Cryo-EM structure of the nucleosome containing the ALB1 enhancer DNA sequence

Yoshimasa Takizawa, Hiroki Tanaka, Shinichi Machida, Masako Koyama, Kazumitsu Maehara, Yasuyuki Ohkawa, Paul A. Wade, Matthias Wolf, Hitoshi Kurumizaka

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6 Citations (Scopus)

Abstract

Pioneer transcription factors specifically target their recognition DNA sequences within nucleosomes. FoxA is the pioneer transcription factor that binds to the ALB1 gene enhancer in liver precursor cells, and is required for liver differentiation in embryos. The ALB1 enhancer DNA sequence is reportedly incorporated into nucleosomes in cells, although the nucleosome structure containing the targeting sites for FoxA has not been clarified yet. In this study, we determined the nucleosome structure containing the ALB1 enhancer (N1) sequence, by cryogenic electron microscopy at 4.0 Å resolution. The nucleosome structure with the ALB1 enhancer DNA is not significantly different from the previously reported nucleosome structure with the Widom 601 DNA. Interestingly, in the nucleosomes, the ALB1 enhancer DNA contains local flexible regions, as compared to the Widom 601 DNA. Consistently, DNaseI treatments revealed that, in the nucleosome, the ALB1 enhancer (N1) DNA is more accessible than the Widom 601 sequence. The histones also associated less strongly with the ALB1 enhancer (N1) DNA than the Widom 601 DNA in the nucleosome. Therefore, the local histone–DNA contacts May be responsible for the enhanced DNA accessibility in the nucleosome with the ALB1 enhancer DNA.

Original languageEnglish
Article number170255
JournalOpen Biology
Volume8
Issue number3
DOIs
Publication statusPublished - 2018 Jan 1

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Keywords

  • FoxA
  • Histone
  • Nucleosome binding
  • Nucleosome positioning
  • Pioneer transcription factor

ASJC Scopus subject areas

  • Neuroscience(all)
  • Immunology
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Takizawa, Y., Tanaka, H., Machida, S., Koyama, M., Maehara, K., Ohkawa, Y., Wade, P. A., Wolf, M., & Kurumizaka, H. (2018). Cryo-EM structure of the nucleosome containing the ALB1 enhancer DNA sequence. Open Biology, 8(3), [170255]. https://doi.org/10.1098/rsob.170255