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Nucleic Acids Research Advance Access originally published online on February 14, 2008
Nucleic Acids Research 2008 36(6):1965-1975; doi:10.1093/nar/gkm1079
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Nucleic Acids Research, 2008, Vol. 36, No. 6 1965-1975
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Molecular Biology

Secondary DNA structure formation for Hoxb9 promoter and identification of its specific binding protein

Takumi Yamagishi1,2, Shigehisa Hirose2 and Takashi Kondo1,*

1Kondo Research Unit, Brain Development Research Group, Brain Science Institute, Institute of Physical and Chemical Research (RIKEN), 2-1 Hirosawa, Wako, Saitama 351-0198 and 2Department of Biological Sciences, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan

*To whom correspondence should be addressed. Tel: +81 48 467 6729; Fax: +81 48 467 6729; Email: TKondo{at}brain.riken.jp

Received July 6, 2007. Revised November 12, 2007. Accepted November 15, 2007.

Hox genes determine anterior–posterior specificity of an animal body. In mammals, these genes map onto four chromosomal loci in a clustered manner, and their expression is regulated in a coordinated manner according to their chromosomal structure. In the present study, we analysed the Hoxb9 promoter and found that promoter activity in cultured cells is linked to secondary structure formation of promoter DNA. In nuclear extracts, we also detected binding activity specific for secondary-structured DNA. We successfully isolated a candidate gene encoding this specific DNA-binding protein, FBXL10, and demonstrated the effects of the gene product on Hoxb9 promoter activity. Our results suggest that DNA can regulate gene expression by other, non-sequence-specific modes of genetic coding.


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