Publications

• 2026
• 2025
• 2024
• 2023
• 2022
• 2021
• 2020
• 2019
• 2018
• 2017
• 2016

2026

• Yasuda Y, Hitomi K, Noda NN, Kotani T, Nakatogawa H (2026) The Atg2-Atg18 complex interacts with the Atg1 complex to localize to the pre-autophagosomal structure in Saccharomyces cerevisiae. Mol. Biol. Cell 37, ar21.
• Xu R, Tang C, Wang JN, Motooka D, Tsubouchi H, Iwasaki H, Nakagawa T (2026) Transcriptional PBR cycles at pericentromeric repeats cause gross chromosomal rearrangements through Rad52-dependent ADR-loop formation. Nucleic Acids Res. 54, gkaf1455.
• Nakayama C, Fang Q, Daigaku Y, Aoi Y, Ito S, Takahashi M, Shimatani R, Minamisawa T, Ozturk Y, Kimura H, Shilatifard A, Tellier M, Nojima T (2026) NELF prevents transcriptional readthrough into DNA replication zones in cancer cells. EMBO Rep. doi:10.1038/s44319-026-00700-z.
• Matsuda C, Ichiki A, Sato Y, Kudo Y, Saotome M, Takayama C, Le KM, Uchino S, Higuchi R, Kawata K, Tomimatsu K, Ozawa M, Ikawa M, Ohkawa Y, Baba Y, Kimura H (2026) Organization and dynamics of transcription elongation foci in mouse tissues. J. Mol. Biol. 438, 169395.
• Kotani T & Nakatogawa H (2026) Core principles of autophagy initiation mechanisms. Nat. Struct. Mol. Biol. doi:10.1038/s41594-026-01752-4.
• Kawaguchi K, Hama Y, Yoshikawa H, Nishino K, Morimoto K, Nakamura T, Koizumi M, Sakamaki Y, Abe K, Kakuta S, Ichimura K, Ikeda F, Kosako H, Fujita N (2026) Linear ubiquitination triggers Amph-mediated T-tubule biogenesis. Sci. Adv. 12, eady4934.
• Galindo G, Maejima D, DeRoo J, Burlingham SR, Fixen G, Morisaki T, Febvre HP, Hasbrook R, Zhao N, Ghosh S, Mayton EH, Snow CD, Geiss BJ, Ohkawa Y, Sato Y, Kimura H, Stasevich TJ (2026) AI-assisted protein design to rapidly convert antibody sequences to intrabodies targeting diverse peptides and histone modifications. Sci. Adv. 12, eadx8352.

2025

• Ohhashi Y, Nishinami S, Shiraki K, Chatani E & Taguchi H (2025) Low-complexity domains in phase-separated droplets suppress the amyloid formation of yeast prion Sup35. npj Biosensing 2, 13. doi:10.1038/s44328-025-00025-2.
• Kosaka N & Kimura H (2025) Techniques for investigating the effect of various wavelengths of light on the behavior of aquatic animals. Am. Biol. Teach. 87, 270–275. doi:10.1525/abt.2025.87.4-5.270.
• Yang C, Arai M, Ariyanto EF, Zhang J, Lubis DM, Ito R, Xie S, Nitta M, Kawashima F, Ishitsuka T, Yang C, Suzuki T, Komatsu T, Sagae H, Jin H, Takahashi H, Kobayashi E, Wei Y, Liu B, Choi H, Wada Y, Tanaka T, Osawa T, Kimura H, Kodama T, Aburatani H, Tachibana M, Shinkai Y, Inagaki T, Soga T, Osborne TF, Yoneshiro T, Matsumura Y, Sakai J (2025) Glucose-activated JMJD1A drives visceral adipogenesis via α-ketoglutarate-dependent chromatin remodeling. Cell Rep. 44, 116060.
• Taoka H, Murakawa T, Kawaguchi K, Koizumi M, Kaminishi T, Sakamaki Y, Tanaka K, Harada A, Inoue K, Kanki T, Ohkawa Y, Fujita N (2025) Transcriptional dynamics uncover the role of BNIP3 in mitophagy during muscle remodeling in Drosophila. eLife 14, RP105834.
• Taniguchi M, Nagaya S, Kirisako H, Ohsumi Y, Nakatogawa H, Okazaki T (2025) Phagophore ceramide promotes LC3 lipidation and autophagy in T-lymphoid cell death. FASEB J. 39, e70668.
• Taniguchi G, May AI, Iwasaki H, Tsubouchi H (2025) Fission yeast Rad54 prevents intergenerational buildup of Rad51 aggregates in proliferating cells. Life Sci. Alliance 8, e202503252.
• Takeda E, May AI, Ohsumi Y (2025) Reconsidering the selectivity of bulk autophagy: cargo hitchhiking specifies cargo for degradation. Autophagy 21, 910–911.
• Sakai R, Takeda E, Kabuta C, Contu VR, Fujiwara Y, Fujikake N, Hashimoto T, Ohsumi Y, Kabuta T (2025) DHX8 regulates degradation of RNA by RNautophagy. Nucleic Acids Res. 53, gkaf801.
• Nozaki T, Onoda M, Habazaki M, Takeuchi Y, Ishida H, Sato Y, Kujirai T, Hanada K, Yamatsugu K, Kurumizaka H, Kimura H, Kono H, Kawashima SA, Kanai M (2025) Designer catalyst-enabled regiodivergent histone acetylation. J. Am. Chem. Soc. 147, 13732–13743.
• Noguchi Y, Kunishige R, Shinozaki-Narikawa N, Yamashita H, Aihara K, Murata M, Kano F (2025) Unveiling and stratifying cell cycle-dependent drug efficacy using a single-cell PLOM-CON approach with correlation anomaly and presage protein signals. Commun. Biol. 8, 1504.
