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Online Journal of Bioinformatics ©
Volume 12(2):329-344, 2011
Epigenomic regulation of genes involved in anti-stress mechanism in Arabidopsis thaliana using high-throughput genomic data
Nitya Singh, Hrishikesh Mishra, Krishna Misra *
Division of Bioinformatics and allied sciences, Indian Institute of Information Technology, Allahabad, India
Singh N, Mishra H, Misra K., Epigenomic regulation of genes involved in anti-stress mechanism in Arabidopsis thaliana using high-throughput genomic data, Online J Bioinformatics, 12(2):329-344, 2011. A correlation among nucleosomal occupancy on promoter regions and enhanced expression of specific genes has been reported. In this study, differential nucleosomal intensity in promoter regions of highly expressed genes of Arabidopsis thaliana plant stressed with salicylic acid was determined using high-throughput genomic data generated by tilling microarray and related genome expression microarray data. Mononucleosomal intensity values obtained from tilling microarray data suggested reshuffling of nucleosomal distribution throughout the genome, indicating epigenomic regulation in response to environmental stress. Genes involved in the anti-stress mechanism were screened using heuristic, graphical and statistical calculations and were found to have considerably higher nucleosomal intensity profile in control plants as compared to test plants. Stepwise specific screening resulted in 45 genes. Functional annotations for these genes were retrieved from NCBI, TAIR and TIGR databases. The present method could recognize an anti-stress role in 27 and suggested annotation of 10 genes for which no functional annotation is available for Arabidopsis. The results confirmed the crucial role of TATA promoters in stress-responsive gene expression. The findings may assist the discovery and characterization of novel genes existing in plants to survive stress conditions.
Keywords: Antistress mechanism; High-throughput genomic data; Salicylic acid; Nucleosomal distribution; TATA promoters.