MAIN


©1996-2011 All Rights Reserved. Online Journal of Bioinformatics . You may not store these pages in any form except for your own personal use. All other usage or distribute on is illegal under international copyright treaties. Permission to use any of these pages in any other way besides the  before mentioned must be gained in writing from the publisher. This article is exclusively copyrighted in its entirety to OJB publications. This article may be copied once but may not be, reproduced or  re-transmitted without the express permission of the editors. This journal satisfies the refereeing requirements (DEST) for the Higher Education Research Data Collection (Australia). Linking:To link to this page or any pages linking to this page you must link directly to this page only here rather than put up your own page.


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.


MAIN

 

FULL-TEXT(SUBSCRIPTION)