• Miwa T, Taguchi H (2025) Revival of the Escherichia coli heat shock response after two decades with a small Hsp in a critical but distinct act. Biol. Chem. 406, 29–33.
• Masuda S, Komatsu T, Atia S, Suzuki T, Hayashi M, Toyoda A, Kimura H, Inagaki T (2025) Iron-dependent JMJD1A-mediated demethylation of H3K9me2 regulates gene expression during adipogenesis in a spatial genome organization-dependent manner. Genes Cells 30, e70023.
• Lin BC, Jankowska KI, Katneni UK, Amarasinghe R, Padhiar N, Hamasaki-Katagiri N, Wu WW, Zhu H, Taguchi H, Ghosh A, Holcomb DD, Phue J-N, Fumagalli SE, Freedberg DI, Kimchi O, Shen R-F, Komar AA, Sauna ZE, Kimchi-Sarfaty C (2025) Therapeutic implications of synonymous gene recoding: insights into mechanisms controlling protein biogenesis and activity. Protein Cell 16, 905–910.
• Kunishige R, Noguchi Y, Okamoto N, Li L, Ono A, Murata M, Kano F (2025) Protein covariation networks for elucidating ferroptosis inducer mechanisms and potential synergistic drug targets. Commun. Biol. 8, 480.
• Kujirai T, Echigoya K, Kishi Y, Saeki M, Ito T, Kato J, Negishi L, Kimura H, Masumoto H, Takizawa Y, Gotoh Y, Kurumizaka H (2025) Structural insights into how DEK nucleosome binding facilitates H3K27 trimethylation in chromatin. Nat. Struct. Mol. Biol. 32, 1183–1192.
• Kosaka Y, Miyawaki Y, Mori M, Aburaya S, Nishizawa C, Chujo T, Niwa T, Miyazaki T, Sugita T, Fukuyama M, Taguchi H, Tomizawa K, Sugase K, Ueda M, Aoki W (2025) Autonomous ribosome biogenesis in vitro. Nat. Commun. 16, 514.
• Ito H, Machida K, Fujino Y, Hasumi M, Sakamoto S, Nagai Y, Imataka H, Taguchi H (2025) Canonical translation factors eIF1A and eIF5B modulate the initiation step of repeat-associated non-AUG translation. Nucleic Acids Res. 53, gkaf994.
• Ikeda T, Nojima T, Yamamoto S, Yamada R, Niwa T, Konno H, Taguchi H (2025) Seesaw protein: design of a protein that adopts interconvertible alternative functional conformations and its dynamics. Proc. Natl. Acad. Sci. U.S.A. 122, e2412117122.
• Ichikawa T, Kono Y, Kudo M, Shimi T, Miyashita N, Maesaka T, Ishibashi K, Sivashanmugan K, Yoshida T, Miyazawa K, Hanayama R, Hirata E, Miyata K, Kimura H, Fukuma T (2025) Probing nanomechanics by direct indentation using nanoendoscopy-AFM reveals the nuclear elasticity transition in cancer cells. ACS Appl. Nano Mater. 8, 20239–20249.
• Ichihara K, Shiraishi T, Chadani Y, Kito Y, Shiraishi C, Hirata M, Takahashi Y, Kobo A, Hatano A, Matsumoto M, Machida K, Imataka H, Toyoda A, Mishiro-Sato E, Nojima T, Ito T, Taguchi H, Nakayama KI, Matsumoto A (2025) eIF2D promotes 40S ribosomal subunit recycling during intrinsic ribosome destabilization. Nucleic Acids Res. 53, gkaf1322.
• Hasumi M, Ito H, Machida K, Niwa T, Taminato T, Nagai Y, Imataka H, Taguchi H (2025) Dissecting the mechanism of NOP56 GGCCUG repeat-associated non-AUG translation using cell-free translation systems. J. Biol. Chem. 301, 108360.
• Fujioka Y, Tsuji T, Kotani T, Kumeta H, Kakuta C, Shimasaki J, Fujimoto T, Nakatogawa H, Noda NN (2025) Phase separation promotes Atg8 lipidation and vesicle condensation for autophagy progression. Nat. Struct. Mol. Biol. 32, 2285–2295.
• Fujii T, Tomimatsu K, Kato M, Ito M, Sato S, Kurumizaka H, Sato Y, Maehara K, Kimura H, Harada A, Ohkawa Y (2025) Reconstructing epigenomic dynamics through a single-cell multi-epigenome data integration framework. Nat. Commun. 16, 11006.
• Ando Y, Kobo A, Niwa T, Yamakawa A, Konoma S, Kobayashi Y, Nureki O, Taguchi H, Itoh Y, Chadani Y (2025) A mini-hairpin shaped nascent peptide blocks translation termination by a distinct mechanism. Nat. Commun. 16, 2323.

2024

• Machii N, Hatashima R, Niwa T, Taguchi H, Kimirei IA, Mrosso HDJ, Aibara M, Nagasawa T & Nikaido M (2024) Pronounced expression of extracellular matrix proteoglycans regulated by Wnt pathway underlies the parallel evolution of lip hypertrophy in East African cichlids. eLife 13, RP99160. doi:10.7554/eLife.99160.
• Yonezawa N, Shindo T, Oda H, Kimura H, Hiraoka Y, Haraguchi T, Yamagata K (2024) Reconstruction of artificial nuclei with nuclear import activity in living mouse oocytes. Genes Cells 29, 820–837. doi: 10.1111/gtc.13175.
• Wada S, Ideno H, Nakashima K, Komatsu K, Demura N, Tomonari H, Kimura H, Tachibana M, Nifuji A (2024) The histone H3K9 methyltransferase G9a regulates tendon formation during development. Sci. Rep. 14, 20771. doi: 10.1038/s41598-024-70742-6.
