Left-handedly curved DNA regulates accessibility to cis-DNA elements in chromatin

Jun Ichi Nishikawa, Miho Amano, Yoshiro Fukue, Shigeo Tanaka, Haruka Kishi, Yoshiko Hirota, Kinya Yoda, Takashi Ohyama

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)6651-6662
Number of pages12
JournalNucleic Acids Research
Volume31
Issue number22
DOIs
Publication statusPublished - 2003 Nov 15
Externally publishedYes

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Chromatin
DNA
Nucleosomes
TATA Box
Trans-Activators
Thymidine Kinase
Nucleic Acid Regulatory Sequences
Simplexvirus
Genetic Promoter Regions
Transcriptional Activation
Plasmids
Transcription Factors

ASJC Scopus subject areas

  • Genetics

Cite this

Nishikawa, J. I., Amano, M., Fukue, Y., Tanaka, S., Kishi, H., Hirota, Y., ... Ohyama, T. (2003). Left-handedly curved DNA regulates accessibility to cis-DNA elements in chromatin. Nucleic Acids Research, 31(22), 6651-6662. https://doi.org/10.1093/nar/gkg854

Left-handedly curved DNA regulates accessibility to cis-DNA elements in chromatin. / Nishikawa, Jun Ichi; Amano, Miho; Fukue, Yoshiro; Tanaka, Shigeo; Kishi, Haruka; Hirota, Yoshiko; Yoda, Kinya; Ohyama, Takashi.

In: Nucleic Acids Research, Vol. 31, No. 22, 15.11.2003, p. 6651-6662.

Research output: Contribution to journalArticle

Nishikawa, JI, Amano, M, Fukue, Y, Tanaka, S, Kishi, H, Hirota, Y, Yoda, K & Ohyama, T 2003, 'Left-handedly curved DNA regulates accessibility to cis-DNA elements in chromatin', Nucleic Acids Research, vol. 31, no. 22, pp. 6651-6662. https://doi.org/10.1093/nar/gkg854
Nishikawa JI, Amano M, Fukue Y, Tanaka S, Kishi H, Hirota Y et al. Left-handedly curved DNA regulates accessibility to cis-DNA elements in chromatin. Nucleic Acids Research. 2003 Nov 15;31(22):6651-6662. https://doi.org/10.1093/nar/gkg854
Nishikawa, Jun Ichi ; Amano, Miho ; Fukue, Yoshiro ; Tanaka, Shigeo ; Kishi, Haruka ; Hirota, Yoshiko ; Yoda, Kinya ; Ohyama, Takashi. / Left-handedly curved DNA regulates accessibility to cis-DNA elements in chromatin. In: Nucleic Acids Research. 2003 ; Vol. 31, No. 22. pp. 6651-6662.
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