An affinity-based genome walking method to find transgene integration loci in transgenic genome

Analytical Biochemistry

Volumn 416, Issue 2, 2011, Pages 196-201

  Thirulogachandar, V ^a   Pandey, Prachi ^a   Vaishnavi, C S ^a   Reddy, Malireddy K ^a  

^a INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY ICGEB   (India)

Author keywords

Agrobacterium mediated transformation; Biotin purification; Genome walking; Particle bombardment; Positional effect

Indexed keywords

BACTERIA; COENZYMES; DNA; GENES; INTEGRATION; PLANTS (BOTANY);

AGROBACTERIUM MEDIATED TRANSFORMATIONS; AGROBACTERIUM TUMEFACIENS; ENRICHMENT TECHNIQUES; GENOME-WALKING; ILLEGITIMATE RECOMBINATION; PARTICLE BOMBARDMENT; POSITIONAL EFFECT; TRANSGENIC RICE PLANTS;

POLYMERASE CHAIN REACTION;

BIOTIN; COMPLEMENTARY DNA; DOUBLE STRANDED DNA; SINGLE STRANDED DNA; BACTERIAL DNA; PLANT DNA; PRIMER DNA; T DNA; T-DNA;

AMPLICON; ARTICLE; CHROMOSOME 1; CHROMOSOME 6; CHROMOSOME WALKING; DNA INTEGRATION; DNA TEMPLATE; DNA TRANSFER; ENRICHMENT CULTURE; GENE LOCUS; HOMOLOGOUS RECOMBINATION; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RHIZOBIUM RADIOBACTER; RICE; TRANSGENE; CHEMISTRY; GENETICS; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PLANT GENOME; TRANSGENIC PLANT;

AGROBACTERIUM; AGROBACTERIUM SP.; AGROBACTERIUM TUMEFACIENS;

BASE SEQUENCE; DNA PRIMERS; DNA, BACTERIAL; DNA, PLANT; GENETIC LOCI; GENOME, PLANT; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; PLANTS, GENETICALLY MODIFIED; POLYMERASE CHAIN REACTION; RHIZOBIUM RADIOBACTER;

EID: 80155147112     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2011.05.021     Document Type: Article

References (26)