• Takeda E, Isoda T, Hosokawa S, Oikawa Y, Hotta-Ren S, May AI, Ohsumi Y (2024) Receptor-mediated cargo hitchhiking on bulk autophagy. EMBO J. 43, 3116–3140. doi: 10.1038/s44318-024-00079-7.
• Takahashi M, Ito K, Iwasaki H, Norden B (2024) Linear dichroism reveals the perpendicular orientation of DNA bases in the RecA and Rad51 recombinase filaments: A possible mechanism for the strand exchange reaction. Chirality 36, e23664. doi: 10.1002/chir.23664.
• Taguchi H, Niwa T (2024) Reconstituted cell-free translation systems for exploring protein folding and aggregation. J. Mol. Biol. 436, 168726. doi: 10.1016/j.jmb.2024.168726.
• Sammani PKT, Yospanya W, Niwa T, Kohata A, Taguchi H, Kinbara K (2024) Monitoring insulin fibrillation kinetics using chromatographic analysis. Int. J. Biol. Macromol. 275, 133660. doi: 10.1016/j.ijbiomac.2024.133660.
• Renodon-Corniere A, Mikawa T, Kuwabara N, Ito K, Levitsky D, Iwasaki H, Takahashi M* (2024) Human Rad51 protein requires higher concentrations of calcium ions for D-Loop formation than for oligonucleotide strand exchange. Int. J. Mol. Sci. 25, 3633. doi: 10.3390/ijms25073633.
• Olan I, Ando-Kuri M, Parry AJ, Handa T, Schoenfelder S, Fraser P, Ohkawa Y, Kimura H, Narita M, Narita M (2024) HMGA1 orchestrates chromatin compartmentalization and sequesters genes into 3D networks coordinating senescence heterogeneity. Nat. Commun. 15, 6891. doi: 10.1038/s41467-024-51136-3.
• Nakane K, Fujimura C, Miyano S, Liu Z, Niwa T, Nishi H, Kadonosono T, Taguchi H, Tomoshige S, Ishikawa M, Sato S (2024) Laccase-catalyzed tyrosine click reaction with 1-methyl-4-arylurazole: rapid labeling on protein surfaces. Chem. Commun. 60, 14208–14211. doi: 10.1039/d4cc04664c.
• Miura K, Niimi H, Niwa T, Taguchi H, Nakamura H (2024) Intracellular photocatalytic proximity labeling (iPPL) for dynamic analysis of chromatin-binding proteins targeting histone H3. ACS Chem. Biol. 19, 2412–2417. doi: 10.1021/acschembio.4c00473.
• Li Z, Nakatogawa H (2024) Methods to monitor nucleophagy in yeast. Methods Mol. Biol. 2845, 15–25. doi: 10.1007/978-1-0716-4027-5_2.
• Li Z, Mochida K, Nakatogawa H (2024) Macronucleophagy maintains cell viability under nitrogen starvation by modulating micronucleophagy. Nat. Commun. 15, 10670. doi: 10.1038/s41467-024-54837-3.
• Lestari B, Fukushima T, Utomo RY, Wahyuningsih MSH (2024) Apoptotic and non-apoptotic roles of caspases in placenta physiology and pathology. Placenta 151, 37–47. doi: 10.1016/j.placenta.2024.06.003.
• Kono Y, Pack CG, Ichikawa T, Komatsubara A, Adam SA, Miyazawa K, Rolas L, Nourshargh S, Medalia O, Goldman RD, Fukuma T, Kimura H, Shimi T (2024) Roles of the lamin A-specific tail region in the localization to sites of nuclear envelope rupture. PNAS Nexus 3, pgae527. doi: 10.1093/pnasnexus/pgae527.
• Komatsu K, Ideno H, Nakashima K, Udagawa N, Kobayashi Y, Kimura H, Tachibana M, Yamashita T, Nifuji A (2024) The G9a histone methyltransferase represses osteoclastogenesis and bone resorption by regulating NFATc1 function. FASEB J. 38, e23779. doi: 10.1096/fj.202401234R.
• Kato A, Pipil S, Ota C, Kusakabe M, Watanabe T, Nagashima A, Chen AP, Islam Z, Hayashi N, Wong MKS, Komada M, Romero MF, Takei Y (2024) Convergent gene losses and pseudogenizations in multiple lineages of stomachless fishes. Commun. Biol. 7, 408. doi: 10.1038/s42003-024-06033-8.
• Kadokura H, Harada N, Yamaki S, Hirai N, Tsukuda R, Azuma K, Amagai Y, Nakamura D, Yanagitani K, Taguchi H, Kohno K, Inaba K (2024) Development of luciferase-based highly sensitive reporters that detect ER-associated protein biogenesis abnormalities. iScience 27, 111189. doi: 10.1016/j.isci.2024.111189.
• Ito K, Maki T, Kanamaru S, Takahashi M, Iwasaki H (2024) The Swi5-Sfr1 complex regulates Dmc1- and Rad51-driven DNA strand exchange proceeding through two distinct three-stranded intermediates by different mechanisms. Nucleic Acids Res. 52, 12517–12533. doi: 10.1093/nar/gkae987.
• Isoda T, Takeda E, Hosokawa S, Hotta-Ren S, Ohsumi Y (2024) Atg45 is an autophagy receptor for glycogen, a non-preferred cargo of bulk autophagy in yeast. iScience 27, 109810. doi: 10.1016/j.isci.2024.109810.
• Hamano T, Nagumo Y, Umehara T, Hirono K, Fujiwara K, Taguchi H, Chadani Y, Doi N (2024) STALL-seq: mRNA-display selection of bacterial and eukaryotic translational arrest sequences from large random-sequence libraries. J. Biol. Chem. 300, 107978. doi: 10.1016/j.jbc.2024.107978.
