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Versatile gene-specific sequence tags for Arabidopsis functional genomics: trancript profiling and reverse genetics applications

Pierre Hilson UGent, Joke Allemeersch, Thomas Altmann, Sébastien Aubourg UGent, Alexandra Avon, Jim Beynon, Rishikesh P Bhalerao, Frédérique Bitton, Michel Caboche, Bernard Cannoot UGent, et al. (2004) GENOME RESEARCH. 14(10B). p.2176-2189
abstract
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
RESTORER GENE, PLANT-GROWTH, THALIANA, DESIGN, WIDE EXPRESSION, ESCHERICHIA-COLI, MICROARRAY ANALYSIS, VACUOLAR H+-ATPASE, REPEAT-CONTAINING GENE, SECONDARY CELL-WALL
journal title
GENOME RESEARCH
Genome Res.
volume
14
issue
10B
pages
2176 - 2189
Web of Science type
Article
Web of Science id
000224514000024
JCR category
BIOTECHNOLOGY & APPLIED MICROBIOLOGY
JCR impact factor
10.382 (2004)
JCR rank
3/133 (2004)
JCR quartile
1 (2004)
ISSN
1088-9051
DOI
10.1101/gr.2544504
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
298896
handle
http://hdl.handle.net/1854/LU-298896
date created
2005-02-18 12:50:00
date last changed
2016-12-19 15:44:53
@article{298896,
  abstract     = {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.},
  author       = {Hilson, Pierre and Allemeersch, Joke and Altmann, Thomas and Aubourg, S{\'e}bastien and Avon, Alexandra and Beynon, Jim and Bhalerao, Rishikesh P and Bitton, Fr{\'e}d{\'e}rique and Caboche, Michel and Cannoot, Bernard and Chardakov, Vasil and Cognet-Holliger, C{\'e}cile and Colot, Vincent and Crowe, Mark and Darimont, Caroline and Durinck, Steffen and Eickhoff, Holger and de Longevialle, And{\'e}ol Falcon and Farmer, Edward E and Grant, Murray and Kuiper, Martin and Lehrach, Hans and L{\'e}on, C{\'e}cile and Leyva, Antonio and Lundeberg, Joakim and Lurin, Claire and Moreau, Yves and Nietfeld, Wilfried and Paz-Ares, Javier and Reymond, Philippe and Rouz{\'e}, Pierre and Sandberg, Goran and Segura, Maria Dolores and Serizet, Carine and Tabrett, Alexandra and Taconnat, Ludivine and Thareau, Vincent and Van Hummelen, Paul and Vercruysse, Steven and Vuylsteke, Marnik and Weingartner, Magdalena and Weisbeek, Peter J and Wirta, Valtter and Wittink, Floyd RA and Zabeau, Marc and Small, Ian},
  issn         = {1088-9051},
  journal      = {GENOME RESEARCH},
  keyword      = {RESTORER GENE,PLANT-GROWTH,THALIANA,DESIGN,WIDE EXPRESSION,ESCHERICHIA-COLI,MICROARRAY ANALYSIS,VACUOLAR H+-ATPASE,REPEAT-CONTAINING GENE,SECONDARY CELL-WALL},
  language     = {eng},
  number       = {10B},
  pages        = {2176--2189},
  title        = {Versatile gene-specific sequence tags for Arabidopsis functional genomics: trancript profiling and reverse genetics applications},
  url          = {http://dx.doi.org/10.1101/gr.2544504},
  volume       = {14},
  year         = {2004},
}

Chicago
Hilson, Pierre, Joke Allemeersch, Thomas Altmann, Sébastien Aubourg, Alexandra Avon, Jim Beynon, Rishikesh P Bhalerao, et al. 2004. “Versatile Gene-specific Sequence Tags for Arabidopsis Functional Genomics: Trancript Profiling and Reverse Genetics Applications.” Genome Research 14 (10B): 2176–2189.
APA
Hilson, P., Allemeersch, J., Altmann, T., Aubourg, S., Avon, A., Beynon, J., Bhalerao, R. P., et al. (2004). Versatile gene-specific sequence tags for Arabidopsis functional genomics: trancript profiling and reverse genetics applications. GENOME RESEARCH, 14(10B), 2176–2189.
Vancouver
1.
Hilson P, Allemeersch J, Altmann T, Aubourg S, Avon A, Beynon J, et al. Versatile gene-specific sequence tags for Arabidopsis functional genomics: trancript profiling and reverse genetics applications. GENOME RESEARCH. 2004;14(10B):2176–89.
MLA
Hilson, Pierre, Joke Allemeersch, Thomas Altmann, et al. “Versatile Gene-specific Sequence Tags for Arabidopsis Functional Genomics: Trancript Profiling and Reverse Genetics Applications.” GENOME RESEARCH 14.10B (2004): 2176–2189. Print.