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Abstract
BackgroundThe nucleosome positioning regulates the gene expression and many other DNA-related processes in eukaryotes. Genome-wide mapping of nucleosome positions and correlation of genome-wide nucleosomal remodeling with the changes in the gene expression can help us understanding gene regulation on genome level.ResultsIn the present study, we correlate the gene expression and the genomic nucleosomal remodeling in response to salicylic acid (SA) treatment in A. thaliana. We have mapped genome-wide nucleosomes by performing tiling microarray using 146 bp mononucleosomal template DNA. The average nucleosomal coverage is approximately 346 bp per nucleosome both under the control and the SA-treated conditions. The nucleosomal coverage is more in the coding region than in the 5′ regulatory regions. We observe approximately 50% nucleosomal remodeling on SA treatment where significant nucleosomal depletion and nucleosomal enrichment around the transcription start site (TSS) occur in SA induced genes and SA repressed genes respectively in response to SA treatment. Especially in the case of the SA-induced group, the nucleosomal remodeling over the minimal promoter in response to SA is especially significant in the Non-expresser of PR1 (NPR1)-dependent genes. A detailed investigation of npr1-1 mutant confirms a distinct role of NPR1 in the nucleosome remodeling over the core promoter. We have also identified several motifs for various hormonal responses; including ABRE elements in the remodeled nucleosomal regions around the promoter region in the SA regulated genes. We have further identified that the W-box and TGACG/C motif, reported to play an important role in SA-mediated induction, are enriched in nucleosome free regions (NFRs) of the promoter region of the SA induced genes.ConclusionsThis is the first study reporting genome-wide effects of SA treatment on the chromatin architecture of A. thaliana. It also reports significant role of NPR1 in genome-wide nucleosomal remodeling in response to SA.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0404-2) contains supplementary material, which is available to authorized users.
Highlights
The nucleosome positioning regulates the gene expression and many other DNA-related processes in eukaryotes
To determine the changes in the nucleosome positions that eventually lead to changes in the gene expression, 2-week old control or salicylic acid (SA)-treated A. thaliana seedlings were used for mononucleosomal DNA preparation
Custom scripts were developed and used for assigning nucleosomes where nucleosomes were identified at different stringency levels
Summary
The nucleosome positioning regulates the gene expression and many other DNA-related processes in eukaryotes. Genome-wide mapping of nucleosome positions and correlation of genome-wide nucleosomal remodeling with the changes in the gene expression can help us understanding gene regulation on genome level. It is well known that the position of the nucleosome along a particular sequence of DNA has profound effects on its accessibility for all DNA processes such as transcription regulation, recombination, and repair [1,2,3]. Genome-wide mapping of nucleosome positions of eukaryotic genomes is a prerequisite to understand the basic mechanism of chromosomal organization. Different techniques have been used to assay nucleosome positioning in chromatin; for example, whole-genome tiling-microarray using mononucleosomal DNA [28], Micrococcal Nuclease (MNase1)sequencing [22,23,24,25,27], which provides in-depth data on genome-wide nucleosomal positioning, etc
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