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Plant and Cell Physiology Advance Access originally published online on February 5, 2007
Plant and Cell Physiology 2007 48(3):459-470; doi:10.1093/pcp/pcm017
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© The Author 2007. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org

Mapping and Characterization of DNase I Hypersensitive Sites in Arabidopsis Chromatin

Yuichi Kodama1, Shingo Nagaya1, Atsuhiko Shinmyo and Ko Kato*

Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192 Japan

*Corresponding author: E-mail, kou{at}bs.naist.jp; Fax, +81-743-72-5469.


  Abstract

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

Abbreviations: ABRE, ABA-responsive elements; BAC, bacterial artificial chromosome; ChIP, chromatin immunoprecipitation; DNase I HS, DNase I hypersensitive site; HSE, heat shock element; HSF, heat shock factor; HSP18.2, heat shock protein 18.2; NIB, nuclei isolation buffer; PCNA1, proliferating cell nuclear antigen; RD29b, responsive to desiccation 29b; V-ATPase, vacuolar-type proton ATPase subunit A.

1 These authors contributed equally to this work.

(Received November 13, 2006; Accepted January 26, 2007)
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