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170 results on '"Arimura, Yasuhiro"'

9. Architecture and flexibility of native kinetochores revealed by structural studies utilizing a thermophilic yeast

Author

Barrero, Daniel J., primary, Wijeratne, Sithara S., additional, Zhao, Xiaowei, additional, Cunningham, Grace F., additional, Yan, Rui, additional, Nelson, Christian R., additional, Arimura, Yasuhiro, additional, Funabiki, Hironori, additional, Asbury, Charles L., additional, Yu, Zhiheng, additional, Subramanian, Radhika, additional, and Biggins, Sue, additional

Published
2024
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14. Crystal structure of the overlapping dinucleosome composed of hexasome and octasome

Author

Kato, Daiki, Osakabe, Akihisa, Arimura, Yasuhiro, Mizukami, Yuka, Horikoshi, Naoki, Saikusa, Kazumi, Akashi, Satoko, Nishimura, Yoshifumi, Park, Sam-Yong, Nogami, Jumpei, Maehara, Kazumitsu, Ohkawa, Yasuyuki, Matsumoto, Atsushi, Kono, Hidetoshi, Inoue, Rintaro, Sugiyama, Masaaki, and Kurumizaka, Hitoshi

Published
2017

22. Histone variant H2A.B-H2B dimers are spontaneously exchanged with canonical H2A-H2B in the nucleosome

Author

80825646, 40812087, 80563840, Hirano, Rina, Arimura, Yasuhiro, Kujirai, Tomoya, Shibata, Mikihiro, Okuda, Aya, Morishima, Ken, Inoue, Rintaro, Sugiyama, Masaaki, Kurumizaka, Hitoshi, 80825646, 40812087, 80563840, Hirano, Rina, Arimura, Yasuhiro, Kujirai, Tomoya, Shibata, Mikihiro, Okuda, Aya, Morishima, Ken, Inoue, Rintaro, Sugiyama, Masaaki, and Kurumizaka, Hitoshi

Abstract

H2A.B is an evolutionarily distant histone H2A variant that accumulates on DNA repair sites, DNA replication sites, and actively transcribing regions in genomes. In cells, H2A.B exchanges rapidly in chromatin, but the mechanism has remained enigmatic. In the present study, we found that the H2A.B-H2B dimer incorporated within the nucleosome exchanges with the canonical H2A-H2B dimer without assistance from additional factors, such as histone chaperones and nucleosome remodelers. High-speed atomic force microscopy revealed that the H2A.B nucleosome, but not the canonical H2A nucleosome, transiently forms an intermediate “open conformation”, in which two H2A.B-H2B dimers may be detached from the H3-H4 tetramer and bind to the DNA regions near the entry/exit sites. Mutational analyses revealed that the H2A.B C-terminal region is responsible for the adoption of the open conformation and the H2A.B-H2B exchange in the nucleosome. These findings provide mechanistic insights into the histone exchange of the H2A.B nucleosome.

Published
2021

25. Cancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome

Author

Arimura, Yasuhiro, Ikura, Masae, Fujita, Risa, Noda, Mamiko, Kobayashi, Wataru, Horikoshi, Naoki, Sun, Jiying, Shi, Lin, Kusakabe, Masayuki, Harata, Masahiko, Ohkawa, Yasuyuki, Tashiro, Satoshi, Kimura, Hiroshi, Ikura, Tsuyoshi, and Kurumizaka, Hitoshi

Subjects
animal structures, embryonic structures, Gene Regulation, Chromatin and Epigenetics
Abstract

Mutations of the Glu76 residue of canonical histone H2B are frequently found in cancer cells. However, it is quite mysterious how a single amino acid substitution in one of the multiple H2B genes affects cell fate. Here we found that the H2B E76K mutation, in which Glu76 is replaced by Lys (E76K), distorted the interface between H2B and H4 in the nucleosome, as revealed by the crystal structure and induced nucleosome instability in vivo and in vitro. Exogenous production of the H2B E76K mutant robustly enhanced the colony formation ability of the expressing cells, indicating that the H2B E76K mutant has the potential to promote oncogenic transformation in the presence of wild-type H2B. We found that other cancer-associated mutations of histones, H3.1 E97K and H2A.Z.1 R80C, also induced nucleosome instability. Interestingly, like the H2B E76K mutant, the H3.1 E97K mutant was minimally incorporated into chromatin in cells, but it enhanced the colony formation ability. In contrast, the H2A.Z.1 R80C mutant was incorporated into chromatin in cells, and had minor effects on the colony formation ability of the cells. These characteristics of histones with cancer-associated mutations may provide important information toward understanding how the mutations promote cancer progression.

