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- The Art of Packaging the Sperm Genome: Molecular and Structural Basis of the Histone-To-Protamine Exchange. Moritz L, Hammoud SS. Front Endocrinol (Lausanne) 13 895502 (2022)
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- Crystallographic analysis of the overlapping dinucleosome as a novel chromatin unit. Nishimura M, Nozawa K, Kurumizaka H. Biophys Physicobiol 15 251-254 (2018)
- Structural studies of functional nucleosome complexes with transacting factors. Kurumizaka H. Proc Jpn Acad Ser B Phys Biol Sci 98 1-14 (2022)
Articles citing this publication (92)
- Crystal structure of the human centromeric nucleosome containing CENP-A. Tachiwana H, Kagawa W, Shiga T, Osakabe A, Miya Y, Saito K, Hayashi-Takanaka Y, Oda T, Sato M, Park SY, Kimura H, Kurumizaka H. Nature 476 232-235 (2011)
- FACT caught in the act of manipulating the nucleosome. Liu Y, Zhou K, Zhang N, Wei H, Tan YZ, Zhang Z, Carragher B, Potter CS, D'Arcy S, Luger K. Nature 577 426-431 (2020)
- The molecular basis of tight nuclear tethering and inactivation of cGAS. Zhao B, Xu P, Rowlett CM, Jing T, Shinde O, Lei Y, West AP, Liu WR, Li P. Nature 587 673-677 (2020)
- Protein interactions, post-translational modifications and topologies in human cells. Chavez JD, Weisbrod CR, Zheng C, Eng JK, Bruce JE. Mol Cell Proteomics 12 1451-1467 (2013)
- Structures of human nucleosomes containing major histone H3 variants. Tachiwana H, Osakabe A, Shiga T, Miya Y, Kimura H, Kagawa W, Kurumizaka H. Acta Crystallogr D Biol Crystallogr 67 578-583 (2011)
- Contribution of histone N-terminal tails to the structure and stability of nucleosomes. Iwasaki W, Miya Y, Horikoshi N, Osakabe A, Taguchi H, Tachiwana H, Shibata T, Kagawa W, Kurumizaka H. FEBS Open Bio 3 363-369 (2013)
- Chd5 orchestrates chromatin remodelling during sperm development. Li W, Wu J, Kim SY, Zhao M, Hearn SA, Zhang MQ, Meistrich ML, Mills AA. Nat Commun 5 3812 (2014)
- Histone chaperone activity of Fanconi anemia proteins, FANCD2 and FANCI, is required for DNA crosslink repair. Sato K, Ishiai M, Toda K, Furukoshi S, Osakabe A, Tachiwana H, Takizawa Y, Kagawa W, Kitao H, Dohmae N, Obuse C, Kimura H, Takata M, Kurumizaka H. EMBO J 31 3524-3536 (2012)
- Environmental Susceptibility of the Sperm Epigenome During Windows of Male Germ Cell Development. Wu H, Hauser R, Krawetz SA, Pilsner JR. Curr Environ Health Rep 2 356-366 (2015)
- Mechanisms of Ubiquitin-Nucleosome Recognition and Regulation of 53BP1 Chromatin Recruitment by RNF168/169 and RAD18. Hu Q, Botuyan MV, Cui G, Zhao D, Mer G. Mol Cell 66 473-487.e9 (2017)
- Crystal structure of the overlapping dinucleosome composed of hexasome and octasome. Kato D, Osakabe A, Arimura Y, Mizukami Y, Horikoshi N, Saikusa K, Akashi S, Nishimura Y, Park SY, Nogami J, Maehara K, Ohkawa Y, Matsumoto A, Kono H, Inoue R, Sugiyama M, Kurumizaka H. Science 356 205-208 (2017)
- Cancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome. Arimura Y, Ikura M, Fujita R, Noda M, Kobayashi W, Horikoshi N, Sun J, Shi L, Kusakabe M, Harata M, Ohkawa Y, Tashiro S, Kimura H, Ikura T, Kurumizaka H. Nucleic Acids Res 46 10007-10018 (2018)
