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 language | English |
|---|---|
| Article number | 170255 |
| Journal | Open Biology |
| Volume | 8 |
| Issue number | 3 |
| DOIs | |
| Publication status | Published - 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
Cryo-EM structure of the nucleosome containing the ALB1 enhancer DNA sequence. / Takizawa, Yoshimasa; Tanaka, Hiroki; Machida, Shinichi; Koyama, Masako; Maehara, Kazumitsu; Ohkawa, Yasuyuki; Wade, Paul A.; Wolf, Matthias; Kurumizaka, Hitoshi.
In: Open Biology, Vol. 8, No. 3, 170255, 01.01.2018.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Cryo-EM structure of the nucleosome containing the ALB1 enhancer DNA sequence
AU - Takizawa, Yoshimasa
AU - Tanaka, Hiroki
AU - Machida, Shinichi
AU - Koyama, Masako
AU - Maehara, Kazumitsu
AU - Ohkawa, Yasuyuki
AU - Wade, Paul A.
AU - Wolf, Matthias
AU - Kurumizaka, Hitoshi
PY - 2018/1/1
Y1 - 2018/1/1
N2 - 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.
AB - 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.
KW - FoxA
KW - Histone
KW - Nucleosome binding
KW - Nucleosome positioning
KW - Pioneer transcription factor
UR - http://www.scopus.com/inward/record.url?scp=85045136109&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85045136109&partnerID=8YFLogxK
U2 - 10.1098/rsob.170255
DO - 10.1098/rsob.170255
M3 - Article
VL - 8
JO - Open Biology
JF - Open Biology
SN - 2046-2441
IS - 3
M1 - 170255
ER -