Research activity information

• Jan. 2024 神戸大学, 神戸大学自然科学系長賞


• Sep. 2016 第89回日本生化学会大会 若手優秀発表賞

  共同研究・競争的資金等の業績IDIRI


• Jul. 2016 クロマチン動構造ワークショップ 優秀発表賞

  共同研究・競争的資金等の業績IDIRI

• ヌクレオチド除去修復のDNA損傷認識を制御するクロマチンダイナミクス

  日下部将之, 菅澤 薫

  Feb. 2025, 生化学, 97(1) (1), 61 - 65, Japanese

  [Refereed]

  Scientific journal


• Epigenetic modulation via the C-terminal tail of H2A.Z.

  László Imre, Péter Nánási Jr, Ibtissem Benhamza, Kata Nóra Enyedi, Gábor Mocsár, Rosevalentine Bosire, Éva Hegedüs, Erfaneh Firouzi Niaki, Ágota Csóti, Zsuzsanna Darula, Éva Csősz, Szilárd Póliska, Beáta Scholtz, Gábor Mező, Zsolt Bacsó, H T Marc Timmers, Masayuki Kusakabe, Margit Balázs, György Vámosi, Juan Ausio, Peter Cheung, Katalin Tóth, David Tremethick, Masahiko Harata, Gábor Szabó

  H2A.Z-nucleosomes are present in both euchromatin and heterochromatin and it has proven difficult to interpret their disparate roles in the context of their stability features. Using an in situ assay of nucleosome stability and DT40 cells expressing engineered forms of the histone variant we show that native H2A.Z, but not C-terminally truncated H2A.Z (H2A.Z∆C), is released from nucleosomes of peripheral heterochromatin at unusually high salt concentrations. H2A.Z and H3K9me3 landscapes are reorganized in H2A.Z∆C-nuclei and overall sensitivity of chromatin to nucleases is increased. These tail-dependent differences are recapitulated upon treatment of HeLa nuclei with the H2A.Z-tail-peptide (C9), with MNase sensitivity being increased genome-wide. Fluorescence correlation spectroscopy revealed C9 binding to reconstituted nucleosomes. When introduced into live cells, C9 elicited chromatin reorganization, overall nucleosome destabilization and changes in gene expression. Thus, H2A.Z-nucleosomes influence global chromatin architecture in a tail-dependent manner, what can be modulated by introducing the tail-peptide into live cells.

  Oct. 2024, Nature communications, 15(1) (1), 9171 - 9171, English, International magazine

  [Refereed]

  Scientific journal


• Fluorescence-microscopy-based assay assessing regulatory mechanisms of global genome nucleotide excision repair in cultured cells.

  Masayuki Kusakabe, Kaoru Sugasawa

  It remains uncertain how global genome nucleotide excision repair (GG-NER) efficiently removes various helix distorting DNA lesions in the cell nucleus. Here, we present a protocol to assess the contribution of factors of interest to GG-NER using two types of fluorescence-microscopy-based techniques. First, we describe steps for analyzing the localization of the factors upon local ultraviolet (UV) irradiation. We then detail the second technique, which quantifies the removal of UV-induced photolesions combined with lesion-specific antibodies and program-based image analysis. For complete details on the use and execution of this protocol, please refer to Kusakabe et al.1.

  Lead, Jun. 2023, STAR protocols, 4(3) (3), 102378 - 102378, English, International magazine

  [Refereed]

  Scientific journal

  Link to Kobe Univ. Repository (Kernel)


• Histone deacetylation regulates nucleotide excision repair through an interaction with the XPC protein.

  Masayuki Kusakabe, Erina Kakumu, Fumika Kurihara, Kazuki Tsuchida, Takumi Maeda, Haruto Tada, Kanako Kusao, Akari Kato, Takeshi Yasuda, Tomonari Matsuda, Mitsuyoshi Nakao, Masayuki Yokoi, Wataru Sakai, Kaoru Sugasawa

  The XPC protein complex plays a central role in DNA lesion recognition for global genome nucleotide excision repair (GG-NER). Lesion recognition can be accomplished in either a UV-DDB-dependent or -independent manner; however, it is unclear how these sub-pathways are regulated in chromatin. Here, we show that histone deacetylases 1 and 2 facilitate UV-DDB-independent recruitment of XPC to DNA damage by inducing histone deacetylation. XPC localizes to hypoacetylated chromatin domains in a DNA damage-independent manner, mediated by its structurally disordered middle (M) region. The M region interacts directly with the N-terminal tail of histone H3, an interaction compromised by H3 acetylation. Although the M region is dispensable for in vitro NER, it promotes DNA damage removal by GG-NER in vivo, particularly in the absence of UV-DDB. We propose that histone deacetylation around DNA damage facilitates the recruitment of XPC through the M region, contributing to efficient lesion recognition and initiation of GG-NER.

