MOLECULAR BEACON PROBE BASED PROMOTER MOTIFS VALIDATION IN ANOXIA RESPONSIVE DIFFERENTIALLY EXPRESSED GENES AND THEIR IN SILICO INTERACTION STUDIES WITH AP2/EREBP TF IN RICE (ORYZA SATIVA L.)
Keywords:
DEGs, Anoxia, DEG, MBP, HADDOCK, SiteMapAbstract
Objective: Progressive evolution in molecular biology revealed the differential expression of genes and their regulatory mechanism in rice under anoxia. In addition to that the consensus promoter motifs (GCC and TCC box) were identified in differentially expressed genes (DEGs) from microarray analysis through in silico study. These promoter motifs need to be validated and their interaction study with the transcription factors (TFs) are essential.
Methods: To unravel the regulatory mechanism in rice during anoxia, we identified and validated the promoter motifs through Molecular Beacon Probes (MBP) based Real Time PCR. In silico protein-DNA interaction was studied between highly up-regulated APETALA2/Ethylene-responsive element binding proteins (AP2/ERBP) TF under anoxia and validated promoter motifs through the HADDOCK and SiteMap module.
Results: It was identified that consensus promoter motif GCC and TCC box were present in highly up-regulated methyl-transferase domain containing protein gene (MT) and down-regulated RhoGAP domain containing protein gene (RG), respectively.
Conclusion: These promoter motifs were validated through MBP and further their interaction with AP2/ERBP shows the significant binding affinity towards GCC and TCC box present on MT and RG, respectively.
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