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OJBTM
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.
ABSTRACT
Singh N, Mishra H, Misra K., Epigenomic regulation
of genes involved in anti-stress mechanism in Arabidopsis thaliana using
high-throughput genomic data, Onl J Bioinform., 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.
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