• Fujiwara K, Inoue T, Kimoto A, Zixian J, Tokuhiro K, Yasukochi Y, Akama TO, Cai CL, Shiojima I, Kimura H, Yoshimura SH, Nakamura T, Hirai M (2024) Spatial organizations of heterochromatin underpin nuclear structural integrity of ventricular cardiomyocytes against mechanical stress. Cell Rep. 43, 115048. doi: 10.1016/j.celrep.2024.115048.
• Endo A, Komada M, Yoshida Y (2024) Ubiquitin-mediated endosomal stress: A novel organelle stress of early endosomes that initiates cellular signaling pathways. BioEssays 46, e2400127. doi: 10.1002/bies.202400127.
• Alam JM, Maruyama T, Noshiro D, Kakuta C, Kotani T, Nakatogawa H, Noda NN (2024) Complete set of the Atg8–E1–E2–E3 conjugation machinery forms an interaction web that mediates membrane shaping. Nat. Struct. Mol. Biol. 31, 170–178. doi: 10.1038/s41594-023-01171-7.
• Renodon-Corniere A, Mikawa T, Kuwabara N, Ito K, Levitsky D, Iwasaki H, Takahashi M* (2024) Human Rad51 protein requires higher concentrations of calcium ions for D-Loop formation than for oligonucleotide strand exchange. Int. J. Mol. Sci. 25, 3633. doi: 10.3390/ijms25073633.
• Takahashi M*, Ito K, Iwasaki H, Norden B (2024) Linear dichroism reveals the perpendicular orientation of DNA bases in the RecA and Rad51 recombinase filaments: A possible mechanism for the strand exchange reaction. Chirality 36, e23664. doi: 10.1002/chir.23664.
• Taguchi Y, Nakaya T, Aizawa K, Noguchi Y, Maiya N, Iwamoto C, Ohba K, Sugawara M, Murata M, Nagai R*, Kano F* (2024) Peptide mimetic NC114 induces growth arrest by preventing PKCδ activation and FOXM1 nuclear translocation in colorectal cancer cells. FEBS Open Bio. 14(4): 695-720. doi: 10.1002/2211-5463.13784
• Goto, N. Suke, K. Yonezawa, N. Nishihara, H. Handa, T. ;Sato, Y. Kujirai, T. Kurumizaka, H. Yamagata, K. Kimura, H. ISWI chromatin remodeling complexes recruit NSD2 and H3K36me2 in pericentromeric heterochromatin. J Cell Biol. (2024 )Aug 5;223(8):e202310084. doi: 10.1083/jcb.202310084.
• Nakao, M. Sato, Y. Aizawa, A. Kimura, H. Mode of SUV420H2 heterochromatin localization through multiple HP1 binding motifs in the heterochromatic targeting module. Genes Cells. (2024) May;29(5):361-379. doi: 10.1111/gtc.13109.
• Sato, Y. Takenoshita, M. Ueoka, M. Ueda, J. Yamagata, K. Kimura, H. Visualizing histone H4K20me1 in knock-in mice expressing the mCherry-tagged modification-specific intracellular antibody. Histochem Cell Biol. (2024) May 19. doi: 10.1007/s00418-024-02296-8.
• Tomimatsu, K. Fujii, T. Bise, R. Hosoda, K. Taniguchi, Y. Ochiai, H. Ohishi, H. Ando, K.Minami, R. Tanaka, K. Tachibana, T. Mori, S. Harada, A. Maehara, K. Nagasaki, M. Uchida, S. Kimura, H. Narita, M. Ohkawa, Y. Precise immunofluorescence canceling for highly multiplexed imaging to capture specific cell states. Nat Commun. (2024) May 8;15(1):3657. doi: 10.1038/s41467-024-47989-9.
• Ugolini, M. Kerlin, M. A. Kuznetsova, K. Oda, H. Kimura, H. Vastenhouw, N. L.Transcription bodies regulate gene expression by sequestering CDK9. Nat Cell Biol. 2024 Apr;26(4):604-612. doi: 10.1038/s41556-024-01389-9.
• Atsumi, Y. Iwata, R. Kimura, H. Vanderhaeghen, P. Yamamoto, N. Sugo, N. Repetitive CREB-DNA interactions at gene loci predetermined by CBP induce activity-dependent gene expression in human cortical neurons. Cell Rep. 2024 Jan 23;43(1):113576. doi: 10.1016/j.celrep.2023.113576.
• Ideno, H. Nakashima, K. Komatsu, K. Kimura, H. Shinkai, Y. Tachibana, M. Nifuji, A. Epigenetic modifier G9a is involved in regulation of mouse tongue development. J Oral Biosci. 2024 Mar;66(1):35-40. doi: 10.1016/j.job.2023.12.007.
• Ito, R. Xie, S. Tumenjargal, M. Sugahara, Y. Yang, C. Takahashi, H. Arai, M. Inoue, S. I. Uchida, A. Nakano, K. Choi, H. Yang, G. Zhao, Y. Yamaguchi, R. Jin, H. Sagae, H. Wada, Y. Tanaka, T. Kimura, H. Kodama, T. Aburatani, H. Takeda, K. Inagaki, T. Osborne, T. F. Yoneshiro, T. Matsumura, Y. Sakai, J.Mitochondrial biogenesis in white adipose tissue mediated by JMJD1A-PGC-1 axis limits age-related metabolic disease. iScience. 2024 Mar 1;27(4):109398. doi: 10.1016/j.isci.2024.109398.
• Kashiwagi, K. Yoshida, J. Kimura, H. Shinjo, K. Kondo, Y. Horie, K.Mutation of the SWI/SNF complex component Smarce1 decreases nucleosome stability in embryonic stem cells and impairs differentiation. J Cell Sci. 2024 Mar 15;137(6):jcs260467. doi: 10.1242/jcs.260467.
• Kimura, H. Lakadamyali, M. Decoding the cell nucleusCurr Opin. Cell Biol. 2024 Feb;86:102319. doi: 10.1016/j.ceb.2023.102319.