  Lead, Apr. 2022, iScience, 25(4) (4), 104040 - 104040, English, International magazine

  [Refereed]

  Scientific journal

  Link to Kobe Univ. Repository (Kernel)


• Analysis of the molecular evolution of histone variant H2A.Z using a linker-mediated complex strategy and yeast genetic complementation.

  Saho Kitagawa, Masayuki Kusakabe, Daisuke Takahashi, Takumi Narimiya, Yu Nakabayashi, Masayuki Seki, Chihiro Horigome, Masahiko Harata

  The histone variant H2A.Z is deposited into chromatin by specific machinery and is required for genome functions. Using a linker-mediated complex strategy combined with yeast genetic complementation, we demonstrate evolutionary conservation of H2A.Z together with its chromatin incorporation and functions. This approach is applicable to the evolutionary analyses of proteins that form complexes with interactors.

  Dec. 2021, Bioscience, biotechnology, and biochemistry, 86(1) (1), 104 - 108, English, International magazine

  [Refereed]

  Scientific journal


• Functional impacts of the ubiquitin-proteasome system on DNA damage recognition in global genome nucleotide excision repair.

  Wataru Sakai, Mayumi Yuasa-Sunagawa, Masayuki Kusakabe, Aiko Kishimoto, Takeshi Matsui, Yuki Kaneko, Jun-Ichi Akagi, Nicolas Huyghe, Masae Ikura, Tsuyoshi Ikura, Fumio Hanaoka, Masayuki Yokoi, Kaoru Sugasawa

  The ubiquitin-proteasome system (UPS) plays crucial roles in regulation of various biological processes, including DNA repair. In mammalian global genome nucleotide excision repair (GG-NER), activation of the DDB2-associated ubiquitin ligase upon UV-induced DNA damage is necessary for efficient recognition of lesions. To date, however, the precise roles of UPS in GG-NER remain incompletely understood. Here, we show that the proteasome subunit PSMD14 and the UPS shuttle factor RAD23B can be recruited to sites with UV-induced photolesions even in the absence of XPC, suggesting that proteolysis occurs at DNA damage sites. Unexpectedly, sustained inhibition of proteasome activity results in aggregation of PSMD14 (presumably with other proteasome components) at the periphery of nucleoli, by which DDB2 is immobilized and sequestered from its lesion recognition functions. Although depletion of PSMD14 alleviates such DDB2 immobilization induced by proteasome inhibitors, recruitment of DDB2 to DNA damage sites is then severely compromised in the absence of PSMD14. Because all of these proteasome dysfunctions selectively impair removal of cyclobutane pyrimidine dimers, but not (6-4) photoproducts, our results indicate that the functional integrity of the proteasome is essential for the DDB2-mediated lesion recognition sub-pathway, but not for GG-NER initiated through direct lesion recognition by XPC.

  Nov. 2020, Scientific reports, 10(1) (1), 19704 - 19704, English, International magazine

  [Refereed]

  Scientific journal

  Link to Kobe Univ. Repository (Kernel)


• K-3. Molecular evolution of the histone variant H2A.Z

  Saho Kitagawa, Masayuki Kusakabe, Hi-Royuki Oku, Daisuke Takahashi, Takumi Narimiya, Yu Nakabayashi, Masayuki Seki, Masahiko Harata

  National Academy of Sciences of Ukraine, 2019, Biopolymers and Cell, 35(3) (3), 217 - 218, English

  Scientific journal


• Common and distinct roles of the isoforms of histone variant H2A.Z in transcriptional regulation

  Daisuke Takahashi, Noboru Ogihara, Ma-Sayuki Kusakabe, Saho Kitagawa, Yukako Oma, Masahiko Harata

  National Academy of Sciences of Ukraine, 2019, Biopolymers and Cell, 35(3) (3), 197, English

  Scientific journal


• Mechanism and regulation of DNA damage recognition in nucleotide excision repair.

  Masayuki Kusakabe, Yuki Onishi, Haruto Tada, Fumika Kurihara, Kanako Kusao, Mari Furukawa, Shigenori Iwai, Masayuki Yokoi, Wataru Sakai, Kaoru Sugasawa

  Nucleotide excision repair (NER) is a versatile DNA repair pathway, which can remove an extremely broad range of base lesions from the genome. In mammalian global genomic NER, the XPC protein complex initiates the repair reaction by recognizing sites of DNA damage, and this depends on detection of disrupted/destabilized base pairs within the DNA duplex. A model has been proposed that XPC first interacts with unpaired bases and then the XPD ATPase/helicase in concert with XPA verifies the presence of a relevant lesion by scanning a DNA strand in 5'-3' direction. Such multi-step strategy for damage recognition would contribute to achieve both versatility and accuracy of the NER system at substantially high levels. In addition, recognition of ultraviolet light (UV)-induced DNA photolesions is facilitated by the UV-damaged DNA-binding protein complex (UV-DDB), which not only promotes recruitment of XPC to the damage sites, but also may contribute to remodeling of chromatin structures such that the DNA lesions gain access to XPC and the following repair proteins. Even in the absence of UV-DDB, however, certain types of histone modifications and/or chromatin remodeling could occur, which eventually enable XPC to find sites with DNA lesions. Exploration of novel factors involved in regulation of the DNA damage recognition process is now ongoing.

