DOI: 10.1098/rsob.170255. Cryo-EM structure of the nucleosome containing the <i>ALB1</i> enhancer DNA sequence

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

10.1098/rsob.170255

Crossref journal-article

The Royal Society

Open Biology (175)

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.

Bibliography

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).

Authors 9

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

References 45 Referenced 38

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Dates

Type	When
Created	7 years, 5 months ago (March 21, 2018, 5 a.m.)
Deposited	2 years, 8 months ago (Dec. 12, 2022, 6:55 a.m.)
Indexed	1 week, 4 days ago (Aug. 26, 2025, 2:56 a.m.)
Issued	7 years, 6 months ago (March 1, 2018)
Published	7 years, 6 months ago (March 1, 2018)
Published Online	7 years, 5 months ago (March 21, 2018)
Published Print	7 years, 6 months ago (March 1, 2018)

Funders 3

JSP CREST
Awards1
1. JPMJCR16G1
the Platform Project for Supporting in Drug Discovery and Life Science Research, from the Japan Agency for Medical Research and Development
JSPS KAKENHI
Awards8
1. JP16K18473
2. JP25116010
3. JP16H01577
4. JP17H03608
5. JP17K15080
6. JP17H01408
7. JP25116002
8. JP16H01550

BibTeX

@article{Takizawa_2018, title={Cryo-EM structure of the nucleosome containing the ALB1 enhancer DNA sequence}, volume={8}, ISSN={2046-2441}, url={http://dx.doi.org/10.1098/rsob.170255}, DOI={10.1098/rsob.170255}, number={3}, journal={Open Biology}, publisher={The Royal Society}, author={Takizawa, Yoshimasa and Tanaka, Hiroki and Machida, Shinichi and Koyama, Masako and Maehara, Kazumitsu and Ohkawa, Yasuyuki and Wade, Paul A. and Wolf, Matthias and Kurumizaka, Hitoshi}, year={2018}, month=mar }

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