• Komiya, H. Sato, Y. Kimura, H. Kawakami, A. Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish. Dev Growth Differ. 2024 Feb;66(2):161-171. doi: 10.1111/dgd.12908.
• Lochs, S. J. A. van der Weide, R. H. de Luca, K. L. Korthout, T. van Beek, R. E. Kimura, H. Kind, J. Combinatorial single-cell profiling of major chromatin types with MAbID. Nat Methods. 2024 Jan;21(1):72-82. doi: 10.1038/s41592-023-02090-9.
• Nakayama, C. Daigaku, Y. Aoi, Y. Fang, Q. Kimura, H. Shilatifard, A. Tellier, M. Nojima, T. NELF coordinates Pol II transcription termination and DNA replication initiation. bioRxiv [Preprint]. 2024 Feb 1:2024.01.31.578294. doi: 10.1101/2024.01.31.578294.
• Endo A, Fukushima T, Takahashi C, Tsuchiya H, Ohtake F, Ono S, Ly T, Yoshida Y, Tanaka K, Saeki Y, Komada M* (2024) USP8 prevents aberrant NF-kappaB and Nrf2 activation by counteracting ubiquitin signals from endosomes. J. Cell Biol. 223(3),e202306013. doi: 10.1083/jcb.202306013.
• Kobo A, Taguchi H*, Chadani Y* (2024) Non-specific N-terminal tetrapeptide insertions disrupt the translation arrest induced by ribosome arresting peptide sequences. J. Biol. Chem. 300(6):107360 doi: 10.1016/j.jbc.2024.107360.
• Chadani Y*, Yamanouchi S, Uemura E, Yamasaki K, Niwa T, Ikeda T, Kurihara M, Iwasaki W, Taguchi H * (2024) The ABCF proteins in Escherichia coli individually cope with 'hard-to-translate' nascent peptide sequences. Nucleic Acids Res. doi: 10.1093/nar/gkae309.
• Fujita, N., Girada, S., Vogler, G., Bodmer, R., Kiger A*.　PI(4,5)P2 role in Transverse-tubule membrane formation and muscle function. bioRxiv (2024) https://doi.org/10.1101/2024.01.31.578124 (J Cell Biol in revision)

2023

• Kagohashi Y, Sasaki M, May AI, Kawamata T*, Ohsumi Y.* The mechanism of Atg15-mediated membrane disruption in autophagy. J Cell Biol. 2023 Dec　4;222(12):e202306120. doi: 10.1083/jcb.202306120. Epub 2023 Nov 2
• Palihati M, Iwasaki H*, Tsubouchi H* (2023) Analysis of the indispensable RAD51 cofactor BRCA2 in Naganishia liquefaciens, a Basidiomycota yeast.. Life Sci. Alliance 7, e202302342. doi: 10.26508/lsa.202302342.
• Lee W, Iwasaki H, Tsubouchi H* (2023) Li HW* Hop2-Mnd1 and Swi5-Sfr1 stimulate Dmc1 filament assembly using distinct mechanisms. Nucleic Acids Res. 51, 8550-8562 doi: 10.1093/nar/gkad561.
• Maki T*, Thon G, Iwasaki H* (2023) Fission yeast Swi2 designates cell-type specific donor and stimulates Rad51-driven strand exchange for mating-type switching. Nucleic Acids Res. 51, 3869-3887 doi:10.1093/nar/gkad204.
• Taguchi Y, Ito K, Kano F* (2023) PKM2 controls the translation of TFE3 to maintain the integrity of the Golgi apparatus for the survival of HeLa and ME-180 cervical cancer cells. The FEBS Journal 290(12):3221-3242. doi: 10.1111/febs.16740
• Nakatsu D, Kunishige R, Taguchi Y, Shinozaki-Narikawa N, Osaka K, Yokomizo K, Ishida M, Takei S, Yamasaki S, Hagiya K, Hattori K, Tsukamoto T, Murata M, Kano F* (2023) BMP4-SMAD1/5/9-RUNX2 pathway activation inhibits neurogenesis and oligodendrogenesis in Alzheimer’s patients’ iPSCs in senescence-related conditions. Stem Cell Reports 18(3): 688–705. doi: 10.1016/j.stemcr.2023.01.004
• Estell, C. Davidson, L. Eaton, J. D. Kimura, H. Gold, V. A. M. West, S.A restrictor complex of ZC3H4, WDR82, and ARS2 integrates with PNUTS to control unproductive transcription. Mol Cell. 2023 Jul 6;83(13):2222-2239.e5. doi: 0.1016/j.molcel.2023.05.029.
• Fukuda, K. Shimi, T. Shimura, C. ;Ono, T. Suzuki, T. ;Onoue, K. Okayama, S. Miura, H. Hiratani, I. Ikeda, K. Okada, Y. Dohmae, N. Yonemura, S. Inoue, A. Kimura, H. Shinkai, Y. Epigenetic plasticity safeguards heterochromatin configuration in mammals. Nucleic Acids Res. 2023 Jul 7;51(12):6190-6207. doi: 10.1093/nar/gkad387.
• Nishino, M. ;Imaizumi, H. ;Yokoyama, Y. ;Katahira, J. ;Kimura, H. ;Matsuura, N. Matsumura, M.Histone methyltransferase SUV39H1 regulates the Golgi complex via the nuclear envelope-spanning LINC complex. PLoS One. 2023 Jul 12;18(7):e0283490. doi: 10.1371/journal.pone.0283490.
• Ochiai, H. Ohishi, H. Sato, Y. Kimura, H. Organization of transcription and 3D genome as revealed by live-cell imaging. Curr Opin Struct Biol. 2023 Aug;81:102615. doi: 10.1016/j.sbi.2023.102615.
