Genome-wide targeted prediction of ABA responsive genes in rice based on over-represented cis-motif in co-expressed genes.
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.
Lenka
Sangram K
SK
National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India.
Lohia
Bikash
B
Kumar
Abhay
A
Chinnusamy
Viswanathan
V
Bansal
Kailash C
KC
D000040:Abscisic Acid / Q000494:pharmacology*; D030541:Databases, Genetic; D018506:Gene Expression Regulation, Plant / Q000187:drug effects / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D012275:Oryza / Q000187:drug effects / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction
D000040:Abscisic Acid