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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,
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.