• Oda, H. Sato, Y. Kawashima, S. A. Fujiwara, Y. Pálfy, M. Wu, E. Vastenhouw, N. L. Kanai, M. Kimura, H. Actin filaments accumulated in the nucleus remain in the vicinity of condensing chromosomes in the zebrafish early embryo. Biol Open. 2023 May 15;12(5):bio059783. doi: 10.1242/bio.059783.
• Saxton, M. N. Morisaki, T. Krapf, D. Kimura, H. Stasevich, T. J. Live-cell imaging uncovers the relationship between histone acetylation, transcription initiation, and nucleosome mobility. Sci Adv. 2023 Oct 6;9(40):eadh4819. doi: 10.1126/sciadv.adh4819.
• Stasevich, T. J. Kimura, H. 　An expanded view of transcription. Science. 2023 Jul 7;381(6653):26-27. doi: 10.1126/science.adi8187.
• Suzuki, T. Komatsu, T. Shibata, H. Tanioka, A. Vargas, D. Kawabata-Iwakawa, R. Miura, F. Masuda, S. Hayashi, M. Tanimura-Inagaki, K. Morita, S. Kohmaru, J. Adachi, K. Tobo, M.Obinata, H. Hirayama, T. Kimura, H. Sakai, J. Nagasawa, H. Itabashi, H. Hatada, I. Ito, T. Inagaki, T. Crucial role of iron in epigenetic rewriting during adipocyte differentiation mediated by JMJD1A and TET2 activity.Nucleic Acids Res. 2023 Jul 7;51(12):6120-6142. doi: 10.1093/nar/gkad342.
• Trakarnphornsombat, W. Kimura, H. Live-cell tracking of γ-H2AX kinetics reveals the distinct modes of ATM and DNA-PK in the immediate response to DNA damage. J Cell Sci. 2023 Apr 15;136(8):jcs260698. doi: 10.1242/jcs.260698.
• Nakamura F, Kimura H, Fusetani N, *Nakao Y. Two Onnamide Analogs from the Marine Sponge Theonella conica: Evaluation of Geometric Effects in the Polyene Systems on Biological Activity. Molecules. 28, 2524 (2023) doi: 10.3390/molecules28062524.
• Kuznetsova K, Chabot NM, Ugolini M, Wu E, Lalit M, Oda H, Sato Y, Kimura H, Jug F, *Vastenhouw NL. Nanog organizes transcription bodies. Curr Biol 33, 164-173.e5 (2023) doi: 10.1016/j.cub.2022.11.015.
• Ozawa H, Kambe A, Hibi K, Murakami S, Oikawa A, Handa T, Fujiki K, Nakato R, Shirahige K, Kimura H, Shiraki N, *Kume S. Transient Methionine Deprivation Triggers Histone Modification and Potentiates Differentiation of Induced Pluripotent Stem Cells. Stem Cells 41, 271-286 (2023) doi: 10.1093/stmcls/sxac082.
• Tanaka M, Harada H, *Kimura H. (2023) The role of H3K9me3 in oral squamous cell carcinoma. Biochem Biophys Res Commun 640, 56-63. doi: 10.1016/j.bbrc.2022.11.102.
• Yomogita H, Ito H, Hashimoto K, Kudo A, Fukushima T, Endo T, Hirate Y, Akimoto Y, Komada M, Kanai Y, Miyasaka N, Kanai-Azuma M* (2023) A possible function of Nik-related kinase in the labyrinth layer of delayed delivery mouse placentas. J. Reprod. Dev. Mol. 69(1): 32-40. doi: 10.1262/jrd.2022-120.
• Adachi J, Oda H, Fukushima T*, Lestari B, Kimura H, Sugai H, Shiraki K, Hamaguchi R, Sato K, Kinbara K* (2023) Dense and Acidic Organelle-Targeted Visualization in Living Cells: Application of Viscosity-Responsive Fluorescence Utilizing Restricted Access to Minimum Energy Conical Intersection. Anal. Chem. 95(12): 5196-5204. doi: 10.1021/acs.analchem.2c04133.
• Chadani Y*, Kanamori T, Niwa T, Ichihara K, Nakayama KI, Matsumoto A, Taguchi H* (2023) Mechanistic dissection of premature translation termination induced by acidic residues-enriched nascent peptide. Cell Rep. 42(12) 113569-113569 doi: 10.1016/j.celrep.2023.113569.
• Soriano JC, Tsutsumi S, Ohara D, Hirota K, Kondoh G, Niwa T, Taguchi H, Kadonosono T*, Kizaka-Kondoh S (2023) Identification of Surface Markers and Functional Characterization of Myeloid Derived Suppressor Cell-Like Adherent Cells. Adv. Biol. (Weinh) e2300159 doi: 10.1002/adbi.202300159.
• Ito H, Machida K, Hasumi M, Ueyama M, Nagai Y, Imataka H and Taguchi, H* (2023) Reconstitution of C9orf72 (GGGGCC) repeat-associated non-AUG translation with purified components. Sci Rep Dec 20;13(1):22826 doi: 10.1038/s41598-023-50188-z.
• Fukuyama M*, Nishinami S, Maruyama Y, Ozawa T, Tomita S, Ohhashi Y, Kasuya M, Gen M, Chatani E, Shiraki K, Hibara A* (2023) Detection of fibril nucleation in micrometer-sized protein condensates and suppression of Sup35NM fibril nucleation by liquid–liquid phase separation. Anal Chem. 95(26), 9855-9862. doi: 10.1021/acs.analchem.3c00766.
• Hashimoto M, Miki T*, Niwa T, Mihara H (2023) Proximity labeling and identification of endogenous client proteins recruited to Y15-based artificial granules tethering a bait protein. J Pept Sci. e3536 doi: 10.1002/psc.3536.
