Functional genomics in Arabidopsis: Large-scale insertional mutagenesis complements the genome sequencing project

Current Opinion in Biotechnology

Volumn 11, Issue 2, 2000, Pages 157-161

  Parinov, Serguei ^a   Sundaresan, Venkatesan ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARABIDOPSIS; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE INSERTION; GENE SEQUENCE; GENETIC SCREENING; KNOCKOUT GENE; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; REVIEW; TRANSPOSON;

ARABIDOPSIS; ARABIDOPSIS THALIANA; EMBRYOPHYTA; MAGNOLIOPHYTA;

EID: 0034030591     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0958-1669(00)00075-6     Document Type: Article

References (26)

1. Lin X., Kaul S., Rounsley S., Shea T.P., Benito M.I., Town C.D., Fujii C.Y., Mason T., Bowman C.L., Barnstead M. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature. 402:1999;761-768.
2. Sequence, and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature. 402:1999;769-777.
3. Bevan M., Bancroft I., Mewes H-M., Martienssen R., McCombie R. Clearing a path through the jungle: progress in Arabidopsis genomics. BioEssays. 21:1999;110-120.
4. Beetham P.R., Kipp P.B., Sawycky X.L., Arntzen C.J., May G.D. A tool for functional plant genomics: chimeric RNA/DNA oligonucleotides cause in vivo gene-specific mutations. Proc Natl Acad Sci USA. 96:1999;8774-8778.
5. Jorgensen R.A., Que Q., Stam M. Do unintended antisense transcripts contribute to sense cosuppression in plants? Trends Genet. 15:1999;11-12.
6. Liu Y.G., Whittier R.F. Thermal asymmetric interlaced PCR: automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking. Genomics. 25:1995;674-681.
7. Krisan P.J., Young J.C., Sussman M.R. T-DNA as an insertional mutagen in Arabidopsis. Plant Cell. 11:1999;2283-2290. A comprehensive review of the strategies for using T-DNA insertional mutagenesis in reverse genetics and a useful introduction to the T-DNA knockout facility recently established by the authors at the University of Wisconsin.
8. Bouchez, D., Granier, F., Bouché, N., Caboche, M., Bechtold, N., Pelletier, G.: T-DNA insertional mutagenesis for reverse genetics in Arabidopsis. 10th International Conference on Arabidopsis Research: 1999 4-8 July: The University of Melbourne, Australia. Report # 4-1. Abstracts can be downloaded from http://www.arabidopsis.org/abstract_australia.pdf.
9. Patton, D., Levin, J., Ashby, C., Aux, G., Barton, J., Budziszewski, G., Cates, E., Cushman, M.A., Franzmann, L., Gregoski, A.: Use of insertional mutagenesis for the identification of essential genes in Arabidopsis. 10th International Conference on Arabidopsis Research: 1999 4-8 July: The University of Melbourne, Australia. Abstract # 4-12. Abstracts can be downloaded from http://www.arabidopsis.org/abstract_australia.pdf.
10. De Buck S., Jacobs A., Van Montagu M., Depicker A. The DNA sequences of T-DNA junctions suggest that complex T-DNA loci are formed by a recombination process resembling T-DNA integration. Plant J. 20:1999;295-304.
11. Kononov M.E., Bassuner B., Gelvin S.B. Integration of T-DNA binary vector 'backbone' sequences into the tobacco genome: evidence for multiple complex patterns of integration. Plant J. 11:1997;945-957.
12. Nacry P., Camilleri C., Courtial B., Caboche M., Bouchez D. Major chromosomal rearrangements induced by T-DNA transformation in Arabidopsis. Genetics. 149:1998;641-650.
13. Laufs P., Autran D., Traas J. A chromosomal paracentric inversion associated with T-DNA integration in Arabidopsis. Plant J. 18:1999;131-139.
14. Clogh S.J., Bent A.F. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16:1998;735-743.
15. Yang W.C., Ye D., Xu J., Sundaresan V. The SPOROCYTELESS gene of Arabidopsis is required for initiation of sporogenesis and encodes a novel nuclear protein. Genes Dev. 15:1999;2108-2117.
16. Speulman E., Metz P.L., van Arkel G., te Lintel Hekkert B., Stiekema W.J., Pereira A. A two-component enhancer-inhibitor transposon mutagenesis system for functional analysis of the arabidopsis genome. Plant Cell. 11:1999;1853-1866. A different application of the Enhancer-Inhibitor En-I (also known as Suppressor-mutator Spm-dSpm) transposon system for functional genomics is described. Seven original 'founder' (starter) lines carrying 7-10 mobile I (dSpm) elements and an En transposase gene were used to generate a series of mutant lines by single-seed descent such that multiple (20-25) I insertions occurred per plant. 'Multiple transposant population' of 2592 lines were produced and combined in pools. DNA from the pools was extracted and can be used for PCR screening using a three-dimensional strategy.
