene disruptions and for generating gene traps, while T-DNA-based agents may be more effective for activation tagging and enhancer trapping. From the patterns of insertion site distributions, we have identified a set of nucleotide sequence motifs that are overrepresented at the transposon insertion sites. These motifs may play a role in the transposon insertion site preferences. These results could help biologists to study the mechanisms of insertions of the insertional mutagenesis agents and to design better strategies for genome-wide insertional mutagenesis.
Erscheinungsjahr
2005
Zeitschriftentitel
Plant Physiology
Band
137
Ausgabe
1
Seite(n)
168-175
ISSN
0032-0889
eISSN
1532-2548
Page URI
https://pub.uni-bielefeld.de/record/1864201

Zitieren

Pan X, Li Y, Stein L. Site preferences of insertional mutagenesis agents in Arabidopsis. Plant Physiology. 2005;137(1):168-175.
Pan, X., Li, Y., & Stein, L. (2005). Site preferences of insertional mutagenesis agents in Arabidopsis. Plant Physiology, 137(1), 168-175. https://doi.org/10.1104/pp.104.053215
Pan, X., Li, Y., and Stein, L. (2005). Site preferences of insertional mutagenesis agents in Arabidopsis. Plant Physiology 137, 168-175.
Pan, X., Li, Y., & Stein, L., 2005. Site preferences of insertional mutagenesis agents in Arabidopsis. Plant Physiology, 137(1), p 168-175.
X. Pan, Y. Li, and L. Stein, “Site preferences of insertional mutagenesis agents in Arabidopsis”, Plant Physiology, vol. 137, 2005, pp. 168-175.
Pan, X., Li, Y., Stein, L.: Site preferences of insertional mutagenesis agents in Arabidopsis. Plant Physiology. 137, 168-175 (2005).
Pan, X., Li, Yong, and Stein, L. “Site preferences of insertional mutagenesis agents in Arabidopsis”. Plant Physiology 137.1 (2005): 168-175.

