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Detection of 91 potential in plant conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes

Eric Bonnet (UGent) , Jan Wuyts (UGent) , Pierre Rouzé (UGent) and Yves Van de Peer (UGent)
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Abstract
MicroRNAs (miRNAs) are an extensive class of tiny RNA molecules that regulate the expression of target genes by means of complementary base pair interactions. Although the first miRNAs were discovered in Caenorhabditis elegans, >300 miRNAs were recently documented in animals and plants, both by cloning methods and computational predictions. We present a genome-wide computational approach to detect miRNA genes in the Arabidopsis thaliana genome. Our method is based on the conservation of short sequences between the genomes of Arabidopsis and rice (Oryza sativa) and on properties of the secondary structure of the miRNA precursor. The method was fine-tuned to take into account plant-specific properties, such as the variable length of the miRNA precursor sequences. In total, 91 potential miRNA genes were identified, of which 58 had at least one nearly perfect match with an Arabidopsis mRNA, constituting the potential targets of those miRNAs. In addition to already known transcription factors involved in plant development, the targets also comprised genes involved in several other cellular processes, such as sulfur assimilation and ubiquitin-dependent protein degradation. These findings considerably broaden the scope of miRNA functions in plants.
Keywords
SYSTEM, DATABASE, MIRNA, SEQUENCE, EXPRESSION, thale cress, comparative genomics, rice, noncoding RNA, C-ELEGANS, CAENORHABDITIS-ELEGANS, RNA INTERFERENCE, PROTEIN, ATP SULFURYLASE

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Citation

Please use this url to cite or link to this publication:

Chicago
Bonnet, Eric, Jan Wuyts, Pierre Rouzé, and Yves Van de Peer. 2004. “Detection of 91 Potential in Plant Conserved Plant microRNAs in Arabidopsis Thaliana and Oryza Sativa Identifies Important Target Genes.” Proceedings of the National Academy of Sciences of the United States of America 101 (31): 11511–11516.
APA
Bonnet, E., Wuyts, J., Rouzé, P., & Van de Peer, Y. (2004). Detection of 91 potential in plant conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 101(31), 11511–11516.
Vancouver
1.
Bonnet E, Wuyts J, Rouzé P, Van de Peer Y. Detection of 91 potential in plant conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2004;101(31):11511–6.
MLA
Bonnet, Eric, Jan Wuyts, Pierre Rouzé, et al. “Detection of 91 Potential in Plant Conserved Plant microRNAs in Arabidopsis Thaliana and Oryza Sativa Identifies Important Target Genes.” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101.31 (2004): 11511–11516. Print.
@article{298761,
  abstract     = {MicroRNAs (miRNAs) are an extensive class of tiny RNA molecules that regulate the expression of target genes by means of complementary base pair interactions. Although the first miRNAs were discovered in Caenorhabditis elegans, >300 miRNAs were recently documented in animals and plants, both by cloning methods and computational predictions. We present a genome-wide computational approach to detect miRNA genes in the Arabidopsis thaliana genome. Our method is based on the conservation of short sequences between the genomes of Arabidopsis and rice (Oryza sativa) and on properties of the secondary structure of the miRNA precursor. The method was fine-tuned to take into account plant-specific properties, such as the variable length of the miRNA precursor sequences. In total, 91 potential miRNA genes were identified, of which 58 had at least one nearly perfect match with an Arabidopsis mRNA, constituting the potential targets of those miRNAs. In addition to already known transcription factors involved in plant development, the targets also comprised genes involved in several other cellular processes, such as sulfur assimilation and ubiquitin-dependent protein degradation. These findings considerably broaden the scope of miRNA functions in plants.},
  author       = {Bonnet, Eric and Wuyts, Jan and Rouzé, Pierre and Van de Peer, Yves},
  issn         = {0027-8424},
  journal      = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA},
  keywords     = {SYSTEM,DATABASE,MIRNA,SEQUENCE,EXPRESSION,thale cress,comparative genomics,rice,noncoding RNA,C-ELEGANS,CAENORHABDITIS-ELEGANS,RNA INTERFERENCE,PROTEIN,ATP SULFURYLASE},
  language     = {eng},
  number       = {31},
  pages        = {11511--11516},
  title        = {Detection of 91 potential in plant conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes},
  url          = {http://dx.doi.org/10.1073/pnas.0404025101},
  volume       = {101},
  year         = {2004},
}

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