Nucleic Acids Research Advance Access published online on April 24, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp258
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Molecular Biology |
IHF-binding sites inhibit DNA loop formation and transcription initiation
1National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, P. R. China, 2Institut Pasteur, Molecular Genetics Unit and CNRS URA-2172, 25 rue du Dr Roux, 75724 Paris Cedex 15, France and 3Department of Life Sciences, Imperial College London, London SW72AZ, UK
*To whom correspondence should be addressed. Tel: +86 10 6275 8490; Fax: +86 10 6275 6325; Email: wangyp{at}pku.edu.cn
Received October 27, 2008. Revised April 5, 2009. Accepted April 7, 2009.
Transcriptional activation of enhancer and 
54-dependent promoters requires efficient interactions between enhancer-binding proteins (EBP) and promoter bound 54-RNA polymerase (E54) achieved by DNA looping, which is usually facilitated by the integration host factor (IHF). Since the lengths of the intervening region supporting DNA-loop formation are similar among IHF-dependent and IHF-independent promoters, the precise reason(s) why IHF is selectively important for the frequency of transcription initiation remain unclear. Here, using kinetic cyclization and in vitro transcription assays we show that, in the absence of IHF protein, the DNA fragments containing an IHF-binding site have much less looping-formation ability than those that lack an IHF-binding site. Furthermore, when an IHF consensus-binding site was introduced into the intervening region between promoter and enhancer of the target DNA fragments, loop formation and DNA-loop-dependent transcriptional activation are significantly reduced in a position-independent manner. DNA-looping-independent transcriptional activation was unaffected. The binding of IHF to its consensus site in the target promoters clearly restored efficient DNA looping formation and looping-dependent transcriptional activation. Our data provide evidence that one function for the IHF protein is to release a communication block set by intrinsic properties of the IHF DNA-binding site.