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Kobayashi W*, Ruangroengkulrith S*, Arslantas EN, Mohanan A, Tachibana K.
Feed-forward loops by NR5A2 ensure robust gene activation during pre-implantation development.
Development. 2026, 153:dev205059. doi:10.1242/dev.205059
Kobayashi W, Michael AK, Ruangroengkulrith S, Kümmecke M, Tachibana K.
Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination.
STAR Protoc. 2025, 7:104295. doi:10.1016/j.xpro.2025.104295
Kobayashi W, Tachibana K.
CUT&Tag for Transcription Factor Binding Profiles During Mammalian Zygotic Genome Activation.
Methods Mol Biol. 2025, 2923:77-87. doi:10.1007/978-1-0716-4522-2_6
Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H.
Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site.
Nature. 2024, 628:212-220. doi:10.1038/s41586-024-07196-4
Kobayashi W, Sappler H. A, Bollschweiler D, Kümmecke M, Basquin J, Arslantas E, Ruangroengkulrith S, Hornberger R, Duderstadt K, Tachibana K.
Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by minor groove anchor competition.
Nat Struct Mol Biol. 2024, 31:757-766. doi:10.1038/s41594-024-01239-0
Gassler J*, Kobayashi W*, Gáspár I*, Ruangroengkulrith S*, Mohanan A, Gómez Hernández L, Kravchenko P, Kümmecke M, Lalic A, Rifel N, Ashburn RJ, Zaczek M, Vallot A, Cuenca Rico L, Ladstätter S, Tachibana K.
Zygotic genome activation by the totipotency pioneer factor Nr5a2.
Science. 2022, 378:1305-1315. doi:10.1126/science.abn7478
Ho CH, Takizawa Y, Kobayashi W, Arimura Y, Kimura H, Kurumizaka H.
Structural basis of nucleosomal histone H4 lysine 20 methylation by SET8 methyltransferase.
Life Sci Alliance. 2021, 4:e202000919. doi:10.26508/lsa.202000919
Kobayashi W, Tachibana K.
Awakening of the zygotic genome by pioneer transcription factors.
Curr Opin Struct Biol. 2021, 71:94-100. doi:10.1016/j.sbi.2021.05.013
Takizawa Y, Ho CH, Tachiwana H, Matsunami H, Kobayashi W, Suzuki M, Arimura Y, Hori T, Fukagawa T, Ohi MD, Wolf M, Kurumizaka H.
Cryo-EM Structures of Centromeric Tri-nucleosomes Containing a Central CENP-A Nucleosome.
Structure. 2020, 28:44-53.e4. doi:10.1016/j.str.2019.10.016
Kobayashi W, Kurumizaka H.
Structural transition of the nucleosome during chromatin remodeling and transcription.
Curr Opin Struct Biol. 2019, 59:107-114. doi:10.1016/j.sbi.2019.07.011
Kobayashi W, Takizawa Y, Aihara M, Negishi L, Ishii H, Kurumizaka H.
Structural and biochemical analyses of the nuclear pore complex component ELYS identify residues responsible for nucleosome binding.
Commun Biol. 2019, 2:163. doi:10.1038/s42003-019-0385-7
Kobayashi W, Liu E, Ishii H, Matsunaga S, Schlögelhofer P, Kurumizaka H.
Homologous pairing activities of Arabidopsis thaliana RAD51 and DMC1.
J. Biochem. 2019, 165:289-295. doi:10.1093/jb/mvy105
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.
Cancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome.
Nucleic Acids Res. 2018, 46:10007-10018. doi:10.1093/nar/gky661
Osakabe A, Lorkovic ZJ, Kobayashi W, Tachiwana H, Yelagandula R, Kurumizaka H, Berger F.
Histone H2A variants confer specific properties to nucleosomes and impact on chromatin accessibility.
