Nucleic Acids Research, 2003, Vol. 31, No. 22 6651-6662
© 2003 Oxford University Press
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Left-handedly curved DNA regulates accessibility to cis-DNA elements in chromatin
1 Department of Biology, Faculty of Science and Engineering, 2 High Technology Research Center, Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan, 3 Laboratory of Cell Genetics, Division of Cell Genetics, National Institute of Genetics, 1-111 Yata, Mishima, Shizuoka 411-8540, Japan, 4 Meiji Institute of Health Science, 540 Naruda, Odawara 250-0862, Japan and 5 Bioscience Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-01, Japan
*To whom correspondence should be addressed at Department of Biology, Faculty of Science and Engineering, and High Technology Research Center, Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan. Tel: +81 78 435 2547; Fax: +81 78 435 2547; Email: ohyama{at}base2.ipc.konan-u.ac.jp
There is little information on chromatin structure that allows access of trans-acting transcription factors. Logically, the target DNA elements become accessible by either exposing themselves towards the environment on the surface of the nucleosome, or making the regulatory region free of the nucleosome. Here, we demonstrate that curved DNA that mimics a negative supercoil can play both roles in the promoter region. By constructing 35 reporter plasmids and using in vivo assay systems, we scrutinized the relationships between upstream DNA geometry, nucleosome positioning and promoter activity. When the left-handedly curved DNA was linked to the herpes simplex virus thymidine kinase (HSV tk) promoter at a specific rotational phase and distance, the curved DNA attracted the nucleosome and the TATA box was thereby left in the linker DNA with its minor groove facing outwards, which led to the activation of transcription. Neither planar curving, nor right-handedly curved DNA nor straight DNA had this effect. Our results seem to provide a clue for solving the problem of why curved DNA is often located near transcriptional control regions.
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