Genome-wide targeted prediction of ABA responsive genes in rice based on over-represented cis-motif in co-expressed genes

Plant Mol Biol. 2009 Feb;69(3):261-71. doi: 10.1007/s11103-008-9423-4. Epub 2008 Nov 8.

Abstract

Abscisic acid (ABA), the popular plant stress hormone, plays a key role in regulation of sub-set of stress responsive genes. These genes respond to ABA through specific transcription factors which bind to cis-regulatory elements present in their promoters. We discovered the ABA Responsive Element (ABRE) core (ACGT) containing CGMCACGTGB motif as over-represented motif among the promoters of ABA responsive co-expressed genes in rice. Targeted gene prediction strategy using this motif led to the identification of 402 protein coding genes potentially regulated by ABA-dependent molecular genetic network. RT-PCR analysis of arbitrarily chosen 45 genes from the predicted 402 genes confirmed 80% accuracy of our prediction. Plant Gene Ontology (GO) analysis of ABA responsive genes showed enrichment of signal transduction and stress related genes among diverse functional categories.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Abscisic Acid / pharmacology*
  • Databases, Genetic
  • Gene Expression Regulation, Plant / drug effects
  • Gene Expression Regulation, Plant / genetics*
  • Genome, Plant / genetics*
  • Oryza / drug effects
  • Oryza / genetics*
  • Reverse Transcriptase Polymerase Chain Reaction

Substances

  • Abscisic Acid