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  The Regulatory Code for Transcriptional Response Diversity and Its Relation to Genome Structural Properties in A. thaliana

Walther, D., Brunnemann, R., & Selbig, J. (2007). The Regulatory Code for Transcriptional Response Diversity and Its Relation to Genome Structural Properties in A. thaliana. PLoS Genetics, 3(2), e11. doi:10.1371/journal.pgen.0030011.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-2833-8 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-2834-6
Genre: Journal Article

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 Creators:
Walther, D.1, Author              
Brunnemann, R.2, Author              
Selbig, J.2, Author              
Affiliations:
1BioinformaticsCIG, Infrastructure Groups and Service Units, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753303              
2BioinformaticsCRG, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753315              

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Free keywords: highly expressed genes arabidopsis gene elements yeast drosophila networks stress DNA identification robustness
 Abstract: Regulation of gene expression via specific cis-regulatory promoter elements has evolved in cellular organisms as a major adaptive mechanism to respond to environmental change. Assuming a simple model of transcriptional regulation, genes that are differentially expressed in response to a large number of different external stimuli should harbor more distinct regulatory elements in their upstream regions than do genes that only respond to few environmental challenges. We tested this hypothesis in Arabidopsis thaliana using the compendium of gene expression profiling data available in AtGenExpress and known cis-element motifs mapped to upstream gene promoter regions and studied the relation of the observed breadth of differential gene expression response with several fundamental genome architectural properties. We observed highly significant positive correlations between the density of cis-elements in upstream regions and the number of conditions in which a gene was differentially regulated. The correlation was most pronounced in regions immediately upstream of the transcription start sites. Multistimuli response genes were observed to be associated with significantly longer upstream intergenic regions, retain more paralogs in the Arabidopsis genome, are shorter, have fewer introns, and are more likely to contain TATA-box motifs in their promoters. In abiotic stress time series data, multistimuli response genes were found to be overrepresented among early-responding genes. Genes involved in the regulation of transcription, stress response, and signaling processes were observed to possess the greatest regulatory capacity. Our results suggest that greater gene expression regulatory complexity appears to be encoded by an increased density of cis-regulatory elements and provide further evidence for an evolutionary adaptation of the regulatory code at the genomic layout level. Larger intergenic spaces preceding multistimuli response genes may have evolved to allow greater regulatory gene expression potential.

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Language(s): eng - English
 Dates: 2007-02-132007
 Publication Status: Published in print
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 Identifiers: ISI: ISI:000244711700006
DOI: 10.1371/journal.pgen.0030011
ISSN: 1553-7404 (Electronic) 1553-7390 (Linking)
URI: ://000244711700006 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1796623/pdf/pgen.0030011.pdf?tool=pmcentrez
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Title: PLoS Genetics
Source Genre: Journal
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Pages: - Volume / Issue: 3 (2) Sequence Number: - Start / End Page: e11 Identifier: -