- Testis-Specific Histone Variant H3t Gene Is Essential for Entry into Spermatogenesis. Ueda J, Harada A, Urahama T, Machida S, Maehara K, Hada M, Makino Y, Nogami J, Horikoshi N, Osakabe A, Taguchi H, Tanaka H, Tachiwana H, Yao T, Yamada M, Iwamoto T, Isotani A, Ikawa M, Tachibana T, Okada Y, Kimura H, Ohkawa Y, Kurumizaka H, Yamagata K. Cell Rep 18 593-600 (2017)
- Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation. Wakamori M, Fujii Y, Suka N, Shirouzu M, Sakamoto K, Umehara T, Yokoyama S. Sci Rep 5 17204 (2015)
- N-terminal phosphorylation of HP1α increases its nucleosome-binding specificity. Nishibuchi G, Machida S, Osakabe A, Murakoshi H, Hiragami-Hamada K, Nakagawa R, Fischle W, Nishimura Y, Kurumizaka H, Tagami H, Nakayama J. Nucleic Acids Res 42 12498-12511 (2014)
- Young Genes out of the Male: An Insight from Evolutionary Age Analysis of the Pollen Transcriptome. Cui X, Lv Y, Chen M, Nikoloski Z, Twell D, Zhang D. Mol Plant 8 935-945 (2015)
- Structural basis of a nucleosome containing histone H2A.B/H2A.Bbd that transiently associates with reorganized chromatin. Arimura Y, Kimura H, Oda T, Sato K, Osakabe A, Tachiwana H, Sato Y, Kinugasa Y, Ikura T, Sugiyama M, Sato M, Kurumizaka H. Sci Rep 3 3510 (2013)
- A method for evaluating nucleosome stability with a protein-binding fluorescent dye. Taguchi H, Horikoshi N, Arimura Y, Kurumizaka H. Methods 70 119-126 (2014)
- Structural polymorphism in the L1 loop regions of human H2A.Z.1 and H2A.Z.2. Horikoshi N, Sato K, Shimada K, Arimura Y, Osakabe A, Tachiwana H, Hayashi-Takanaka Y, Iwasaki W, Kagawa W, Harata M, Kimura H, Kurumizaka H. Acta Crystallogr D Biol Crystallogr 69 2431-2439 (2013)
- Bivalent interaction of the PZP domain of BRPF1 with the nucleosome impacts chromatin dynamics and acetylation. Klein BJ, Muthurajan UM, Lalonde ME, Gibson MD, Andrews FH, Hepler M, Machida S, Yan K, Kurumizaka H, Poirier MG, Côté J, Luger K, Kutateladze TG. Nucleic Acids Res 44 472-484 (2016)
- Stable complex formation of CENP-B with the CENP-A nucleosome. Fujita R, Otake K, Arimura Y, Horikoshi N, Miya Y, Shiga T, Osakabe A, Tachiwana H, Ohzeki J, Larionov V, Masumoto H, Kurumizaka H. Nucleic Acids Res 43 4909-4922 (2015)
- Tissue-specific expression of histone H3 variants diversified after species separation. Maehara K, Harada A, Sato Y, Matsumoto M, Nakayama KI, Kimura H, Ohkawa Y. Epigenetics Chromatin 8 35 (2015)
- Comprehensive structural analysis of mutant nucleosomes containing lysine to glutamine (KQ) substitutions in the H3 and H4 histone-fold domains. Iwasaki W, Tachiwana H, Kawaguchi K, Shibata T, Kagawa W, Kurumizaka H. Biochemistry 50 7822-7832 (2011)
- Structure and function of human histone H3.Y nucleosome. Kujirai T, Horikoshi N, Sato K, Maehara K, Machida S, Osakabe A, Kimura H, Ohkawa Y, Kurumizaka H. Nucleic Acids Res 44 6127-6141 (2016)
- Histone H2A variants confer specific properties to nucleosomes and impact on chromatin accessibility. Osakabe A, Lorkovic ZJ, Kobayashi W, Tachiwana H, Yelagandula R, Kurumizaka H, Berger F. Nucleic Acids Res 46 7675-7685 (2018)
- Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis. Urahama T, Harada A, Maehara K, Horikoshi N, Sato K, Sato Y, Shiraishi K, Sugino N, Osakabe A, Tachiwana H, Kagawa W, Kimura H, Ohkawa Y, Kurumizaka H. Epigenetics Chromatin 9 2 (2016)
- The chromatin remodeler DDM1 prevents transposon mobility through deposition of histone variant H2A.W. Osakabe A, Jamge B, Axelsson E, Montgomery SA, Akimcheva S, Kuehn AL, Pisupati R, Lorković ZJ, Yelagandula R, Kakutani T, Berger F. Nat Cell Biol 23 391-400 (2021)
- Two Populations of Viral Minichromosomes Are Present in a Geminivirus-Infected Plant Showing Symptom Remission (Recovery). Ceniceros-Ojeda EA, Rodríguez-Negrete EA, Rivera-Bustamante RF. J Virol 90 3828-3838 (2016)
- Interaction of the pioneer transcription factor GATA3 with nucleosomes. Tanaka H, Takizawa Y, Takaku M, Kato D, Kumagawa Y, Grimm SA, Wade PA, Kurumizaka H. Nat Commun 11 4136 (2020)
- Structural basis of pyrimidine-pyrimidone (6-4) photoproduct recognition by UV-DDB in the nucleosome. Osakabe A, Tachiwana H, Kagawa W, Horikoshi N, Matsumoto S, Hasegawa M, Matsumoto N, Toga T, Yamamoto J, Hanaoka F, Thomä NH, Sugasawa K, Iwai S, Kurumizaka H. Sci Rep 5 16330 (2015)
- Dynamics of DOT1L localization and H3K79 methylation during meiotic prophase I in mouse spermatocytes. Ontoso D, Kauppi L, Keeney S, San-Segundo PA. Chromosoma 123 147-164 (2014)
- H3K14 ubiquitylation promotes H3K9 methylation for heterochromatin assembly. Oya E, Nakagawa R, Yoshimura Y, Tanaka M, Nishibuchi G, Machida S, Shirai A, Ekwall K, Kurumizaka H, Tagami H, Nakayama JI. EMBO Rep 20 e48111 (2019)
- The evolution and functional divergence of the histone H2B family in plants. Jiang D, Borg M, Lorković ZJ, Montgomery SA, Osakabe A, Yelagandula R, Axelsson E, Berger F. PLoS Genet 16 e1008964 (2020)
- DUX4-Induced Histone Variants H3.X and H3.Y Mark DUX4 Target Genes for Expression. Resnick R, Wong CJ, Hamm DC, Bennett SR, Skene PJ, Hake SB, Henikoff S, van der Maarel SM, Tapscott SJ. Cell Rep 29 1812-1820.e5 (2019)
- Nuclear reprogramming of sperm and somatic nuclei in eggs and oocytes. Teperek M, Miyamoto K. Reprod Med Biol 12 133-149 (2013)
- Phosphorylation of CBX2 controls its nucleosome-binding specificity. Kawaguchi T, Machida S, Kurumizaka H, Tagami H, Nakayama JI. J Biochem 162 343-355 (2017)
- Comparative analysis of histone H3 and H4 post-translational modifications of esophageal squamous cell carcinoma with different invasive capabilities. Zhang K, Li L, Zhu M, Wang G, Xie J, Zhao Y, Fan E, Xu L, Li E. J Proteomics 112 180-189 (2015)
- Comparison between the CENP-A and histone H3 structures in nucleosomes. Tachiwana H, Kagawa W, Kurumizaka H. Nucleus 3 6-11 (2012)
- Nap1 stimulates homologous recombination by RAD51 and RAD54 in higher-ordered chromatin containing histone H1. Machida S, Takaku M, Ikura M, Sun J, Suzuki H, Kobayashi W, Kinomura A, Osakabe A, Tachiwana H, Horikoshi Y, Fukuto A, Matsuda R, Ura K, Tashiro S, Ikura T, Kurumizaka H. Sci Rep 4 4863 (2014)