• Matsumoto R, Niwa T, Shimane Y, Kuruma Y, Taguchi H, Kanamori T* (2023) Regulated N-Terminal Modification of Proteins Synthesized Using a Reconstituted Cell-Free Protein Synthesis System. ACS Synth.Biol. doi: 10.1021/acssynbio.3c00191.
• Inoue R, Fukutani Y, Niwa T, Matsunami H, Yohda M* (2023) Identification and Characterization of Proteins That Are Involved in RTP1S-Dependent Transport of Olfactory Receptors. Int. J. Mol. Sci. 24(9) doi: 10.3390/ijms24097829
• Yajie C, Miwa T, Taguchi H* (2023) The mRNA binding-mediated self-regulatory function of small heat shock protein IbpA in γ-proteobacteria is conferred by a conserved arginine. J Biol Chem. 299, (9):105108. doi: 10.1016/j.jbc.2023.105108.
• Miwa T, Taguchi H* (2023) Escherichia coli small heat shock protein IbpA plays a role in regulating the heat shock response by controlling the translation of σ32. Proc Natl Acad Sci U S A., 120, e2304841120. doi: 10.1073/pnas.2304841120
• Minami S, Niwa T, Uemura E, Koike R, Taguchi H, Ota M* (2023) Prediction of chaperonin GroE substrates using small structural patterns of proteins. FEBS Open Bio. doi: 10.1002/2211-5463.13590.
• Yamakawa A, Niwa T*, Chadani Y*, Kobo A, Taguchi H * (2023) A method to enrich polypeptidyl-tRNAs to capture snapshots of translation in the cell. Nucleic Acids Res. doi: 10.1093/nar/gkac1276.
• Shen HK, Morishita K, Hashim PK, Okuro K, Kashiwagi D, Kimura A, Yanagisawa H, KikkawaM, Niwa T, Taguchi, H, Aida T*. (2023) ATP-Responsive Nanoparticles Covered with Biomolecular Machine "Chaperonin GroEL". Angew Chem Int Ed 62:e202304894 doi: 10.1002/anie.202304894.
• Shin J*, Lee C* (2023) Profiling of Secreted Proteins in Serum-Containing Media Using BONCAT and Pulsed SILAC. Methods Mol Biol. 2603:235-243. doi: 10.1007/978-1-0716-2863-8_19.
• Kotani T, Sakai Y, Kirisako H, Kakuta C, Kakuta S, Ohsumi Y, Nakatogawa H* (2023) A mechanism that ensures non-selective cytoplasm degradation by autophagy. Nat. Commun. 14, Article number: 5815
• Hitomi K, Kotani T, Noda N.N, Kimura Y, Nakatogawa H* (2023) The Atg1 complex, Atg9, and Vac8 recruit PI3K complex I to the pre-autophagosomal structure. J. Cell Biol. 222, e202210017.
• Shioda, T., Takahashi, I., Ikenaka, K., Fujita, N., Kanki, T., Oka, T., Mochizuki, H., Antebi, A., Yoshimori, T.*, and Nakamura, S*. Neuronal MML-1/MXL-2 regulates systemic aging via glutamate transporter and cell nonautonomous autophagic and peroxidase activity. PNAS (2023) 120 (39): e2221553120

2022

• Jin Y*, Jin N, Oikawa Y, Benyair R, Koizumi M, Wilson TE, Ohsumi Y*, Weisman　LS*. Bur1 functions with TORC1 for vacuole-mediated cell cycle progression. EMBO Rep. 2022 Feb 15:e53477 Epub ahead of print.
• Kawamata T*, Makino S, Kagohashi Y, Sasaki M, Ohsumi Y*. A method for the isolation and characterization of autophagic bodies from yeast provides a key tool to investigate cargos of autophagy. J. Biol. Chem. Available online 25 October 2022, 102641.
• Esquivel-Chávez A, Maki T, Tsubouchi H, Handa T, Kimura H, Haber JE, Thon G, Iwasaki H* (2022) Euchromatin factors HULC and Set1C affect heterochromatin organization and mating-type switching in fission yeast Schizosaccharomyces pombe. Genes Genet. Syst. 97, 123-138. doi: 10.1266/ggs.22-00012. GGS prize awarded.
• Zhu B, Nosaka N, Kanamaru S, Dong J, Dai Y, Inoue A, Yang Y, Kobayashi K, Kitaguchi T, Iwasaki H, Koike R, Wakabayashi K, Ueda H*(2022) Rapid and sensitive SARS-CoV-2 detection using a homogeneous fluorescent immunosensor Quenchbody with crowding agents. Analyst 147, 4971-4979. doi: 10.1039/d2an01051h.
• Kunishige R, Murata M, Kano F* (2022) Targeted protein degradation by Trim-Away using cell resealing coupled with microscopic image-based quantitative analysis. Front. Cell Dev. Biol. 10:1027043. doi: 10.3389/fcell.2022.1027043
• Noguchi Y, Murakami M, Murata M, Kano F* (2022) Microscopic image-based classification of adipocyte differentiation by machine learning. Histochem. Cell Biol. 159(4):313-327. doi: 10.1007/s00418-022-02168-z
• Ohishi H, Shimada S, Uchino S, Li J, Sato Y, Shintani M, Owada H, Ohkawa Y, Pertsinidis A, Yamamoto T, *Kimura H, *Ochiai H. (2022) STREAMING-tag system reveals spatiotemporal relationships between transcriptional regulatory factors and transcriptional activity. Nat Commun. 13(1):7672. doi: 10.1038/s41467-022-35286-2.
• Kamiya N, Kuramoto K, Takishima K, Yumoto T, Oda H, Shimi T, Kimura H, Matsushita M, *Fujiyoshi S. (2022) Superfluid helium nanoscope insert with millimeter working range. Rev Sci Instrum 93, 103703 (2022) doi: 10.1063/5.0107395.