27 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

A collection of enhancer trap insertional mutants for functional genomics in tomato.
Pérez-Martín F, Yuste-Lisbona FJ, Pineda B, Angarita-Díaz MP, García-Sogo B, Antón T, Sánchez S, Giménez E, Atarés A, Fernández-Lozano A, Ortíz-Atienza A, García-Alcázar M, Castañeda L, Fonseca R, Capel C, Goergen G, Sánchez J, Quispe JL, Capel J, Angosto T, Moreno V, Lozano R., Plant Biotechnol J 15(11), 2017
PMID: 28317264
The neutral metallopeptidase NMP1 of Trichoderma guizhouense is required for mycotrophy and self-defence.
Zhang J, Bayram Akcapinar G, Atanasova L, Rahimi MJ, Przylucka A, Yang D, Kubicek CP, Zhang R, Shen Q, Druzhinina IS., Environ Microbiol 18(2), 2016
PMID: 26118314
Spectrum of T-DNA integrations for insertional mutagenesis of Histoplasma capsulatum.
Kemski MM, Stevens B, Rappleye CA., Fungal Biol 117(1), 2013
PMID: 23332832
How important are transposons for plant evolution?
Lisch D., Nat Rev Genet 14(1), 2013
PMID: 23247435
Production of a high-efficiency TILLING population through polyploidization.
Tsai H, Missirian V, Ngo KJ, Tran RK, Chan SR, Sundaresan V, Comai L., Plant Physiol 161(4), 2013
PMID: 23417087
Analysis of selected singleton transposable elements (SSTEs) and their application for the development of land PATE markers in Magnaporthe oryzae
Zhang Hy, He Dy, Kasetsomboon T, Zhou H, Li P, Li Xl, Jantasuriyarat C, Zhou B., J. Gen. Plant Pathol. 79(2), 2013
PMID: IND500635846
A versatile gene trap to visualize and interrogate the function of the vertebrate proteome.
Trinh le A, Hochgreb T, Graham M, Wu D, Ruf-Zamojski F, Jayasena CS, Saxena A, Hawk R, Gonzalez-Serricchio A, Dixson A, Chow E, Gonzales C, Leung HY, Solomon I, Bronner-Fraser M, Megason SG, Fraser SE., Genes Dev 25(21), 2011
PMID: 22056673
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
Epigenetic regulation of transposable elements in plants.
Lisch D., Annu Rev Plant Biol 60(), 2009
PMID: 19007329
The Lmgpi15 gene, encoding a component of the glycosylphosphatidylinositol anchor biosynthesis pathway, is required for morphogenesis and pathogenicity in Leptosphaeria maculans.
Remy E, Meyer M, Blaise F, Simon UK, Kuhn D, Chabirand M, Riquelme M, Balesdent MH, Rouxel T., New Phytol 179(4), 2008
PMID: 18557818
Many or most genes in Arabidopsis transposed after the origin of the order Brassicales.
Freeling M, Lyons E, Pedersen B, Alam M, Ming R, Lisch D., Genome Res 18(12), 2008
PMID: 18836034
Transposition-based plant transformation.
Yan H, Rommens CM., Plant Physiol 143(2), 2007
PMID: 17142486
An efficient method for producing an indexed, insertional-mutant library in rice.
He C, Dey M, Lin Z, Duan F, Li F, Wu R., Genomics 89(4), 2007
PMID: 17229544
Discovery of chemically induced mutations in rice by TILLING.
Till BJ, Cooper J, Tai TH, Colowit P, Greene EA, Henikoff S, Comai L., BMC Plant Biol 7(), 2007
PMID: 17428339
Genetic transformation in potato: Approaches and strategies.
Chakravarty B, Wang-Pruski G, Flinn B, Gustafson V, Regan S., Am. J. Potato Res. 84(4), 2007
PMID: IND43959874
Genome-wide analysis of T-DNA integration into the chromosomes of Magnaporthe oryzae.
Choi J, Park J, Jeon J, Chi MH, Goh J, Yoo SY, Park J, Jung K, Kim H, Park SY, Rho HS, Kim S, Kim BR, Han SS, Kang S, Lee YH., Mol Microbiol 66(2), 2007
PMID: 17850257
A systematic analysis of T-DNA insertion events in Magnaporthe oryzae.
Meng Y, Patel G, Heist M, Betts MF, Tucker SL, Galadima N, Donofrio NM, Brown D, Mitchell TK, Li L, Xu JR, Orbach M, Thon M, Dean RA, Farman ML., Fungal Genet Biol 44(10), 2007
PMID: 17544743
Diverse developmental mutants revealed in an activation-tagged population of poplar
Harrison EJ, Bush M, Plett JM, McPhee DP, Vitez R, O'Malley B, Sharma V, Bosnich W, Séguin A, MacKay J., Can J Bot 85(11), 2007
PMID: IND44007647
Mapped Ds/T-DNA launch pads for functional genomics in barley.
Zhao T, Palotta M, Langridge P, Prasad M, Graner A, Schulze-Lefert P, Koprek T., Plant J 47(5), 2006
PMID: 16889649
An alpha-(1,4)-amylase is essential for alpha-(1,3)-glucan production and virulence in Histoplasma capsulatum.
Marion CL, Rappleye CA, Engle JT, Goldman WE., Mol Microbiol 62(4), 2006
PMID: 17038119
Gene trap lines define domains of gene regulation in Arabidopsis petals and stamens.
Nakayama N, Arroyo JM, Simorowski J, May B, Martienssen R, Irish VF., Plant Cell 17(9), 2005
PMID: 16055634
Novel gene functions required for melanization of the human pathogen Cryptococcus neoformans.
Walton FJ, Idnurm A, Heitman J., Mol Microbiol 57(5), 2005
PMID: 16102007

30 References

Daten bereitgestellt von Europe PubMed Central.