- The specification and global reprogramming of histone epigenetic marks during gamete formation and early embryo development in C. elegans. Samson M, Jow MM, Wong CC, Fitzpatrick C, Aslanian A, Saucedo I, Estrada R, Ito T, Park SK, Yates JR, Chu DS. PLoS Genet 10 e1004588 (2014)
- Retroviruses integrate into a shared, non-palindromic DNA motif. Kirk PD, Huvet M, Melamed A, Maertens GN, Bangham CR. Nat Microbiol 2 16212 (2016)
- Two arginine residues suppress the flexibility of nucleosomal DNA in the canonical nucleosome core. Kono H, Shirayama K, Arimura Y, Tachiwana H, Kurumizaka H. PLoS One 10 e0120635 (2015)
- Crystal structures of heterotypic nucleosomes containing histones H2A.Z and H2A. Horikoshi N, Arimura Y, Taguchi H, Kurumizaka H. Open Biol 6 160127 (2016)
- Evaluation of potential protein biomarkers in patients with high sperm DNA damage. Behrouzi B, Kenigsberg S, Alladin N, Swanson S, Zicherman J, Hong SH, Moskovtsev SI, Librach CL. Syst Biol Reprod Med 59 153-163 (2013)
- A Brownian ratchet model for DNA loop extrusion by the cohesin complex. Higashi TL, Pobegalov G, Tang M, Molodtsov MI, Uhlmann F. Elife 10 e67530 (2021)
- Structural and functional analyses of nucleosome complexes with mouse histone variants TH2a and TH2b, involved in reprogramming. Padavattan S, Shinagawa T, Hasegawa K, Kumasaka T, Ishii S, Kumarevel T. Biochem Biophys Res Commun 464 929-935 (2015)
- Distinct features of the histone core structure in nucleosomes containing the histone H2A.B variant. Sugiyama M, Arimura Y, Shirayama K, Fujita R, Oba Y, Sato N, Inoue R, Oda T, Sato M, Heenan RK, Kurumizaka H. Biophys J 106 2206-2213 (2014)
- A Basic Post-SET Extension of NSDs Is Essential for Nucleosome Binding In Vitro. Allali-Hassani A, Kuznetsova E, Hajian T, Wu H, Dombrovski L, Li Y, Gräslund S, Arrowsmith CH, Schapira M, Vedadi M. J Biomol Screen 19 928-935 (2014)
- Nap1 regulates proper CENP-B binding to nucleosomes. Tachiwana H, Miya Y, Shono N, Ohzeki J, Osakabe A, Otake K, Larionov V, Earnshaw WC, Kimura H, Masumoto H, Kurumizaka H. Nucleic Acids Res 41 2869-2880 (2013)
- The CENP-A centromere targeting domain facilitates H4K20 monomethylation in the nucleosome by structural polymorphism. Arimura Y, Tachiwana H, Takagi H, Hori T, Kimura H, Fukagawa T, Kurumizaka H. Nat Commun 10 576 (2019)
- The Tudor domain of the PHD finger protein 1 is a dual reader of lysine trimethylation at lysine 36 of histone H3 and lysine 27 of histone variant H3t. Kycia I, Kudithipudi S, Tamas R, Kungulovski G, Dhayalan A, Jeltsch A. J Mol Biol 426 1651-1660 (2014)
- Histone variant innovation in a rapidly evolving chordate lineage. Moosmann A, Campsteijn C, Jansen PW, Nasrallah C, Raasholm M, Stunnenberg HG, Thompson EM. BMC Evol Biol 11 208 (2011)
- Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA. Osakabe A, Adachi F, Arimura Y, Maehara K, Ohkawa Y, Kurumizaka H. Open Biol 5 150128 (2015)
- Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration. Harada A, Maehara K, Ono Y, Taguchi H, Yoshioka K, Kitajima Y, Xie Y, Sato Y, Iwasaki T, Nogami J, Okada S, Komatsu T, Semba Y, Takemoto T, Kimura H, Kurumizaka H, Kurumizaka H, Ohkawa Y. Nat Commun 9 1400 (2018)