Nucleic Acids Res. 2018, 46:7675-7685. doi:10.1093/nar/gky540
Higgs MR, Sato K, Reynolds JJ, Begum S, Bayley R, Goula A, Vernet A, Paquin KL, Skalnik DG, Kobayashi W, Takata M, Howlett NG, Kurumizaka H, Kimura H, Stewart GS.
Histone Methylation by SETD1A Protects Nascent DNA through the Nucleosome Chaperone Activity of FANCD2.
Mol Cell. 2018, 71:25-41.e6. doi:10.1016/j.molcel.2018.05.018
Okamoto Y, Iwasaki WM, Kugou K, Takahashi KK, Oda A, Sato K, Kobayashi W, Kawai H, Sakasai R, Takaori-Kondo A, Yamamoto T, Kanemaki MT, Taoka M, Isobe T, Kurumizaka H, Innan H, Ohta K, Ishiai M, Takata M.
Replication stress induces accumulation of FANCD2 at central region of large fragile genes.
Nucleic Acids Res. 2018, 46(6):2932-2944. doi:10.1093/nar/gky058
Kobayashi W, Hosoya N, Machida S, Miyagawa K. and Kurumizaka H.
SYCP3 regulates strand invasion activities of RAD51 and DMC1.
Genes Cells. 2017, 22:799-809. doi:10.1111/gtc.12513
Inano S, Sato K, Katsuki Y, Kobayashi W, Tanaka H, Nakajima K, Nakada S, Miyoshi H, Knies K, Takaori-Kondo A, Schindler D, Ishiai M, Kurumizaka H, Takata M.
RFWD3-Mediated Ubiquitination Promotes Timely Removal of Both RPA and RAD51 from DNA Damage Sites to Facilitate Homologous Recombination.
Mol Cell. 2017, 66:622-634.e8. doi:10.1016/j.molcel.2017.04.022
Kakumu E, Nakanishi S, Shiratori HM, Kato A, Kobayashi W, Machida S, Yasuda T, Adachi N, Saito N, Ikura T, Kurumizaka H, Kimura H, Yokoi M, Sakai W, Sugasawa K.
Xeroderma pigmentosum group C protein interacts with histones: regulation by acetylated states of histone H3.
Genes Cells. 2017, 22:310-327. doi:10.1111/gtc.12479
Sato K, Shimomuki M, Katsuki Y, Takahashi D, Kobayashi W, Ishiai M, Miyoshi H, Takata M, Kurumizaka H.
FANCI-FANCD2 stabilizes the RAD51-DNA complex by binding RAD51 and protects the 5′-DNA end.
Nucleic Acids Res. 2016, 44:10758-10771. doi:10.1093/nar/gkw876
Kobayashi W, Takaku M, Machida S, Tachiwana H, Maehara K, Ohkawa Y, Kurumizaka H.
Chromatin architecture may dictate the target site for DMC1, but not for RAD51, during homologous pairing.
Sci Rep. 2016, 6:24228. doi:10.1038/srep24228
Kobayashi W, Sekine S, Machida S, Kurumizaka H.
Green fluorescent protein fused to the C-terminal end of RAD51 specifically interferes with secondary DNA binding by the RAD51-ssDNA complex.
Genes Genet Syst. 2014, 89:169-179. doi:10.1266/ggs.89.169
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.
Nap1 stimulates homologous recombination by RAD51 and RAD54 in higher-ordered chromatin containing histone H1.
Sci Rep. 2014, 4:4863. doi:10.1038/srep04863
Uanschou C, Ronceret A, Von Harder M, De Muyt A, Vezon D, Pereira L, Chelysheva L, Kobayashi W, Kurumizaka H, Schlögelhofer P, Grelon M.
Sufficient amounts of functional HOP2/MND1 complex promote interhomolog DNA repair but are dispensable for intersister DNA repair during meiosis in Arabidopsis.
Plant Cell. 2013, 25:4924-4940. doi:10.1105/tpc.113.118521