  Lead, 2019, Genes and environment : the official journal of the Japanese Environmental Mutagen Society, 41, 2 - 2, English, International magazine

  [Refereed]

  Scientific journal

  Link to Kobe Univ. Repository (Kernel)


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

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

  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.

  Nov. 2018, Nucleic acids research, 46(19) (19), 10007 - 10018, English, International magazine

  [Refereed]

  Scientific journal


• SUMO modification system facilitates the exchange of histone variant H2A.Z-2 at DNA damage sites.

  Atsuhiko Fukuto, Masae Ikura, Tsuyoshi Ikura, Jiying Sun, Yasunori Horikoshi, Hiroki Shima, Kazuhiko Igarashi, Masayuki Kusakabe, Masahiko Harata, Naoki Horikoshi, Hitoshi Kurumizaka, Yoshiaki Kiuchi, Satoshi Tashiro

  Histone exchange and histone post-translational modifications play important roles in the regulation of DNA metabolism, by re-organizing the chromatin configuration. We previously demonstrated that the histone variant H2A.Z-2 is rapidly exchanged at damaged sites after DNA double strand break induction in human cells. In yeast, the small ubiquitin-like modifier (SUMO) modification of H2A.Z is involved in the DNA damage response. However, whether the SUMO modification regulates the exchange of human H2A.Z-2 at DNA damage sites remains unclear. Here, we show that H2A.Z-2 is SUMOylated in a damage-dependent manner, and the SUMOylation of H2A.Z-2 is suppressed by the depletion of the SUMO E3 ligase, PIAS4. Moreover, PIAS4 depletion represses the incorporation and eviction of H2A.Z-2 at damaged sites. These findings demonstrate that the PIAS4-mediated SUMOylation regulates the exchange of H2A.Z-2 at DNA damage sites.

  Jan. 2018, Nucleus (Austin, Tex.), 9(1) (1), 87 - 94, English, International magazine

  [Refereed]

  Scientific journal


• Quantitative regulation of histone variant H2A.Z during cell cycle by ubiquitin proteasome system and SUMO-targeted ubiquitin ligases.

  Daisuke Takahashi, Yuki Orihara, Saho Kitagawa, Masayuki Kusakabe, Takahiro Shintani, Yukako Oma, Masahiko Harata

  Quantitative control of histones and histone variants during cell cycle is relevant to their epigenetic functions. We found that the level of yeast histone variant H2A.Z in the G2/M-phase is actively kept low by the ubiquitin proteasome system and SUMO-targeted ubiquitin ligases. Overexpression of H2A.Z induced defects in mitotic progression, suggesting functional importance of this quantitative control.

  Aug. 2017, Bioscience, biotechnology, and biochemistry, 81(8) (8), 1557 - 1560, English, International magazine

  [Refereed]

  Scientific journal


• Multivalent binding of PWWP2A to H2A.Z regulates mitosis and neural crest differentiation.

  Sebastian Pünzeler, Stephanie Link, Gabriele Wagner, Eva C Keilhauer, Nina Kronbeck, Ramona Mm Spitzer, Susanne Leidescher, Yolanda Markaki, Edith Mentele, Catherine Regnard, Katrin Schneider, Daisuke Takahashi, Masayuki Kusakabe, Chiara Vardabasso, Lisa M Zink, Tobias Straub, Emily Bernstein, Masahiko Harata, Heinrich Leonhardt, Matthias Mann, Ralph Aw Rupp, Sandra B Hake

  Replacement of canonical histones with specialized histone variants promotes altering of chromatin structure and function. The essential histone variant H2A.Z affects various DNA-based processes via poorly understood mechanisms. Here, we determine the comprehensive interactome of H2A.Z and identify PWWP2A as a novel H2A.Z-nucleosome binder. PWWP2A is a functionally uncharacterized, vertebrate-specific protein that binds very tightly to chromatin through a concerted multivalent binding mode. Two internal protein regions mediate H2A.Z-specificity and nucleosome interaction, whereas the PWWP domain exhibits direct DNA binding. Genome-wide mapping reveals that PWWP2A binds selectively to H2A.Z-containing nucleosomes with strong preference for promoters of highly transcribed genes. In human cells, its depletion affects gene expression and impairs proliferation via a mitotic delay. While PWWP2A does not influence H2A.Z occupancy, the C-terminal tail of H2A.Z is one important mediator to recruit PWWP2A to chromatin. Knockdown of PWWP2A in Xenopus results in severe cranial facial defects, arising from neural crest cell differentiation and migration problems. Thus, PWWP2A is a novel H2A.Z-specific multivalent chromatin binder providing a surprising link between H2A.Z, chromosome segregation, and organ development.

