Journal Article

Mapping and Characterization of DNase I Hypersensitive Sites in <i>Arabidopsis</i> Chromatin

Yuichi Kodama, Shingo Nagaya, Atsuhiko Shinmyo and Ko Kato

in Plant and Cell Physiology

Published on behalf of Japanese Society of Plant Physiologists

Volume 48, issue 3, pages 459-470
Published in print March 2007 | ISSN: 0032-0781
Published online March 2007 | e-ISSN: 1471-9053 | DOI: http://dx.doi.org/10.1093/pcp/pcm017
Mapping and Characterization of DNase I Hypersensitive Sites in Arabidopsis Chromatin

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Recent genome-wide analyses of yeast and human chromatin revealed the widespread prevalence of DNase I hypersensitive sites (DNase I HSs) at gene regulatory regions with possible roles in eukaryotic gene regulation. The presence of DNase I HSs in plants has been described for only a few genes, and we analyzed the chromatin structure of an 80 kb genomic region containing 30 variably expressed genes by DNase I sensitivity assay at 500 bp resolution in Arabidopsis. Distinct DNase I HSs were found at the 5′ and/or 3′ ends of most genes irrespective of their expression levels. Further analysis of well-characterized genes showed that the DNase I HSs occurred near cis-regulatory elements in the promoters of these genes. Upon transcriptional activation of a heat-inducible gene, the DNase I HS was extended into the vicinity of a cis-element and adjacent TATA element in the promoter. Concomitant with this change in DNase I HS, histones were acetylated, removed from the promoter, and a transcription activator bound to this cis-element. These results suggest that the DNase I HSs participate in the transcriptional regulation of Arabidopsis genes by enhancing the access of chromatin remodeling factors and/or transcription factors to their target sites as seen in yeast and human chromatin.

Keywords: Arabidopsis thaliana; Chromatin structure; DNase I-hypersensitive site; Gene expression; Histone acetylation; Transcription regulation

Journal Article.  7111 words.  Illustrated.

Subjects: Biochemistry ; Molecular and Cell Biology ; Plant Sciences and Forestry

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