17. Meissner R.C., Jin H., Cominelli E., Denekamp M., Fuertes A., Greco R., Kranz H.D., Penfield S., Petroni K., Urzainqui A. Function search in a large transcription factor gene family in arabidopsis. Assessing the potential of reverse genetics to identify insertional mutations in r2r3 myb genes. Plant Cell. 11:1999;1827-1840. This work demonstrates the current feasibility of available insertion lines for reverse genetics screening. Several collections of T-DNA and dSpm (mobile and immobile) insertion lines were subjected to PCR and hybridization-based screening for disrupted genes of encoding MYB transcription factors. Insertions into 36 distinct MYB genes were isolated by screening a total of 73 genes.
18. Machida C., Onouchi H., Koizumi J., Hamada S., Semiarti E., Torikai S., Machida Y. Characterization of the transposition pattern of the Ac element in Arabidopsis thaliana using endonuclease I-SceI. Proc Natl Acad Sci USA. 94:1997;8675-8680.
19. Ito T., Seki M., Hayashida N., Shibata D., Shinozaki K. Regional insertional mutagenesis of genes on Arabidopsis thaliana chromosome V using the Ac/Ds transposon in combination with a cDNA scanning method. Plant J. 17:1999;433-444.
20. Seki M., Ito T., Shibata D., Shinozaki K. Regional insertional mutagenesis of specific genes on the CIC5F11/CIC2B9 locus of Arabidopsis thaliana chromosome 5 using the Ac/Ds transposon in combination with the cDNA scanning method. Plant Cell Physiol. 40:1999;624-639.
21. Parinov S., Sevugan M., Ye D., Yang W.C., Kumaran M., Sundaresan V. Analysis of flanking sequences from dissociation insertion lines: a database for reverse genetics in Arabidopsis. Plant Cell. 11:1999;2263-2270. The authors present results of molecular analysis using a collection of lines containing independent Dissociation (Ds) element insertions distributed throughout the Arabidopsis genome. Distribution of Ds transpositions shows significant (~10%) preference to the regions adjacent to nucleolus organizer regions on chromosomes 2 and 4, but were otherwise random. The sequences of over 500 lines with characterized insertion position by reference to GenBank sequences are presented as a database, with the corresponding lines available from Nottingham Arabidopsis Stock Center http://nasc.nott.ac.uk/ima.html .
22. Tissier A.F., Marillonnet S., Klimyuk V., Patel K., Torres M.A., Murphy G., Jones J.D. Multiple independent defective suppressor-mutator transposon insertions in Arabidopsis. A tool for functional genomics. Plant Cell. 11:1999;1841-1852. A new system for insertional mutagenesis based on the maize Enhancer/Suppressor-mutator (En/Spm) element was introduced into Arabidopsis. A total of 48,000 lines in pools of 50 were produced of which ~80% result from independent insertion events. DNA extracted from the pools can be used for reverse genetics screening by PCR using primers from the transposon and the targeted gene. Authors sequenced PCR-amplified fragments adjacent to inserts and database of 1200 sequences flanking the dSpm insertions has been established.
23. Sundaresan V., Springer P., Volpe T., Haward S., Jones J.D., Dean C., Ma H., Martienssen R. Patterns of gene action in plant development revealed by enhancer trap and gene trap transposable elements. Genes Dev. 9:1995;1797-1810.
24. Scholl, R., Rivero, L., Crist, D., Ware, D., Davis, K.: Progress of ABRC in obtaining new T-DNA stocks and preparing DNA from T-DNA populations for PCR screening. 10th International Conference on Arabidopsis Research: 1999 4-8 July; The University of Melbourne, Australia. Abstract # 4-15. Abstracts can be downloaded from http://www.arabidopsis.org/abstract_australia.pdf.
25. Wilson, F., Dennis, P., Hall, C., Kincaid, J., Kitchingman, S., Searle, K., Walsh, S. May, S.: N.A.S.C. (Nottingham Arabidopsis Stock Centre). 10th International Conference on Arabidopsis Research: 1999 4-8 July; The University of Melbourne, Australia. Abstract # 4-18. Abstracts can be downloaded from http://www.arabidopsis.org/abstract_australia.pdf.
26. Bellen H.J. Ten years of enhancer detection. Lessons from the fly. Plant Cell. 11:1999;2271-2282.