  Aug. 2017, The EMBO journal, 36(15) (15), 2263 - 2279, English, International magazine

  [Refereed]

  Scientific journal


• Genetic complementation analysis showed distinct contributions of the N-terminal tail of H2A.Z to epigenetic regulations.

  Masayuki Kusakabe, Hiroyuki Oku, Ryo Matsuda, Tetsuya Hori, Akihiko Muto, Kazuhiko Igarashi, Tatsuo Fukagawa, Masahiko Harata

  H2A.Z is one of the most evolutionally conserved histone variants. In vertebrates, this histone variant has two isoforms, H2A.Z.1 and H2A.Z.2, each of which is coded by an individual gene. H2A.Z is involved in multiple epigenetic regulations, and in humans, it also has relevance to carcinogenesis. In this study, we used the H2A.Z DKO cells, in which both H2A.Z isoform genes could be inducibly knocked out, for the functional analysis of H2A.Z by a genetic complementation assay, as the first example of its kind in vertebrates. Ectopically expressed wild-type H2A.Z and two N-terminal mutants, a nonacetylable H2A.Z mutant and a chimera in which the N-terminal tail of H2A.Z.1 was replaced with that of the canonical H2A, complemented the mitotic defects of H2A.Z DKO cells similarly, suggesting that both acetylation and distinctive sequence of the N-terminal tail of H2A.Z are not required for mitotic progression. In contrast, each one of these three forms of H2A.Z complemented the transcriptional defects of H2A.Z DKO cells differently. These results suggest that the N-terminal tail of vertebrate H2A.Z makes distinctively different contributions to these epigenetic events. Our results also imply that this genetic complementation system is a novel and useful tool for the functional analysis of H2A.Z.

  Lead, Feb. 2016, Genes to cells : devoted to molecular & cellular mechanisms, 21(2) (2), 122 - 35, English, International magazine

  [Refereed]

  Scientific journal


• Reorganization of damaged chromatin by the exchange of histone variant H2A.Z-2.

  Ikuno Nishibuchi, Hidekazu Suzuki, Aiko Kinomura, Jiying Sun, Ning-Ang Liu, Yasunori Horikoshi, Hiroki Shima, Masayuki Kusakabe, Masahiko Harata, Tatsuo Fukagawa, Tsuyoshi Ikura, Takafumi Ishida, Yasushi Nagata, Satoshi Tashiro

  PURPOSE: The reorganization of damaged chromatin plays an important role in the regulation of the DNA damage response. A recent study revealed the presence of 2 vertebrate H2A.Z isoforms, H2A.Z-1 and H2A.Z-2. However, the roles of the vertebrate H2A.Z isoforms are still unclear. Thus, in this study we examined the roles of the vertebrate H2A.Z isoforms in chromatin reorganization after the induction of DNA double-strand breaks (DSBs). METHODS AND MATERIALS: To examine the dynamics of H2A.Z isoforms at damaged sites, we constructed GM0637 cells stably expressing each of the green fluorescent protein (GFP)-labeled H2A.Z isoforms, and performed fluorescence recovery after photobleaching (FRAP) analysis and inverted FRAP analysis in combination with microirradiation. Immunofluorescence staining using an anti-RAD51 antibody was performed to study the kinetics of RAD51 foci formation after 2-Gy irradiation of wild-type (WT), H2A.Z-1- and H2A.Z-2-deficient DT40 cells. Colony-forming assays were also performed to compare the survival rates of WT, H2A.Z-1-, and H2A.Z-2-deficient DT40 cells with control, and H2A.Z-1- and H2A.Z-2-depleted U2OS cells after irradiation. RESULTS: FRAP analysis revealed that H2A.Z-2 was incorporated into damaged chromatin just after the induction of DSBs, whereas H2A.Z-1 remained essentially unchanged. Inverted FRAP analysis showed that H2A.Z-2 was released from damaged chromatin. These findings indicated that H2A.Z-2 was exchanged at DSB sites immediately after the induction of DSBs. RAD51 focus formation after ionizing irradiation was disturbed in H2A.Z-2-deficient DT40 cells but not in H2A.Z-1-deficient cells. The survival rate of H2A.Z-2-deficient cells after irradiation was lower than those of WT and H2A.Z-1- DT40 cells. Similar to DT40 cells, H2A.Z-2-depleted U2OS cells were also radiation-sensitive compared to control and H2A.Z-1-depleted cells. CONCLUSIONS: We found that vertebrate H2A.Z-2 is involved in the regulation of the DNA damage response at a very early stage, via the damaged chromatin reorganization required for RAD51 focus formation.

