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Plant and Cell Physiology Advance Access originally published online on July 19, 2008
Plant and Cell Physiology 2008 49(9):1306-1315; doi:10.1093/pcp/pcn105
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© The Author 2008. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org

Isolation of Heat Shock Factor HsfA1a-Binding Sites in vivo Revealed Variations of Heat Shock Elements in Arabidopsis thaliana

Lihong Guo1,2,3,4, Shanna Chen3,4, Kaihui Liu1, Yanfang Liu1, Lianghua Ni1, Keqin Zhang1 and Lemin Zhang1,*

1 Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China
2 Department of Biology, Kunming College, Kunming 650031, China
3 School of Life Sciences, Yunnan University, Kunming 650091, China

*Corresponding author: E-mail, zhanglm{at}ynu.edu.cn; Fax, +86-871-5034838.


  Abstract

The information about DNA-binding sites of regulatory protein is important to understanding the regulatory network of DNA–protein interactions in the genome. In this report we integrated chromatin immunoprecipitation with DNA cloning to isolate genomic sites bound in vivo by heat shock factor HsfA1a in Arabidopsis thaliana. Plantlets were subjected to formaldehyde crosslinking, followed by immunoprecipitation of chromatin. The immunoprecipitated DNA was amplified by PCR and cloned. From a library enriched in putative HsfA1a-binding sites, 21 different genomic fragments were identified (65–332 bp). Six fragments contained known HsfA1a-binding motif (perfect heat shock element). Six fragments contained novel HsfA1a-binding motifs: (1) gap-type, (2) TTC-rich-type, (3) stress responsive element (STRE). Representatives of each were verified by in vitro electrophoretic mobility shift assay. About 81% of the isolated fragments contained the HsfA1a-binding motifs, and/or could be bound by HsfA1a, demonstrating that the method is efficient in the isolation of genomic binding sites of a regulatory protein. The nearest downstream genes to the HsfA1a-binding fragments, which were considered as potential HsfA1a target genes, include a set of classical heat shock protein genes: Hsp17.4, Hsp18.2, Hsp21, Hsp81–1, Hsp101, and several novel genes encoding a non-race specific disease resistance protein and a transmembrane CLPTM1 family protein.

Keywords: Arabidopsis thaliana - Chromatin immunoprecipitation - Heat shock element - Heat shock factor - Protein–DNA interaction

Abbreviations: HSE, heat shock element; HSF, heat shock factor; STRE, stress responsive element.

4These authors contributed equally to this work.

(Received May 17, 2008; Accepted July 17, 2008)
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