title: Global nucleosome positioning regulates salicylic acid mediated transcription in Arabidopsis thaliana.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  In 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.
  
  
  CONCLUSIONS
  This 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.
authors.affiliation: CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India. singhmala21@gmail.com.
authors.forename: Mala
authors.initials: M
authors.lastname: Singh
authors.affiliation: CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India. sumit.bag@nbri.res.in.|Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110 001, India. sumit.bag@nbri.res.in.
authors.forename: Sumit Kumar
authors.initials: SK
authors.lastname: Bag
authors.affiliation: CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India. archana2287@gmail.com.|Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110 001, India. archana2287@gmail.com.
authors.forename: Archana
authors.initials: A
authors.lastname: Bhardwaj
authors.affiliation: CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India. amolranjan@yahoo.co.in.
authors.forename: Amol
authors.initials: A
authors.lastname: Ranjan
authors.affiliation: CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India. shrikant@nabi.res.in.
authors.forename: Shrikant
authors.initials: S
authors.lastname: Mantri
authors.affiliation: CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India. deept_mbi@yahoo.co.in.
authors.forename: Deepti
authors.initials: D
authors.lastname: Nigam
authors.affiliation: Department of Botany, Lucknow University, Lucknow, 226007, India. yogesh_s26@yahoo.com.
authors.forename: Yogesh Kumar
authors.initials: YK
authors.lastname: Sharma
authors.affiliation: CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India. samirsawant@nbri.res.in.|Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110 001, India. samirsawant@nbri.res.in.
authors.forename: Samir Vishwanath
authors.initials: SV
authors.lastname: Sawant
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000276:immunology; D029681:Arabidopsis Proteins / Q000378:metabolism; D020029:Base Pairing / Q000235:genetics; D001483:Base Sequence; D045584:Chromosome Positioning / Q000235:genetics*; D032461:Chromosomes, Plant / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D056426:Genetic Loci; D008969:Molecular Sequence Data; D009707:Nucleosomes / Q000378:metabolism*; D059372:Nucleotide Motifs; D011401:Promoter Regions, Genetic; D020156:Salicylic Acid / Q000378:metabolism*; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: D029681:Arabidopsis Proteins; C105496:NPR1 protein, Arabidopsis; D009707:Nucleosomes; D020156:Salicylic Acid