  Jul. 2014, International journal of radiation oncology, biology, physics, 89(4) (4), 736 - 44, English, International magazine

  [Refereed]

  Scientific journal

• 細胞周期におけるヒストンバリアントH2A.Zの量的制御と染色体分配への関与

  高橋大輔, 日下部将之, 北川紗帆, 尾間由佳子, 原田昌彦

  生命科学系学会合同年次大会運営事務局, Dec. 2017, 日本生化学会大会(Web), 90th, ROMBUNNO.1P‐0651 (WEB ONLY) - 0651], Japanese


• 核構造タンパク質によるクロマチン時空間制御の理解とマニピュレーション introduction アクチンファミリーによる細胞核とクロマチンの機能構造制御

  原田 昌彦, 山崎 祥他, 日下部 将之, 高橋 裕一朗, 尾間 由佳子

  (公社)日本生化学会, Oct. 2014, 日本生化学会大会プログラム・講演要旨集, 87回, [4S12p - 1], Japanese

• DNA damage surveillance mechanism of nucleotide excision repair in vivo

  Masayuki Kusakabe, Kaoru Sugasawa

  Joint work, (株)羊土社, Aug. 2022, Japanese, ISBN: 9784758104043

  [Refereed]

• DNA の構造的要因から探るヌクレオチド除去修復制御機構

  古園英嗣, 松山宏生, 多田遥人, 日下部将之, 松本翔太, 鯨井智也, 越後谷健太, 胡桃坂仁志, 菅澤薫

  第42回染色体ワークショップ・第23回核ダイナミクス研究会, Jan. 2025, Japanese

  Poster presentation


• CRL4Cdt2のDNA合成部位への適切な集積と解離が細胞周期進行を制御する

  戸次龍哉, 日下部将之, 上野晃子, 塩見泰史, 菅澤薫, 林晃世, 西谷秀男

  第47回日本分子生物学会年会, Nov. 2024, Japanese

  Poster presentation


• ヌクレオチド除去修復のDNA損傷認識制御におけるヒストン修飾の役割

  綿田瑞希, 日下部将之, 前田拓海, 各務恵理菜, 横井雅幸, 酒井恒, 菅澤薫

  第47回日本分子生物学会年会, Nov. 2024, Japanese

  Poster presentation


• ヌクレオチド除去修復のDNA損傷認識を制御するクロマチン構造変換機構

  藤原叶枝, 槌田千輝, 日下部将之, 草尾佳那子, 八鍬聖, 横井雅幸, 酒井恒, 菅澤薫

  第47回日本分子生物学会年会, Nov. 2024, Japanese

  Poster presentation


• The involvement of chromatin remodeling factor SMACRAD1 in response to DNA double strand breaks

  Miou Takasu, Masayuki Kusanabe, Atsushi Shibata, Wataru Sakai, Kaoru Sugasawa, Masayuki Yokoi

  The12th 3R+3C International Symposium, Nov. 2024, English

  Poster presentation


• Impact of histone modifications on damage recognition process of global genome nucleotide excision repair

  Masayuki Kusakabe, Mizuki Watada, Takumi Maeda, Erina Kakumu, Kanae Fujiwara, Mizuki Otobe, Wataru Sakai, Masayuki Yokoi, Kaoru Sugasawa

  The12th 3R+3C International Symposium, Nov. 2024, English

  Poster presentation


• Cooperation of Cdt2 C-terminal motifs in regulating CRL4Cdt2 dynamics at the DNA replication site

  Akiyo Hayashi, Tatsuya Bekki, Masayuki Kusanabe, Akiko Ueno, Yasushi Shiomi, Kaoru Sugasawa, Hideo Nishitani

  The12th 3R+3C International Symposium, Nov. 2024, English

  Poster presentation


• Effects of DNA substrate structures on lesion excision by nucleotide excision repair in vitro

  Hidetsugu Kozono, Hiroo Matsuyama, Haruto Tada, Masayuki Kusakabe, Syota Matsumoto, Tomoya Kujirai, Kenta Echigoya, Hitoshi Kurumizaka, Kaoru Sugasawa

  The12th 3R+3C International Symposium, Nov. 2024, English

  Poster presentation


• Roles of histone modifications in regulation of damage recognition process of nucleotide excision repair

  Masayuki KUSAKAB, Mizuki WATADA, Takumi MAEDA, Erina KAKUMU, Kanae FUJIWARA, Mei TAGUCHI, Wataru SAKAI, Masayuki YOKOI, Kaoru SUGASAWA

  The 67th Annual Meeting of the Japanese Radiation Research Society, Sep. 2024, Japanese

  [Invited]

  Invited oral presentation


• Molecular mechanism that regulates DNA damage recognition in nucleotide excision repair

  Hidetsugu KOZONO, Hiroo MATSUYAMA, Haruto TADA, Masayuki KUSAKABE, Syota MATSUMOTO, Tomoya KUJIRAI, Kenta ECHIGOYA, Hitoshi KURUMIZAKA, Kaoru SUGASAWA

  The 67th Annual Meeting of the Japanese Radiation Research Society, Sep. 2024, Japanese

  [Invited]