T-DNA insertional mutagenesis in Arabidopsis.
Koncz C, Nemeth K, Redei GP, Schell J., Plant Mol. Biol. 20(5), 1992
PMID: 1463832
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
Analysis of the chromosomal distribution of transposon-carrying T-DNAs in tomato using the inverse polymerase chain reaction.
Thomas CM, Jones DA, English JJ, Carroll BJ, Bennetzen JL, Harrison K, Burbidge A, Bishop GJ, Jones JD., Mol. Gen. Genet. 242(5), 1994
PMID: 7907167
Directed tagging of the Arabidopsis FATTY ACID ELONGATION1 (FAE1) gene with the maize transposon activator.
James DW Jr, Lim E, Keller J, Plooy I, Ralston E, Dooner HK., Plant Cell 7(3), 1995
PMID: 7734965
Patterns of gene action in plant development revealed by enhancer trap and gene trap transposable elements.
Sundaresan V, Springer P, Volpe T, Haward S, Jones JD, Dean C, Ma H, Martienssen R., Genes Dev. 9(14), 1995
PMID: 7622040
Fitting a mixture model by expectation maximization to discover motifs in biopolymers.
Bailey TL, Elkan C., Proc Int Conf Intell Syst Mol Biol 2(), 1994
PMID: 7584402
Characterization and mapping of Ds-GUS-T-DNA lines for targeted insertional mutagenesis.
Smith D, Yanai Y, Liu YG, Ishiguro S, Okada K, Shibata D, Whittier RF, Fedoroff NV., Plant J. 10(4), 1996
PMID: 8893547
T-DNA insertion mutagenesis in Arabidopsis: going back and forth.
Azpiroz-Leehan R, Feldmann KA., Trends Genet. 13(4), 1997
PMID: 9097726
Target site selection in transposition.
Craig NL., Annu. Rev. Biochem. 66(), 1997
PMID: 9242914
Predicting gene regulatory elements in silico on a genomic scale.
Brazma A, Jonassen I, Vilo J, Ukkonen E., Genome Res. 8(11), 1998
PMID: 9847082
Multiple independent defective suppressor-mutator transposon insertions in Arabidopsis: a tool for functional genomics.
Tissier AF, Marillonnet S, Klimyuk V, Patel K, Torres MA, Murphy G, Jones JD., Plant Cell 11(10), 1999
PMID: 10521516
Characterization of the transposition pattern of the Ac element in Arabidopsis thaliana using endonuclease I-SceI.
Machida C, Onouchi H, Koizumi J, Hamada S, Semiarti E, Torikai S, Machida Y., Proc. Natl. Acad. Sci. U.S.A. 94(16), 1997
PMID: 11038561
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
A collection of 11 800 single-copy Ds transposon insertion lines in Arabidopsis.
Kuromori T, Hirayama T, Kiyosue Y, Takabe H, Mizukado S, Sakurai T, Akiyama K, Kamiya A, Ito T, Shinozaki K., Plant J. 37(6), 2004
PMID: 14996221
Genetic transformation of Drosophila with transposable element vectors.
Rubin GM, Spradling AC., Science 218(4570), 1982
PMID: 6289436
Preferential transposition of the maize element Activator to linked chromosomal locations in tobacco.
Jones JD, Carland F, Lim E, Ralston E, Dooner HK., Plant Cell 2(8), 1990
PMID: 1967054
Analysis of flanking sequences from dissociation insertion lines: a database for reverse genetics in Arabidopsis.
Parinov S, Sevugan M, Ye D, Yang WC, Kumaran M, Sundaresan V., Plant Cell 11(12), 1999
PMID: 10590156
A web site for the computational analysis of yeast regulatory sequences.
van Helden J, Andre B, Collado-Vides J., Yeast 16(2), 2000
PMID: 10641039
Insertion site preferences of the P transposable element in Drosophila melanogaster.
Liao GC, Rehm EJ, Rubin GM., Proc. Natl. Acad. Sci. U.S.A. 97(7), 2000
PMID: 10716700
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
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
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
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
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
ATIDB: Arabidopsis thaliana insertion database.
Pan X, Liu H, Clarke J, Jones J, Bevan M, Stein L., Nucleic Acids Res. 31(4), 2003
PMID: 12582244
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
Transposition pattern of the maize element Ds in Arabidopsis thaliana.
Bancroft I, Dean C., Genetics 134(4), 1993
PMID: 8397137

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 15618417
PubMed | Europe PMC

Suchen in

Google Scholar