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Versatile gene-specific sequence tags for Arabidopsis functional genomics: Trancript profiling and reverse genetics applications
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2004 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 14, no 10B, 2176-2189 p.Article in journal (Refereed) Published
Abstract [en]

Microarray transcript profiling and RNA interference are two new technologies crucial for large-scale gene function studies in multicellular eukaryotes. Both rely on sequence-specific hybridization between complementary nucleic acid strands, inciting us to create a collection of gene-specific sequence tags (GSTs) representing at least 21,500 Arabidopsis genes and which are compatible with both approaches. The GSTs were carefully selected to ensure that each of them shared no significant similarity with any other region in the Arabidopsis genome. They were synthesized by PCR amplification from genomic DNA. Spotted microarrays fabricated from the GSTs show good dynamic range, specificity, and sensitivity in transcript profiling experiments. The GSTs have also been transferred to bacterial plasmid vectors via recombinational cloning protocols. These cloned GSTs constitute the ideal starting point for a variety of functional approaches, including reverse genetics. We have subcloned GSTs on a large scale into vectors designed for gene silencing in plant cells. We show that in planta expression of GST hairpin RNA results in the expected phenotypes in silenced Arabidopsis lines. These versatile GST resources provide novel and powerful tools for functional genomics.

Place, publisher, year, edition, pages
2004. Vol. 14, no 10B, 2176-2189 p.
Keyword [en]
repeat-containing gene, secondary cell-wall, vacuolar h+-atpase, microarray analysis, escherichia-coli, wide expression, restorer gene, plant-growth, design, thaliana
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:kth:diva-23815DOI: 10.1101/gr.2544504ISI: 000224514000024PubMedID: 15489341Scopus ID: 2-s2.0-4043153341OAI: oai:DiVA.org:kth-23815DiVA: diva2:342514
Note

QC 20100525 QC 20110922

Available from: 2010-08-10 Created: 2010-08-10 Last updated: 2017-12-12Bibliographically approved

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Wirta, Valtteri

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