  Invited oral presentation


• 損傷クロマチン基質を用いたヌクレオチド除去修復制御機構の生化学的解析

  古園英嗣, 多田遥人, 日下部将之, 松本翔太, 横井雅幸, 酒井 恒, 鯨井智也, 胡桃坂仁志, 菅澤 薫

  第41回染色体ワークショップ・第22回核ダイナミクス研究会, Jan. 2024, Japanese

  Poster presentation


• ヌクレオチド除去修復の損傷監視制御におけるヒストン修飾の役割

  日下部将之, 綿田瑞希, 前田拓海, 各務恵理菜, 藤原叶枝, 乙部瑞貴, 酒井 恒, 横井雅幸, 菅澤 薫

  第41回染色体ワークショップ・第22回核ダイナミクス研究会, Jan. 2024, Japanese

  Oral presentation


• ヌクレオチド除去修復のDNA損傷認識制御におけるヒストンH3K9メチル化修飾の役割

  綿田瑞希, 日下部将之, 前田拓海, 各務恵理菜, 横井雅幸, 酒井 恒, 菅澤 薫

  第46回日本分子生物学会年会, Dec. 2023, Japanese

  Poster presentation


• 紫外線誘発DNA損傷に対する細胞応答におけるクロマチンリモデリング因⼦SMARCAD1の関与

  高須美央, 坂口友美, 酒井麻衣, 鹿谷有由希, 福永 匠, 酒井 恒, 日下部将之, 菅澤 薫, 花岡文雄, 横井雅幸

  第46回日本分子生物学会年会, Dec. 2023, Japanese

  Poster presentation


• ヒストン翻訳後修飾を介したXPCタンパク質の核内局在制御

  乙部瑞貴, 日下部将之, 各務恵理菜, 槌田千輝, 塩月陽人, 酒井 恒, 横井雅幸, 菅澤 薫

  第46回日本分子生物学会年会, Dec. 2023, Japanese

  Poster presentation


• ゲノム全体を対象としたヌクレオチド除去修復の損傷認識制御におけるヒストン修飾の役割

  日下部将之, 前田拓海, 綿田瑞希, 各務恵理菜, 乙部瑞貴, 藤原叶枝, 菅澤 薫

  日本放射線影響学会第66回大会, Nov. 2023, Japanese

  Oral presentation


• 損傷クロマチン基質を用いたヌクレオチド除去修復制御機構の生化学的解析

  古園英嗣, 多田遥人, 日下部将之, 菅澤 薫

  日本遺伝学会第95回大会, Sep. 2023, Japanese

  Poster presentation


• ゲノム全体を対象としたヌクレオチド除去修復の損傷認識を制御するクロマチン動態

  日下部将之, 前田拓海, 綿田瑞希, 藤原叶枝, 各務恵理菜, 乙部瑞貴, 酒井 恒, 横井雅幸, 菅澤 薫

  第46回日本分子生物学会年会, Dec. 2023, Japanese

  Oral presentation


• ヌクレオチド除去修復のDNA損傷認識を制御するクロマチン構造変換機構

  藤原叶枝, 槌田千輝, 日下部将之, 草尾佳那子, 八鍬 聖, 酒井 恒, 横井雅幸, 菅澤 薫

  第46回日本分子生物学会年会, Jun. 2023, Japanese

  Poster presentation


• ヌクレオチド除去修復の損傷認識制御におけるヒストン修復の役割

  日下部将之, 前田拓海, 綿田瑞希, 各務恵理菜, 菅澤 薫

  第27回DNA複製・組換え・修復ワークショップ, Jun. 2023, Japanese

  Oral presentation


• Histone modifications regulating the initiation of global genome nucleotide excision repair

  Masayuki. Kusakabe, Takumi. Maeda, Erina. Kakumu, Mizuki ,Watada, Kaoru. Sugasawa

  The 19th Ataxia-Telangiectasia Workshop (ATW2023）, Mar. 2023, English

  Poster presentation


• 損傷クロマチン基質におけるヌクレオチド除去修復開始制御機構の解析

  古園英嗣, 多田遥人, 日下部将之, 菅澤 薫

  若手フロンティア研究会2022, Dec. 2022, Japanese

  Poster presentation


• ヒストン修飾を介したヌクレオチド除去修復の損傷認識促進機構

  日下部将之, 前田拓海, 各務恵理菜, 綿田瑞希, 菅澤 薫

  第45回日本分子生物学会年会, Dec. 2022, Japanese

  Poster presentation


• ヒストン修飾を介したヌクレオチド除去修復の損傷認識促進機構

  日下部将之, 前田拓海, 各務恵理菜, 綿田瑞希, 菅澤 薫

  第45回日本分子生物学会年会, Dec. 2022, Japanese

  Oral presentation


• ヌクレオチド除去修復におけるDNA損傷認識を制御するクロマチン構造変換因子複合体

  槌田千輝, 日下部将之, 各務恵理菜, 栗原文佳, 草尾佳那子, 前田拓海, 横井雅幸, 酒井 恒, 菅澤 薫

  第45回日本分子生物学会年会, Nov. 2022, Japanese

  Poster presentation


• Roles of of histone modifications in DNA damage recognition initiating global genome nucleotide excision repair

