Structural Basis of Heterochromatin Formation by Human HP1

Heterochromatin plays important roles in transcriptional silencing and genome maintenance by the formation of condensed chromatin structures, which determine the epigenetic status of eukaryotic cells. The trimethylation of histone H3 lysine 9 (H3K9me3), a target of heterochromatin protein 1 (HP1), i...

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Published in	Molecular cell Vol. 69; no. 3; pp. 385 - 397.e8
Main Authors	Machida, Shinichi, Takizawa, Yoshimasa, Ishimaru, Masakazu, Sugita, Yukihiko, Sekine, Satoshi, Nakayama, Jun-ichi, Wolf, Matthias, Kurumizaka, Hitoshi
Format	Journal Article
Language	English
Published	United States Elsevier Inc 01.02.2018
Subjects	ACF chromatin cryo-EM DNA electron microscopy epigenetics eukaryotic cells genome H3K9me3 heterochromatin histone histones HP1 humans lysine nucleosome nucleosomes transcription (genetics) ACF H3K9me3 HP1 nucleosome histone chromatin cryo-EM epigenetics heterochromatin
Online Access	Get full text
ISSN	1097-2765 1097-4164 1097-4164
DOI	10.1016/j.molcel.2017.12.011

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Abstract	Heterochromatin plays important roles in transcriptional silencing and genome maintenance by the formation of condensed chromatin structures, which determine the epigenetic status of eukaryotic cells. The trimethylation of histone H3 lysine 9 (H3K9me3), a target of heterochromatin protein 1 (HP1), is a hallmark of heterochromatin formation. However, the mechanism by which HP1 folds chromatin-containing H3K9me3 into a higher-order structure has not been elucidated. Here we report the three-dimensional structure of the H3K9me3-containing dinucleosomes complexed with human HP1α, HP1β, and HP1γ, determined by cryogenic electron microscopy with a Volta phase plate. In the structures, two H3K9me3 nucleosomes are bridged by a symmetric HP1 dimer. Surprisingly, the linker DNA between the nucleosomes does not directly interact with HP1, thus allowing nucleosome remodeling by the ATP-utilizing chromatin assembly and remodeling factor (ACF). The structure depicts the fundamental architecture of heterochromatin. [Display omitted] •The HP1-H3K9me3 dinucleosome complex structure determined by the cryo-EM method•HP1 forms a symmetric dimer and bridges two H3K9me3 nucleosomes in the complex•The HP1 chromoshadow domain dimer exists in an accessible location in the complex•The linker DNA between nucleosomes does not directly interact with HP1 HP1 and H3 Lys9 trimethylations (H3K9me3) are hallmarks of heterochromatin, and they play pivotal roles in the epigenetic propagation of heterochromatin. Machida et al. describe the structure of the H3K9me3-containing dinucleosome complexed with human HP1, obtained by the cryo-EM technique.
AbstractList	Heterochromatin plays important roles in transcriptional silencing and genome maintenance by the formation of condensed chromatin structures, which determine the epigenetic status of eukaryotic cells. The trimethylation of histone H3 lysine 9 (H3K9me3), a target of heterochromatin protein 1 (HP1), is a hallmark of heterochromatin formation. However, the mechanism by which HP1 folds chromatin-containing H3K9me3 into a higher-order structure has not been elucidated. Here we report the three-dimensional structure of the H3K9me3-containing dinucleosomes complexed with human HP1α, HP1β, and HP1γ, determined by cryogenic electron microscopy with a Volta phase plate. In the structures, two H3K9me3 nucleosomes are bridged by a symmetric HP1 dimer. Surprisingly, the linker DNA between the nucleosomes does not directly interact with HP1, thus allowing nucleosome remodeling by the ATP-utilizing chromatin assembly and remodeling factor (ACF). The structure depicts the fundamental architecture of heterochromatin. [Display omitted] •The HP1-H3K9me3 dinucleosome complex structure determined by the cryo-EM method•HP1 forms a symmetric dimer and bridges two H3K9me3 nucleosomes in the complex•The HP1 chromoshadow domain dimer exists in an accessible location in the complex•The linker DNA between nucleosomes does not directly interact with HP1 HP1 and H3 Lys9 trimethylations (H3K9me3) are hallmarks of heterochromatin, and they play pivotal roles in the epigenetic propagation of heterochromatin. Machida et al. describe the structure of the H3K9me3-containing dinucleosome complexed with human HP1, obtained by the cryo-EM technique. Heterochromatin plays important roles in transcriptional silencing and genome maintenance by the formation of condensed chromatin structures, which determine the epigenetic status of eukaryotic cells. The trimethylation of histone H3 lysine 9 (H3K9me3), a target of heterochromatin protein 1 (HP1), is a hallmark of heterochromatin formation. However, the mechanism by which HP1 folds chromatin-containing H3K9me3 into a higher-order structure has not been elucidated. Here we report the three-dimensional structure of the H3K9me3-containing dinucleosomes complexed with human HP1α, HP1β, and HP1γ, determined by cryogenic electron microscopy with a Volta phase plate. In the structures, two H3K9me3 nucleosomes are bridged by a symmetric HP1 dimer. Surprisingly, the linker DNA between the nucleosomes