Published
2018

31. Model building of overlapping dinucleosome based on SAXS and SANS profiles

Author

Matsumoto, Atsushi, Kono, Hidetoshi, Inoue, Rintaro, Sugiyama, Masaaki, Arimura, Yasuhiro, and Kurumizaka, Hitoshi

Subjects
Astrophysics::High Energy Astrophysical Phenomena
Abstract

We built the atomic models of the overlapping dinucleosome in solution based on the experimental profiles of the small-angle X-ray scattering (SAXS) and the small-angle neutron scattering (SANS) by the computational approach., 量子生命科学会第１回大会

Published
2019

32. Supplementary Information from Biochemical analysis of nucleosome targeting by Tn5 transposase

Author

Sato, Shoko, Arimura, Yasuhiro, Kujirai, Tomoya, Harada, Akihito, Maehara, Kazumitsu, Nogami, Jumpei, Ohkawa, Yasuyuki, and Kurumizaka, Hitoshi

Subjects
bacteria, biochemical phenomena, metabolism, and nutrition
Abstract

Tn5 transposase is a bacterial enzyme that integrates a DNA fragment into genomic DNA, and is used as a tool for detecting nucleosome-free regions of genomic DNA in eukaryotes. However, in chromatin, the DNA targeting by Tn5 transposase has remained unclear. In the present study, we reconstituted well-positioned 601 dinucleosomes, in which two nucleosomes are connected with a linker DNA, and studied the DNA integration sites in the dinucleosomes by Tn5 transposase in vitro. We found that Tn5 transposase preferentially targets near the entry–exit DNA regions within the nucleosome. Tn5 transposase minimally cleaved the dinucleosome without a linker DNA, indicating that the linker DNA between two nucleosomes is important for the Tn5 transposase activity. In the presence of a 30 base-pair linker DNA, Tn5 transposase targets the middle of the linker DNA, in addition to the entry–exit sites of the nucleosome. Intriguingly, this Tn5-targeting characteristic is conserved in a dinucleosome substrate with a different DNA sequence from the 601 sequence. Therefore, the Tn5-targeting preference in the nucleosomal templates reported here provides important information for the interpretation of Tn5 transposase-based genomics methods, such as ATAC-seq.

Published
2019
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35. Cancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome

Author

40535275, 70335686, Arimura, Yasuhiro, Ikura, Masae, Fujita, Risa, Noda, Mamiko, Kobayashi, Wataru, Horikoshi, Naoki, Sun, Jiying, Shi, Lin, Kusakabe, Masayuki, Harata, Masahiko, Ohkawa, Yasuyuki, Tashiro, Satoshi, Kimura, Hiroshi, Ikura, Tsuyoshi, Kurumizaka, Hitoshi, 40535275, 70335686, Arimura, Yasuhiro, Ikura, Masae, Fujita, Risa, Noda, Mamiko, Kobayashi, Wataru, Horikoshi, Naoki, Sun, Jiying, Shi, Lin, Kusakabe, Masayuki, Harata, Masahiko, Ohkawa, Yasuyuki, Tashiro, Satoshi, Kimura, Hiroshi, Ikura, Tsuyoshi, and Kurumizaka, Hitoshi

Abstract

Mutations of the Glu76 residue of canonical histone H2B are frequently found in cancer cells. However, it is quite mysterious how a single amino acid substitution in one of the multiple H2B genes affects cell fate. Here we found that the H2B E76K mutation, in which Glu76 is replaced by Lys (E76K), distorted the interface between H2B and H4 in the nucleosome, as revealed by the crystal structure and induced nucleosome instability in vivo and in vitro. Exogenous production of the H2B E76K mutant robustly enhanced the colony formation ability of the expressing cells, indicating that the H2B E76K mutant has the potential to promote oncogenic transformation in the presence of wild-type H2B. We found that other cancer-associated mutations of histones, H3.1 E97K and H2A.Z.1 R80C, also induced nucleosome instability. Interestingly, like the H2B E76K mutant, the H3.1 E97K mutant was minimally incorporated into chromatin in cells, but it enhanced the colony formation ability. In contrast, the H2A.Z.1 R80C mutant was incorporated into chromatin in cells, and had minor effects on the colony formation ability of the cells. These characteristics of histones with cancer-associated mutations may provide important information toward understanding how the mutations promote cancer progression.