  Masayuki Kusakabe, Takumi Maeda, Erina Kakumu, Mizuki Watada, Kaoru Sugasawa

  2022 International IBS Conference for Genomic Integrity, Oct. 2022, English

  Poster presentation


• Chromatin dynamics regulating initiation of nucleotide excision repair

  Masayuki Kusakabe, Erina Kakumu, Fumika Kurihara, Kazuki Tsuchida, Takumi Maeda, Mizuki Otobe, Kaoru Sugasawa

  2022 International IBS Conference for Genomic Integrity, Oct. 2022, English

  [Invited]

  Invited oral presentation


• Chromatin dynamics regulating initiation of nucleotide excision repair

  Masayuki Kusakabe, Kaoru Sugasawa

  International Conference of the Genetics Society of Korea 2022 (ICGSK2022), Oct. 2022, English

  [Invited]

  Invited oral presentation


• Roles of of histone modifications in DNA damage recognition initiating global genome nucleotide excision repair

  Masayuki Kusakabe, Takumi Maeda, Erina Kakumu, Mizuki Watada, Kaoru Sugasawa

  International Conference of the Genetics Society of Korea 2022 (ICGSK2022), Oct. 2022, English

  Poster presentation


• Contribution of histone modifications to efficient recognition of UV-induced DNA lesions in nucleotide excision repair

  Masayuki Kusakabe, Takumi Maeda, Erina Kakumu, Mizuki Watada, Wataru Sakai, Masayuki Yokoi, Kaoru Sugasawa

  The 65th Annual Meeting of the Japanese Radiation Research Society, Sep. 2022

  Oral presentation


• Roles of histone modifications ensuring efficient recognition and repair of UV-induced DNA lesions

  Masayuki Kusakabe, Erina Kakumu, Fumika Kurihara, Kazuki Tsuchida, Haruto Tada, Takumi Maeda, Kaoru Sugasawa

  The 64th Annual Meeting of the JAPANESE RADIATION RESEARCH SOCIETY, Sep. 2021

  [Invited]

  Invited oral presentation


• Functional analysis of histone modifications regulating recognition of UV-induced DNA lesions in nucleotide excision repair

  Masayuki Kusakabe, Erina Kakumu, Manami Kobayashi, Kaoru Sugasawa

  The 62th Annual Meeting of the JAPANESE RADIATION RESEARCH SOCIETY, Nov. 2019

  [Invited]

  Invited oral presentation


• ヌクレオチド除去修復の損傷認識を制御するヒストン修飾の解析

  日下部 将之, 前田 拓海, 各務 恵理菜, 菅澤 薫

  第25回 DNA複製・組換え・修復ワークショップ, Nov. 2019

  Oral presentation


• Functional analysis of histone modification in DNA damage recognition process of nucleotide excision repair.

  Masayuki Kusakabe, Fumika Kurihara, Akari Kato, Erina Kakumu, Manami Kobayashi, Kaoru Sugasawa

  The 11th 3R&3C Symposium, Nov. 2018, English, Kanazawa Japan, International conference

  Poster presentation


• ヌクレオチド除去修復の損傷認識を制御するクロマチン構造変換機構の解明

  日下部将之, 各務恵理菜, 小林真奈美, 菅澤 薫

  第91回日本生化学会大会, Sep. 2018, Japanese, 京都, Domestic conference

  Oral presentation


• クロマチン構造を介したヌクレオチド除去修復の高次制御機構

  日下部将之, 各務恵理菜, 加藤安佳梨, 栗原文佳, 草尾佳那子, 横井雅幸, 酒井 恒, SUGASAWA KAORU

  第91回生化学会大会, Sep. 2018, Japanese, 京都, Domestic conference

  Oral presentation


• ヌクレオチド除去修復の開始を制御するクロマチン構造の役割

  KATO Akari, KAKUMU Erina, NAKANISHI Seiya, KUSAKABE Masayuki, KURIHARA Fumika, SAKAI Wataru, SUGASAWA Kaoru

  2017年度生命科学系学会合同年次大会, Dec. 2017, Japanese, 神戸国際会議場, Domestic conference

  Oral presentation


• ヌクレオチド除去修復の開始を制御するクロマチン構造の役割

  KATO Akari, KAKUMU Erina, NAKANISHI Seiya, KUSAKABE Masayuki, KURIHARA Fumika, SAKAI Wataru, SUGASAWA Kaoru

  第24回DNA複製・組換え・修復ワークショップ, Nov. 2017, Japanese, 長良川国際会議場, Domestic conference

  Oral presentation

• 日本遺伝学会

  2024 - Present


• 日本分子生物学会

  2022 - Present


• 日本放射線影響学会

  2019 - Present


• 日本生化学会

  2014 - Present

• 環境変異原によって誘発されるエピゲノム情報の変動機構

  公益財団法人 パブリックヘルスリサーチセンター, 2025年度パブリックヘルス科学研究助成金 生命医科学分野, Apr. 2025 - Mar. 2026, Principal investigator

