Prediction of new abiotic stress genes in Arabidopsis thaliana and Oryza sativa according to enumeration-based statistical analysis

Mátyás Cserháti, Zoltán Turóczy, Zoltán Zombori, Miklós Cserzo, D. Dudits, Sándor Pongor, J. Györgyey

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Plants undergo an extensive change in gene regulation during abiotic stress. It is of great agricultural importance to know which genes are affected during stress response. The genome sequence of a number of plant species has been determined, among them Arabidopsis and Oryza sativa, whose genome has been annotated most completely as of yet, and are well-known organisms widely used as experimental systems. This paper applies a statistical algorithm for predicting new stress-induced motifs and genes by analyzing promoter sets co-regulated by abiotic stress in the previously mentioned two species. After identifying characteristic putative regulatory motif sequence pairs (dyads) in the promoters of 125 stress-regulated Arabidopsis genes and 87 O. sativa genes, these dyads were used to screen the entire Arabidopsis and O. sativa promoteromes to find related stress-induced genes whose promoters contained a large number of these dyads found by our algorithm. We were able to predict a number of putative dyads, characteristic of a large number of stress-regulated genes, some of them newly discovered by our algorithm and serve as putative transcription factor binding sites. Our new motif prediction algorithm comes complete with a stand-alone program. This algorithm may be used in motif discovery in the future in other species. The more than 1,200 Arabidopsis and 1,700 Orzya sativa genes found by our algorithm are good candidates for further experimental studies in abiotic stress.

Original languageEnglish
Pages (from-to)375-391
Number of pages17
JournalMolecular Genetics and Genomics
Volume285
Issue number5
DOIs
Publication statusPublished - May 2011

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Arabidopsis
Genes
Genome
Oryza
Transcription Factors
Binding Sites

Keywords

  • Abiotic stress
  • Arabidopsis thaliana
  • Dyad
  • Oryza sativa
  • Promoter
  • Transcription factor binding site

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology

Cite this

Prediction of new abiotic stress genes in Arabidopsis thaliana and Oryza sativa according to enumeration-based statistical analysis. / Cserháti, Mátyás; Turóczy, Zoltán; Zombori, Zoltán; Cserzo, Miklós; Dudits, D.; Pongor, Sándor; Györgyey, J.

In: Molecular Genetics and Genomics, Vol. 285, No. 5, 05.2011, p. 375-391.

Research output: Contribution to journalArticle

Cserháti, Mátyás ; Turóczy, Zoltán ; Zombori, Zoltán ; Cserzo, Miklós ; Dudits, D. ; Pongor, Sándor ; Györgyey, J. / Prediction of new abiotic stress genes in Arabidopsis thaliana and Oryza sativa according to enumeration-based statistical analysis. In: Molecular Genetics and Genomics. 2011 ; Vol. 285, No. 5. pp. 375-391.
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