Published
2018

36. Model building of overlapping dinucleosome from SAXS and SANS data

Author

Matsumoto, Atsushi, Kono, Hidetoshi, Inoue, Rintaro, Sugiyama, Masaaki, Kato, Daiki, Arimura, Yasuhiro, and Kurumizaka, Hitoshi

Subjects
Astrophysics::High Energy Astrophysical Phenomena
Abstract

In this study, we built the atomic models of the overlapping dinucleosome in solution by the computational approach based on the experimental data of the small-angle X-ray scattering (SAXS) and the small-angle neutron scattering (SANS). In this computational approach, first, the initial atomic model is deformed by the simulation techniques to generate a lot of deformed atomic models with different conformations. Then, the SAXS and SANS profiles are computed from each deformed atomic model. Finally, these computed profiles are compared with the experimental ones to find the best-fitting atomic models. For the accurate reproduction of the experimental data, it was important to model correctly the histone tails, which are not observed in the X-ray crystal structure., 日本生物物理学会第55回年会

Published
2017

39. Synthetic Posttranslational Modifications: Chemical Catalyst-Driven Regioselective Histone Acylation of Native Chromatin

Author

Amamoto, Yoshifumi, primary, Aoi, Yuki, additional, Nagashima, Nozomu, additional, Suto, Hiroki, additional, Yoshidome, Daisuke, additional, Arimura, Yasuhiro, additional, Osakabe, Akihisa, additional, Kato, Daiki, additional, Kurumizaka, Hitoshi, additional, Kawashima, Shigehiro A., additional, Yamatsugu, Kenzo, additional, and Kanai, Motomu, additional

Published
2017
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40. Crystal Structure and Characterization of Novel Human Histone H3 Variants, H3.6, H3.7, and H3.8

Author

Taguchi, Hiroyuki, primary, Xie, Yan, additional, Horikoshi, Naoki, additional, Maehara, Kazumitsu, additional, Harada, Akihito, additional, Nogami, Jumpei, additional, Sato, Koichi, additional, Arimura, Yasuhiro, additional, Osakabe, Akihisa, additional, Kujirai, Tomoya, additional, Iwasaki, Takeshi, additional, Semba, Yuichiro, additional, Tachibana, Taro, additional, Kimura, Hiroshi, additional, Ohkawa, Yasuyuki, additional, and Kurumizaka, Hitoshi, additional

Published
2017
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45. Correction: Corrigendum: Structural basis of a nucleosome containing histone H2A.B/H2A.Bbd that transiently associates with reorganized chromatin

Author

Arimura, Yasuhiro, primary, Kimura, Hiroshi, additional, Oda, Takashi, additional, Sato, Koichi, additional, Osakabe, Akihisa, additional, Tachiwana, Hiroaki, additional, Sato, Yuko, additional, Kinugasa, Yasuha, additional, Ikura, Tsuyoshi, additional, Sugiyama, Masaaki, additional, Sato, Mamoru, additional, and Kurumizaka, Hitoshi, additional

Published
2015
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46. Stable complex formation of CENP-B with the CENP-A nucleosome

Author

Fujita, Risa, primary, Otake, Koichiro, additional, Arimura, Yasuhiro, additional, Horikoshi, Naoki, additional, Miya, Yuta, additional, Shiga, Tatsuya, additional, Osakabe, Akihisa, additional, Tachiwana, Hiroaki, additional, Ohzeki, Jun-ichirou, additional, Larionov, Vladimir, additional, Masumoto, Hiroshi, additional, and Kurumizaka, Hitoshi, additional

Published
2015
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50. Structural basis of a nucleosome containing histone H2A.B/H2A.Bbd that transiently associates with reorganized chromatin

Author

Arimura, Yasuhiro, primary, Kimura, Hiroshi, additional, Oda, Takashi, additional, Sato, Koichi, additional, Osakabe, Akihisa, additional, Tachiwana, Hiroaki, additional, Sato, Yuko, additional, Kinugasa, Yasuha, additional, Ikura, Tsuyoshi, additional, Sugiyama, Masaaki, additional, Sato, Mamoru, additional, and Kurumizaka, Hitoshi, additional

Published
2013
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