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Download Hi-Res ImageDownload to MS-PowerPointCite This:Biochemistry 2017, 56, 16, 2184-2196
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Crystal Structure and Characterization of Novel Human Histone H3 Variants, H3.6, H3.7, and H3.8

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† Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Research Institute for Science and Engineering, and Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
‡ Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
§ Department of Bioengineering, Graduate School of Engineering, Osaka City University, Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
∥ Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
*Telephone: +81-92-642-6384. Fax: +81-92-642-6562. E-mail: [email protected]
*Telephone: +81-3-5369-7315. Fax: +81-3-5367-2820. E-mail: [email protected]
Cite this: Biochemistry 2017, 56, 16, 2184–2196
Publication Date (Web):April 4, 2017
https://doi.org/10.1021/acs.biochem.6b01098
Copyright © 2017 American Chemical Society
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Abstract

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Non-allelic histone variants are considered as epigenetic factors that regulate genomic DNA functions in eukaryotic chromosomes. In this study, we identified three new human histone H3 variants (named H3.6, H3.7, and H3.8), which were previously annotated as pseudogenes. H3.6 and H3.8 conserve the H3.3-specific amino acid residues, but H3.7 shares the specific amino acid residues with H3.1. We successfully reconstituted the nucleosome containing H3.6 in vitro and determined its crystal structure. In the H3.6 nucleosome, the H3.6-specific Val62 residue hydrophobically contacts the cognate H4 molecule, but its contact area is smaller than that of the corresponding H3.3 Ile62 residue. The thermal stability assay revealed that the H3.6 nucleosome is substantially unstable, as compared to the H3.3 nucleosome. Interestingly, mutational analysis demonstrated that the H3.6 Val62 residue is fully responsible for the H3.6 nucleosome instability, probably because of the weakened hydrophobic interaction with H4. We also reconstituted the nucleosome containing H3.8, but its thermal stability was quite low. In contrast, purified H3.7 failed to form nucleosomes in vitro. The identification and characterization of these novel human histone H3 variants provide important new insights into understanding the epigenetic regulation of the human genome.

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Cited By

This article is cited by 12 publications.

  1. Rina Hirano, Yasuhiro Arimura, Tomoya Kujirai, Mikihiro Shibata, Aya Okuda, Ken Morishima, Rintaro Inoue, Masaaki Sugiyama, Hitoshi Kurumizaka. Histone variant H2A.B-H2B dimers are spontaneously exchanged with canonical H2A-H2B in the nucleosome. Communications Biology 2021, 4 (1) https://doi.org/10.1038/s42003-021-01707-z
  2. Benjamin Loppin, Frédéric Berger. Histone Variants: The Nexus of Developmental Decisions and Epigenetic Memory. Annual Review of Genetics 2020, 54 (1) , 121-149. https://doi.org/10.1146/annurev-genet-022620-100039
  3. Hitoshi Kurumizaka, Tomoya Kujirai, Yoshimasa Takizawa. Contributions of Histone Variants in Nucleosome Structure and Function. Journal of Molecular Biology 2020, , 166678. https://doi.org/10.1016/j.jmb.2020.10.012
  4. Aline V Probst, Bénédicte Desvoyes, Crisanto Gutierrez, . Similar yet critically different: the distribution, dynamics and function of histone variants. Journal of Experimental Botany 2020, 71 (17) , 5191-5204. https://doi.org/10.1093/jxb/eraa230
  5. William A. Scott, Eric I. Campos. Interactions With Histone H3 & Tools to Study Them. Frontiers in Cell and Developmental Biology 2020, 8 https://doi.org/10.3389/fcell.2020.00701
  6. Akihisa Osakabe, Zdravko J Lorković, Wataru Kobayashi, Hiroaki Tachiwana, Ramesh Yelagandula, Hitoshi Kurumizaka, Frédéric Berger. Histone H2A variants confer specific properties to nucleosomes and impact on chromatin accessibility. Nucleic Acids Research 2018, 46 (15) , 7675-7685. https://doi.org/10.1093/nar/gky540
  7. Masako Koyama, Hitoshi Kurumizaka. Structural diversity of the nucleosome. The Journal of Biochemistry 2018, 163 (2) , 85-95. https://doi.org/10.1093/jb/mvx081
  8. Tomoya Kujirai, Yasuhiro Arimura, Risa Fujita, Naoki Horikoshi, Shinichi Machida, Hitoshi Kurumizaka. Methods for Preparing Nucleosomes Containing Histone Variants. 2018,,, 3-20. https://doi.org/10.1007/978-1-4939-8663-7_1
  9. , . Histone Variants. 2018,,https://doi.org/10.1007/978-1-4939-8663-7
  10. Delphine Quénet. Histone Variants and Disease. 2018,,, 1-39. https://doi.org/10.1016/bs.ircmb.2017.07.006
  11. . Transcriptional Gene Regulation in Health and Disease. 2018,,https://doi.org/
  12. Stefan J. Tekel, Karmella A. Haynes. Molecular structures guide the engineering of chromatin. Nucleic Acids Research 2017, 45 (13) , 7555-7570. https://doi.org/10.1093/nar/gkx531

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