  Competitive research funding


• Elucidating repair mechanism of benzo[a]pyrene-DNA adduct in vivo

  Smoking Research Foundation, 若手研究, Apr. 2024 - Mar. 2026, Principal investigator

  Competitive research funding


• ヌクレオチド除去修復の損傷認識を促進する新規機構の解明

  日下部 将之

  日本学術振興会, 科学研究費助成事業 若手研究, 若手研究, 神戸大学, 01 Apr. 2021 - 31 Mar. 2025

  本研究は、ゲノム全体を対象としたヌクレオチド除去修復の損傷認識因子XPCが、生体内において発生した損傷を効率よく認識するための補助機構を解明することを目的としている。代表者の所属する研究室は、DNA損傷部位のヒストン脱アセチル化を介してXPCの呼び込みが促進されることを示唆する結果を得ていた。しかし、DNA損傷部位のヒストン脱アセチル化を引き起こす因子や、XPCと低アセチル化ヒストンとの相互作用様式は明らかになっておらず、この補助機構の詳細は不明であった。代表者は脱アセチル化酵素阻害剤やsiRNAを用いた発現抑制を行い、HDAC1/2がDNA損傷部位のヒストン脱アセチル化を引き起こす因子であることを同定した。また、ヒストンが低アセチル化状態であり、DNA染色色素によって視覚化可能な高度なヘテロクロマチン構造を保有するマウス胎児由来繊維芽細胞を用いることで、XPCがヘテロクロマチンに局在することを見出した。この特徴的な局在を指標として、XPCにおけるヒストンとの相互作用領域を探索したところ、XPCの中央に存在する天然変性領域(XPC-M)が低アセチル化ヒストンとの相互作用領域であることが見出された。昆虫細胞を用いてXPC-Mを発現・精製しペプチドプルダウンアッセイを行った結果、XPC-Mは非アセチル化状態のH3テールと直接結合し、アセチル化修飾の導入によって相互作用が減弱することが見出された。さらに、XPC-Mの生理的意義を明らかにするため、XPC-Mを欠失した変異体XPCと野生型XPCを内在性XPCを欠損した細胞に発現させ、損傷部位への集積や紫外線誘発損傷の修復速度を定量したところ、変異体を発現する細胞では両定量結果ともに減弱することが示された。これらは、XPC-Mを介した非アセチル化H3との相互作用は生体内における効率的な損傷認識に重要であることを強く示唆している。


• 天然変性領域を介したDNA損傷認識機構の解明

  公益財団法人 川西記念新明和教育財団, 2023年度 研究助成金, Jun. 2023 - Mar. 2024, Principal investigator

  Competitive research funding


• エピジェネティック制御におけるヒストンバリアントH2A.Zアセチル化の機能解析

  日下部 将之

  日本学術振興会, 科学研究費助成事業 特別研究員奨励費, 特別研究員奨励費, 東北大学, Apr. 2015 - Mar. 2017

  クロマチン構造の変換には、通常のヒストンに代わってヌクレオソーム中に導入されるヒストンバリアントが重要な枠割を果たすことが知られている。ヒストンバリアントH2A.Zは酵母からヒトにまで進化的に高度に保存されたヒストンバリアントであり、生物学的に重要な機能を持つと考えられている。これまでの研究により、H2A.ZのN末端ヒストンテールはアセチル化修飾を受けることが報告されていたが、その機能は不明であった。本研究室ではこれまでに、遺伝子破壊細胞の樹立が可能な培養細胞ニワトリDT40細胞を用いることによって、H2A.Z遺伝子破壊(H2A.Z KO)細胞を樹立した。昨年度の研究によって、H2A.Z KO細胞に対して外来生H2A.Z遺伝子を安定発現させることで、H2A.Z KO細胞の表現型を相補することを利用した「遺伝学的機能相補系」を樹立し、H2A.Zへのアセチル化修飾は転写制御特異的に寄与することを示した。本年度はこの細胞生物学的解析を用いて、H2A.Zアセチル化修飾の転写制御への寄与をさらに詳細に解析した。具体的には、野生型H2A.Z (wtH2A.Z)、アセチル化修飾の起こらないH2A.Z (5KR-H2A.Z)を安定発現するH2A.Z KO細胞を樹立し、細胞外刺激によって転写が誘導されるEGR1遺伝子に着目して解析を行った。クロマチン免疫沈降解析によりEGR1遺伝子領域のアセチル化H2A.Zの存在量を比較したところ、細胞外刺激後にアセチル化H2A.Zの存在量が増加することが示された。重要なことに、EGR1遺伝子の転写誘導はwtH2A.Z発現細胞では観察されたが、5KR-H2A.Z発現細胞では観察されなかった。これらの結果より、H2A.Zアセチル化修飾は転写誘導において重要な機能を持つことが示唆された。