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SIG1, a Sigma Factor for the Chloroplast RNA Polymerase, Differently Associates with Multiple DNA Regions in the Chloroplast Chromosomes in Vivo
Division of Applied Biological Chemistry, Graduate School of Horticulture, Chiba University, Matsudo 648, Matsudo, Chiba 271-8510, Japan
Division of Bioresources, Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259-R1-29, Midori-Ku, Yokohama 226-8503, Japan
* Author to whom correspondence should be addressed.
Received: 1 June 2012; in revised form: 5 September 2012 / Accepted: 11 September 2012 / Published: 25 September 2012
Abstract: Chloroplasts have their own DNA and gene expression systems. Transcription in chloroplasts is regulated by two types of RNA polymerase, nuclear-encoded plastid RNA polymerase (NEP) and plastid-encoded plastid RNA polymerase (PEP), and multiple sigma factors for PEP. To study transcriptional regulation in chloroplasts, a molecular genetic approach has extensively been used. However, this method may include indirect effects, and it cannot be applied to the analysis of factors essential to survival. These limitations make understanding specific regulation by transcription factors difficult. Chromatin immunoprecipitation (ChIP) is a powerful and useful tool for obtaining information on transcription-factor binding sites; it can directly detect dynamic changes in their interaction patterns in vivo. To further understand transcriptional regulation in chloroplasts, we here established a ChIP-based method in Arabidopsis thaliana and analyzed the binding pattern of a chloroplast sigma factor, SIG1. We found that SIG1 specifically binds to newly identified target promoters as well as to a set of promoters of genes whose mRNA expression is dependent on OsSIG1 in rice and that this binding changed in response to high-light stress. These results suggested that the ChIP-based approach is very useful in understanding transcriptional regulation of chloroplast genes and can overcome several problems posed by conventional methods.
Keywords: chloroplast; chromatin immunoprecipitation; transcriptional regulation; sigma factor; SIG1; high-light stress; Arabidopsis thaliana
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MDPI and ACS Style
Hanaoka, M.; Kato, M.; Anma, M.; Tanaka, K. SIG1, a Sigma Factor for the Chloroplast RNA Polymerase, Differently Associates with Multiple DNA Regions in the Chloroplast Chromosomes in Vivo. Int. J. Mol. Sci. 2012, 13, 12182-12194.
Hanaoka M, Kato M, Anma M, Tanaka K. SIG1, a Sigma Factor for the Chloroplast RNA Polymerase, Differently Associates with Multiple DNA Regions in the Chloroplast Chromosomes in Vivo. International Journal of Molecular Sciences. 2012; 13(10):12182-12194.
Hanaoka, Mitsumasa; Kato, Maiko; Anma, Misato; Tanaka, Kan. 2012. "SIG1, a Sigma Factor for the Chloroplast RNA Polymerase, Differently Associates with Multiple DNA Regions in the Chloroplast Chromosomes in Vivo." Int. J. Mol. Sci. 13, no. 10: 12182-12194.