does not directly interact with HP1, thus allowing nucleosome remodeling by the ATP-utilizing chromatin assembly and remodeling factor (ACF). The structure depicts the fundamental architecture of heterochromatin. Heterochromatin plays important roles in transcriptional silencing and genome maintenance by the formation of condensed chromatin structures, which determine the epigenetic status of eukaryotic cells. The trimethylation of histone H3 lysine 9 (H3K9me3), a target of heterochromatin protein 1 (HP1), is a hallmark of heterochromatin formation. However, the mechanism by which HP1 folds chromatin-containing H3K9me3 into a higher-order structure has not been elucidated. Here we report the three-dimensional structure of the H3K9me3-containing dinucleosomes complexed with human HP1α, HP1β, and HP1γ, determined by cryogenic electron microscopy with a Volta phase plate. In the structures, two H3K9me3 nucleosomes are bridged by a symmetric HP1 dimer. Surprisingly, the linker DNA between the nucleosomes does not directly interact with HP1, thus allowing nucleosome remodeling by the ATP-utilizing chromatin assembly and remodeling factor (ACF). The structure depicts the fundamental architecture of heterochromatin.Heterochromatin plays important roles in transcriptional silencing and genome maintenance by the formation of condensed chromatin structures, which determine the epigenetic status of eukaryotic cells. The trimethylation of histone H3 lysine 9 (H3K9me3), a target of heterochromatin protein 1 (HP1), is a hallmark of heterochromatin formation. However, the mechanism by which HP1 folds chromatin-containing H3K9me3 into a higher-order structure has not been elucidated. Here we report the three-dimensional structure of the H3K9me3-containing dinucleosomes complexed with human HP1α, HP1β, and HP1γ, determined by cryogenic electron microscopy with a Volta phase plate. In the structures, two H3K9me3 nucleosomes are bridged by a symmetric HP1 dimer. Surprisingly, the linker DNA between the nucleosomes does not directly interact with HP1, thus allowing nucleosome remodeling by the ATP-utilizing chromatin assembly and remodeling factor (ACF). The structure depicts the fundamental architecture of heterochromatin. Heterochromatin plays important roles in transcriptional silencing and genome maintenance by the formation of condensed chromatin structures, which determine the epigenetic status of eukaryotic cells. The trimethylation of histone H3 lysine 9 (H3K9me3), a target of heterochromatin protein 1 (HP1), is a hallmark of heterochromatin formation. However, the mechanism by which HP1 folds chromatin-containing H3K9me3 into a higher-order structure has not been elucidated. Here we report the three-dimensional structure of the H3K9me3-containing dinucleosomes complexed with human HP1α, HP1β, and HP1γ, determined by cryogenic electron microscopy with a Volta phase plate. In the structures, two H3K9me3 nucleosomes are bridged by a symmetric HP1 dimer. Surprisingly, the linker DNA between the nucleosomes does not directly interact with HP1, thus allowing nucleosome remodeling by the ATP-utilizing chromatin assembly and remodeling factor (ACF). The structure depicts the fundamental architecture of heterochromatin.
Author	Ishimaru, Masakazu Nakayama, Jun-ichi Sugita, Yukihiko Wolf, Matthias Machida, Shinichi Kurumizaka, Hitoshi Takizawa, Yoshimasa Sekine, Satoshi
Author_xml	– sequence: 1 givenname: Shinichi surname: Machida fullname: Machida, Shinichi organization: Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan – sequence: 2 givenname: Yoshimasa surname: Takizawa fullname: Takizawa, Yoshimasa organization: Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan – sequence: 3 givenname: Masakazu surname: Ishimaru fullname: Ishimaru, Masakazu organization: Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan – sequence: 4 givenname: Yukihiko surname: Sugita fullname: Sugita, Yukihiko organization: Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan – sequence: 5 givenname: Satoshi surname: Sekine fullname: Sekine, Satoshi organization: Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan – sequence: 6 givenname: Jun-ichi surname: Nakayama fullname: Nakayama, Jun-ichi organization: National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan – sequence: 7 givenname: Matthias surname: Wolf fullname: Wolf, Matthias email: matthias.wolf@oist.jp organization: Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan – sequence: 8 givenname: Hitoshi surname: Kurumizaka fullname: Kurumizaka, Hitoshi email: kurumizaka@waseda.jp organization: Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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Snippet	Heterochromatin plays important roles in transcriptional silencing and genome maintenance by the formation of condensed chromatin structures, which determine...
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SubjectTerms	ACF chromatin cryo-EM DNA electron microscopy epigenetics eukaryotic cells genome H3K9me3 heterochromatin histone histones HP1 humans lysine nucleosome nucleosomes transcription (genetics)
Title	Structural Basis of Heterochromatin Formation by Human HP1
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