- Structural basis for histone variant H3tK27me3 recognition by PHF1 and PHF19. Dong C, Nakagawa R, Oyama K, Yamamoto Y, Zhang W, Dong A, Li Y, Yoshimura Y, Kamiya H, Nakayama JI, Ueda J, Min J. Elife 9 e58675 (2020)
- Structure of human nucleosome containing the testis-specific histone variant TSH2B. Urahama T, Horikoshi N, Osakabe A, Tachiwana H, Kurumizaka H. Acta Crystallogr F Struct Biol Commun 70 444-449 (2014)
- Thermodynamic stability of histone H3 is a necessary but not sufficient driving force for its evolutionary conservation. Ramachandran S, Vogel L, Strahl BD, Dokholyan NV. PLoS Comput Biol 7 e1001042 (2011)
- Structural basis of nucleosomal histone H4 lysine 20 methylation by SET8 methyltransferase. Ho CH, Takizawa Y, Kobayashi W, Arimura Y, Kimura H, Kurumizaka H. Life Sci Alliance 4 e202000919 (2021)
- Histone variant H2A.B-H2B dimers are spontaneously exchanged with canonical H2A-H2B in the nucleosome. Hirano R, Arimura Y, Kujirai T, Shibata M, Okuda A, Morishima K, Inoue R, Sugiyama M, Kurumizaka H. Commun Biol 4 191 (2021)
- Structural Studies of Overlapping Dinucleosomes in Solution. Matsumoto A, Sugiyama M, Li Z, Martel A, Porcar L, Inoue R, Kato D, Osakabe A, Kurumizaka H, Kono H. Biophys J 118 2209-2219 (2020)
- Modeling DNA-bending in the nucleosome: role of AA periodicity. Prytkova TR, Zhu X, Widom J, Schatz GC. J Phys Chem B 115 8638-8644 (2011)
- Nuclear PKC-θ facilitates rapid transcriptional responses in human memory CD4+ T cells through p65 and H2B phosphorylation. Li J, Hardy K, Phetsouphanh C, Tu WJ, Sutcliffe EL, McCuaig R, Sutton CR, Zafar A, Munier CM, Zaunders JJ, Xu Y, Theodoratos A, Tan A, Lim PS, Knaute T, Masch A, Zerweck J, Brezar V, Milburn PJ, Dunn J, Casarotto MG, Turner SJ, Seddiki N, Kelleher AD, Rao S. J Cell Sci 129 2448-2461 (2016)
- Structural and biochemical analyses of the nuclear pore complex component ELYS identify residues responsible for nucleosome binding. Kobayashi W, Takizawa Y, Aihara M, Negishi L, Ishii H, Kurumizaka H. Commun Biol 2 163 (2019)
- The role of histone tails in nucleosome stability: An electrostatic perspective. Bendandi A, Patelli AS, Diaspro A, Rocchia W. Comput Struct Biotechnol J 18 2799-2809 (2020)
- FLASH/casp8ap2 is indispensable for early embryogenesis but dispensable for proliferation and differentiation of ES cells. Minamida Y, Someda M, Yonehara S. PLoS One 9 e108032 (2014)
- MNase, as a probe to study the sequence-dependent site exposures in the +1 nucleosomes of yeast. Luo D, Kato D, Nogami J, Ohkawa Y, Kurumizaka H, Kono H. Nucleic Acids Res 46 7124-7137 (2018)
- Structural analyses of the nucleosome complexes with human testis-specific histone variants, hTh2a and hTh2b. Padavattan S, Thiruselvam V, Shinagawa T, Hasegawa K, Kumasaka T, Ishii S, Kumarevel T. Biophys Chem 221 41-48 (2017)
- Chromatin architecture may dictate the target site for DMC1, but not for RAD51, during homologous pairing. Kobayashi W, Takaku M, Machida S, Tachiwana H, Maehara K, Ohkawa Y, Kurumizaka H. Sci Rep 6 24228 (2016)