1. D.A. Somers, I. Makarevitch, Transgene integration in plants: Poking or patching holes in promiscuous genomes?, Curr Opin. Biotechnol. 15 (2004) 126-131. (Pubitemid 38469994)
2. S.K. Svitashev, D.A. Somers, Genomic interspersions determine the size and complexity of transgene loci in transgenic plants produced by microprojectile bombardment, Genome 44 (2001) 691-697. (Pubitemid 32773646)
3. A. Rosati, P. Bogani, A. Santarlasci, M. Buiatt, Characterisation of 3′ transgene insertion site and derived mRNAs in MON810 YieldGard maize, Plant Mol. Biol. 67 (2008) 271-281.
4. J. Singh, M. Freeling, D. Lisch, A position effect on the heritability of epigenetic silencing, PLoS Genet. 4 (2008) 1-17.
5. E.C. Bryda, B.A. Bauer, A restriction enzyme-PCR-based technique to determine transgene insertion sites, Methods Mol. Biol. 597 (2010) 287-299.
6. Z. Liang, A.M. Breman, B.R. Grimes, E.D. Rosen, Identifying and genotyping transgene integration loci, Transgenic Res. 17 (2008) 979-983.
7. A. Paruzynski, A. Arens, R. Gabriel, C.C. Bartholomae, S. Scholz, W. Wang, S. Wolf, H. Glimm, M. Schmidt, C. von-Kalle, Genome-wide high-throughput integrome analyses by nrLAM-PCR and next-generation sequencing, Nat. Protoc. 5 (2010) 1379-1395.
8. T. Triglia, M.G. Peterson, D.J. Kemp, A procedure for in vitro amplification of DNA segments that lie outside the boundaries of known sequences, Nucleic Acids Res. 16 (1988) 8186.
9. Y.G. Liu, R.F. Whittier, Thermal asymmetric interlaced PCR: automatable amplification and sequencing of insert end fragments from PI and YAC clones for chromosome walking, Genomics 25 (1995) 674-681.
10. G. Tan, Y. Gao, M. Shi, X. Zhang, S. He, Z. Chen, C. An, SiteFinding-PCR: a simple and efficient PCR method for chromosome walking, Nucleic Acids Res. 33 (2005) e122.
11. C. Arnold, I.J. Hodgson, Vectorette PCR: a novel approach to genomic walking, Genome Res. 1 (1991) 39-42.
12. H. Guo, J. Xiong, A specific and versatile genome walking technique, Gene 381 (2006) 18-23. (Pubitemid 44436764)
13. M.D. Curtis, U. Grossniklaus, A gateway cloning vector set for high-throughput functional analysis of genes in planta, Plant Physiol. 133 (2003) 462-469. (Pubitemid 37325657)
14. J.J. Doyle, J.L. Doyle, Isolation of plant DNA from fresh tissue, Focus 12 (1990) 13-15.
15. R.N. Mishra, S.L. Singla-Pareek, S. Nair, S.K. Sopory, M.K. Reddy, Directional genome walking using PCR, BioTechniques 33 (2002) 830-834. (Pubitemid 35168068)
16. P.S. Reddy, S. Mahanty, T. Kaul, S. Nair, S.K. Sopory, M.K. Reddy, A highthroughput genome-walking method and its use for cloning unknown flanking sequences, Anal. Biochem. 381 (2008) 248-253.
17. J. Bae, J. Sohn, Template-blocking PCR: an advanced PCR technique for genome walking, Anal. Biochem. 398 (2009) 112-116.
18. Y. Yuanxin, A. Chengcai, L. Li, G. Jiayu, T. Guihong, C. Zhangliang, T-linker-specific ligation PCR (T-linker PCR): an advanced PCR technique for chromosome walking or for isolation of tagged DNA ends, Nucleic Acids Res. 31 (2003) e68.
19. D.H. Jones, S.C. Winistorfer, Genome walking with 2-4-kb steps using panhandle PCR, Genome Res. 2 (1993) 197-203. (Pubitemid 23159560)
20. S. Wang, J. He, Z. Cui, S. Li, Self-formed adaptor PCR: a simple and efficient method for chromosome walking, Appl. Environ. Microbiol. 73 (2007) 5048-5051. (Pubitemid 47237257)
21. J. Ji, J. Braam, Restriction site extension PCR: a novel method for highthroughput characterization of tagged DNA fragments and genome walking, PLoS ONE 5 (2010) e10577.
22. P. Bundock, P.J.J. Hooykaas, Integration of Agrobacterium tumefaciens T-DNA in the Saccharomyces cerevisiae genome by illegitimate recombination, Proc. Natl Acad. Sci. USA 93 (1996) 15272-15275. (Pubitemid 27009589)
23. G. Gheysen, R. Villarroel, M. Van Montagu, Illegitimate recombination in plants: a model for T-DNA integration, Genes Dev. 5 (1991) 287-297. (Pubitemid 21905953)
24. F. Durrenberger, A. Crameri, B. Hohn, Z. Koukolfkova-Nicola, Covalently bound VirD2 protein of Agrobacterium tumefaciens protects the T-DNA from exonucleolytic degradation, Proc. Natl Acad. Sci. USA 86 (1989) 9154-9158. (Pubitemid 20010383)
25. R. Offringa, M.J. de Groot, H.J. Haagsman, M.P. Does, P.J.M. van den Elzen, P.J.J. Hooykaas, Extrachromosomal homologous recombination and gene targeting in plant cells after Agrobacterium mediated transformation, EMBO J. 9 (1990) 3077-3084.
26. J. Paszkowski, M. Baur, A. Bogucki, I. Potrykus, Gene targeting in plants, EMBO J. 7 (1988) 4021-4026.