Analysis of flanking sequences from Dissociation insertion lines: A database for reverse genetics in Arabidopsis

Plant Cell

Volumn 11, Issue 12, 1999, Pages 2263-2270

  Parinov, Serguei ^a   Sevugan, Mayalagu ^a   Ye, De ^a   Yang, Wei Cai ^a   Kumaran, Mande ^a   Sundaresan, Venkatesan ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOME ANALYSIS; DNA FLANKING REGION; GENE FUNCTION; INSERTIONAL MUTAGENESIS; PLANT GENETICS; PLANT GENOME; SEQUENCE ANALYSIS;

ARABIDOPSIS;

EID: 0033391313     PISSN: 10404651     EISSN: None     Source Type: Journal    
DOI: 10.1105/tpc.11.12.2263     Document Type: Article

References (29)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
2. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
3. Benson, D.A., Boguski, M.S., Lipman, D.J., Ostell, J., and Ouellette, B.F. (1998). GenBank. Nucleic Acids Res. 26, 1-7.
4. Bevan, M., et al. (1998). Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana. Nature 391, 485-488.
5. Bevan, M., Bancroft, I., Mewes, H.W., Martienssen, R., and McCombie, R. (1999). Clearing a path through the jungle: Progress in Arabidopsis genomics. Bioessays 21, 110-120.
6. Copenhaver, G.P., and Pikaard, C.S. (1996a). RFLP and physical mapping with an rDNA-specific endonuclease reveals that nucleolus organizer regions of Arabidopsis thaliana adjoin telomeres on chromosomes 2 and 4. Plant J. 9, 259-272.
7. Copenhaver, G.P., and Pikaard, C.S. (1996b). Two-dimensional RFLP analyses reveal megabase-sized clusters of rRNA gene variants in Arabidopsis thaliana, suggesting local spreading of variants as the mode for gene homogenization during concerted evolution. Plant J. 9, 273-282.
8. Das, L., and Martienssen, R. (1995). Site-selected transposon mutagenesis at the hcf106 locus in maize. Plant Cell 7, 287-294.
9. Devic, M., Albert, S., Delseny, M., and Roscoe, T.J. (1997). Efficient PCR walking on plant genomic DNA. Plant Physiol. Biochem. 35, 331-339.
10. Dooner, H.K., Belachew, A., Burgess, D., Harding, S., Ralston, M., and Ralston, E. (1994). Distribution of unlinked receptor sites for transposed Ac elements from the bz-m2(Ac) allele in maize. Genetics 136, 261-279.
11. Flanders, D., Weng, S., Petel, F.X., and Cherry, J.M. (1998). AtDB, the Arabidopsis thaliana database, and graphical-web-display of progress by the Arabidopsis Genome Initiative. Nucleic Acids Res. 26, 80-84.
12. Grossniklaus, U., Vielle-Calzada, J.P., Hoeppner, M.A., and Gagliano, W.B. (1998). Maternal control of embryogenesis by MEDEA, a polycomb group gene in Arabidopsis. Science 280, 446-450.
13. Hui, E.K., Wang, P.C., and Lo, S.J. (1998). Strategies for cloning unknown cellular flanking DNA sequences from foreign integrants. Cell. Mol. Life Sci. 54, 1403-1411.
14. Iba, K., Gibson, S., Nishiuchi, T., Fuse, T., Nishimura, M., Arondel, V., Hugly, S., and Somerville, C. (1993). A gene encoding a chloroplast omega-3 fatty acid desaturase complements alterations in fatty acid desaturation and chloroplast copy number of the fad7 mutant of Arabidopsis thaliana. J. Biol. Chem. 268, 24099-24105.
15. Kotani, H., Sato, S., Fukami, M., Hosouchi, T., Nakazaki, N., Okumura, S., Wada, T., Liu, Y.G., Shibata, D., and Tabata, S. (1997). A fine physical map of Arabidopsis thaliana chromosome 5: Construction of a sequence-ready contig map. DNA Res. 4, 371-378.
16. Liebman, S.W., and Newnam, G. (1993). A ubiquitin-conjugating enzyme, RAD6, affects the distribution of Ty1 retrotransposon integration positions. Genetics 133, 499-508.
17. Liu, Y.G., and Whittier, R.F. (1995). Thermal asymmetric interlaced PCR: Automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking. Genomics 25, 674-681.
18. Liu, Y.G., Mitsukawa, N., Oosumi, T., and Whittier, R.F. (1995). Efficient isolation and mapping of Arabidopsis thaliana T-DNA insert junctions by thermal asymmetric interlaced PCR. Plant J. 8, 457-463.
19. Machida, C., Onouchi, H., Koizumi, J., Hamada, S., Semiarti, E., Torikai, S., and Machida, Y. (1997). Characterization of the transposition pattern of the Ac element in Arabidopsis thaliana using endonuclease I-Scel. Proc. Natl. Acad. Sci. USA 94, 8675-8680.
20. Sato, S., Kaneko, T., Kotani, H., Nakamura, Y., Asamizu, E., Miyajima, N., and Tabata, S. (1998). Structural analysis of Arabidopsis thaliana chromosome 5. IV. Sequence features of the regions of 1,456,315 bp covered by nineteen physically assigned P1 and TAC clones. DNA Res. 28, 41-54.
21. Smith, D., Yanai, Y., Liu, Y.-G., Ishiguro, S., Okada, K., Shibata, D., Whittier, R.F., and Fedoroff, N.V. (1996). Characterization and mapping of Ds-GUS-T-DNA lines for targeted insertional mutagenesis. Plant J. 10, 721-732.
22. Spradling, A.C., Stern, D.M., Kiss, I., Roote, J., Laverty, T., and Rubin, G.M. (1995). Gene disruptions using P transposable elements: An integral component of the Drosophila genome project. Proc. Natl. Acad. Sci. USA 92, 10824-10830.
23. Sundaresan, V. (1996). Horizontal spread of transposon mutagenesis: New uses for old elements. Trends Plant Sci. 1, 184-190.
24. Sundaresan, V., Springer, P., Volpe, T., Haward, S., Jones, J.D., Dean, C., Ma, H., and Martienssen, R. (1995). Patterns of gene action in plant development revealed by enhancer trap and gene trap transposable elements. Genes Dev. 9, 1797-1810.
25. Tissier, A.F., Marillonnet, S., Klimyuk, V., Patel, K., Torres, M.A., Murphy, G., and Jones, J.D.G. (1999). Multiple independent defective Suppressor-mutator transposon insertions in Arabidopsis. A tool for functional genomics. Plant Cell 11, 1841-1852.
26. Townley, D.J., Avery, B.J., Rosen, B., and Skarnes, W.C. (1997). Rapid sequence analysis of gene trap integrations to generate a resource of insertional mutations in mice. Genome Res. 7, 293-298.
27. Tsugeki, R., Kochieva, E.Z., and Fedoroff, N.V. (1996). A transposon insertion in the Arabidopsis SSR16 gene causes an embryo-defective lethal mutation. Plant J. 10, 479-489.
28. Zambrowicz, B.P., Friedrich, G.A., Buxton, E.G., Lilleberg, S.L., Person, C., and Sands, A.T. (1998). Disruption and sequence identification of 2,000 genes in mouse embryonic stem cells. Nature 392, 608-611.
29. Zwaal, R.R., Broeks, A., van Meurs, J., Groenen, J.T., and Plasterk, R.H. (1993). Target-selected gene inactivation in Caenorhabditis elegans by using a frozen transposon insertion mutant bank. Proc. Natl. Acad. Sci. USA 15, 7431-7435.