- Mitotic phosphorylation of HP1α regulates its cell cycle-dependent chromatin binding. Nishibuchi G, Machida S, Nakagawa R, Yoshimura Y, Hiragami-Hamada K, Abe Y, Kurumizaka H, Tagami H, Nakayama JI. J Biochem 165 433-446 (2019)
- Molecular mechanism of histone variant H2A.B on stability and assembly of nucleosome and chromatin structures. Peng J, Yuan C, Hua X, Zhang Z. Epigenetics Chromatin 13 28 (2020)
- Polymorphism of apyrimidinic DNA structures in the nucleosome. Osakabe A, Arimura Y, Matsumoto S, Horikoshi N, Sugasawa K, Kurumizaka H. Sci Rep 7 41783 (2017)
- The N-terminal and C-terminal halves of histone H2A.Z independently function in nucleosome positioning and stability. Sato S, Tanaka N, Arimura Y, Kujirai T, Kurumizaka H. Genes Cells 25 538-546 (2020)
- Influence of polynucleosome preparation methods on sedimentation velocity analysis of chromatin. Kujirai T, Machida S, Osakabe A, Kurumizaka H. J Biochem 161 381-388 (2017)
- In vitro reconstitution and biochemical analyses of the Schizosaccharomyces pombe nucleosome. Koyama M, Nagakura W, Tanaka H, Kujirai T, Chikashige Y, Haraguchi T, Hiraoka Y, Kurumizaka H. Biochem Biophys Res Commun 482 896-901 (2017)
- Nucleosome destabilization by nuclear non-coding RNAs. Fujita R, Yamamoto T, Arimura Y, Fujiwara S, Tachiwana H, Ichikawa Y, Sakata Y, Yang L, Maruyama R, Hamada M, Nakao M, Saitoh N, Kurumizaka H. Commun Biol 3 60 (2020)
- Biochemical characterization of the placeholder nucleosome for DNA hypomethylation maintenance. Hirano R, Kujirai T, Negishi L, Kurumizaka H. Biochem Biophys Rep 18 100634 (2019)
- Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS. Papanastasiou M, Mullahoo J, DeRuff KC, Bajrami B, Karageorgos I, Johnston SE, Peckner R, Myers SA, Carr SA, Jaffe JD. Mol Cell Proteomics 18 2089-2098 (2019)
- Crosstalk between H2A variant-specific modifications impacts vital cell functions. Schmücker A, Lei B, Lorković ZJ, Capella M, Braun S, Bourguet P, Mathieu O, Mechtler K, Berger F. PLoS Genet 17 e1009601 (2021)
- Defective FANCI binding by a fanconi anemia-related FANCD2 mutant. Sato K, Ishiai M, Takata M, Kurumizaka H. PLoS One 9 e114752 (2014)
- Identification of the amino acid residues responsible for stable nucleosome formation by histone H3.Y. Kujirai T, Horikoshi N, Xie Y, Taguchi H, Kurumizaka H. Nucleus 8 239-248 (2017)
- Chromatin structure-dependent histone incorporation revealed by a genome-wide deposition assay. Tachiwana H, Dacher M, Maehara K, Harada A, Seto Y, Katayama R, Ohkawa Y, Kimura H, Kurumizaka H, Saitoh N. Elife 10 e66290 (2021)
- Combination of coarse-grained molecular dynamics simulations and small-angle X-ray scattering experiments. Ekimoto T, Kokabu Y, Oroguchi T, Ikeguchi M. Biophys Physicobiol 16 377-390 (2019)
- Unusual nucleosome formation and transcriptome influence by the histone H3mm18 variant. Hirai S, Tomimatsu K, Miyawaki-Kuwakado A, Takizawa Y, Komatsu T, Tachibana T, Fukushima Y, Takeda Y, Negishi L, Kujirai T, Koyama M, Ohkawa Y, Kurumizaka H. Nucleic Acids Res 50 72-91 (2022)
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