• Kono Y, Adam SA, Sato Y, Reddy KL, Zheng Y, Medalia O, Goldman RD, Kimura H, *Shimi T. Nucleoplasmic lamin C rapidly accumulates at sites of nuclear envelope rupture with BAF and cGAS. J Cell Biol 221, e202201024 (2022) doi: 10.1083/jcb.202201024.
• Takahashi H, Yang G, Yoneshiro T, Abe Y, Ito R, Yang C, Nakazono J, Okamoto-Katsuyama M, Uchida A, Arai M, Jin H, Choi H, Tumenjargal M, Xie S, Zhang J, Sagae H, Zhao Y, Yamaguchi R, Nomura Y, Shimizu Y, Yamada K, Yasuda S, Kimura H, Tanaka T, Wada Y, Kodama T, Aburatani H, Zhu MS, Inagaki T, Osborne TF, Kawamura T, Ishihama Y, Matsumura Y, *Sakai J. MYPT1-PP1β phosphatase negatively regulates both chromatin landscape and co-activator recruitment for beige adipogenesis. Nat Commun 13, 5715 (2022) doi: 10.1038/s41467-022-33363-0.
• Dai Y, Sato Y, Zhu B, Kitaguchi T, Kimura H, Ghadessy FJ, *Ueda H. Intra Q-body: an antibody-based fluorogenic probe for intracellular proteins that allows live cell imaging and sorting. Chem Sci 13, 9739-9748 (2022) doi: 10.1039/d2sc02355e.
• Rang FJ, de Luca KL, de Vries SS, Valdes-Quezada C, Boele E, Nguyen PD, Guerreiro I, Sato Y, Kimura H, Bakkers J, *Kind J. Single-cell profiling of transcriptome and histone modifications with EpiDamID. Mol Cell 82, 1956-1970.e14 (2022) doi: 10.1016/j.molcel.2022.03.009.
• Tomimatsu K, Bihary D, Olan I, Parry AJ, Schoenfelder S, Chan ASL, Slater GSC, Ito Y, Rugg-Gunn PJ, Kirschner K, Bermejo-Rodriguez C, Seko T, Kugoh H, Shiraishi K, Sayama K, Kimura H, Fraser P, Narita M, Samarajiwa SA, *Narita M. Locus-specific induction of gene expression from heterochromatin loci during cellular senescence. Nat Aging 2, 31-45 (2022) doi: 10.1038/s43587-021-00147-y.
• Uchino S, Ito Y, Sato Y, Handa T, Ohkawa Y, Tokunaga M, *Kimura H. Live imaging of transcription sites using an elongating RNA polymerase II-specific probe. J Cell Biol 221, e202104134 (2022) doi: 10.1083/jcb.202104134.
• Lestari B, Naito S, Endo A, Nishihara H, Kato A, Watanabe E, Denda K, Komada M*, Fukushima T* (2022) Placental mammals acquired functional sequences in NRK for regulating the CK2-PTEN-AKT pathway and placental cell proliferation. Mol. Biol. Evol. msab371. doi: 10.1093/molbev/msab371.
• Kimura Y‡, Shin J‡, Nakai Y, Takahashi M, Ino Y, Akiyama T, Goto K, Nagata N, Yamaoka Y, Miyakawa K, Kimura H, Ryo A＊ (‡co-first author) (2022) Development of Parallel Reaction Monitoring Mass Spectrometry Assay for the Detection of Human Norovirus Major Capsid Protein. Viruses. 2022 Jun 28;14(7):1416. doi: 10.3390/v14071416.
• Onodera H, Niwa T, Taguchi H*, Chadani Y* (2022) Prophage excision switches the primary ribosome rescue pathway and rescue-associated gene regulations in Escherichia coli. Mol. Microbiol. 119(1) 44-58 doi: 10.1111/mmi.15003.
• Ito Y, Chadani Y*, Niwa T, Yamakawa A, Machida K, Imataka H, Taguchi H* (2022) Nascent peptide-induced translation discontinuation in eukaryotes impacts biased amino acid usage in proteomes. Nat. Commun. 13(1) 7451-7451 doi: 10.1038/s41467-022-35156-x.
• Niwa T, Nakazawa K, Hoshi K, Tadakuma H, Ito K, Taguchi H* (2022) Application of fluorescence correlation spectroscopy to investigate the dynamics of a ribosome-associated trigger factor in Escherichia coli. Front. Mol. Biosci. 9 891128-891128 doi: 10.3389/fmolb.2022.891128.
• Niwa T, Chadani Y, Taguchi H* (2022) Shotgun Proteomics Revealed Preferential Degradation of Misfolded In Vivo Obligate GroE Substrates by Lon Protease in Escherichia coli. Molecules 27(12) doi: 10.3390/molecules27123772.
• Hirai K, Yamashita H, Tomoshige S*, Mishima Y, Niwa T, Ohgane K, Ishii M, Kanamitsu K, Ikemi Y, Nakagawa S, Taguchi H, Sato S, Hashimoto Y, Ishikawa M* (2022) Conversion of a PROTAC Mutant Huntingtin Degrader into Small-Molecule Hydrophobic Tags Focusing on Drug-like Properties. ACS Med. Chem. Lett. 13(3) 396-402 doi: 10.1021/acsmedchemlett.1c00500
• Nakane K, Niwa T, Tsushima M, Tomoshige S, Taguchi H, Nakamura H, Ishikawa M, Sato S* (2022) BODIPY Catalyzes Proximity‐Dependent Histidine Labelling. Chem. Cat. Chem. 14(9) doi: 10.1002/cctc.202200077.
• Nakagawa Y, Shen HC, Komi Y, Sugiyama S, Kurinomaru T, Tomabechi Y, Krayukhina E, Okamoto K, Yokoyama T, Shirouzu M, Uchiyama S, Inaba M, Niwa T, Sako Y, Taguchi H*, Tanaka M* (2022) Amyloid conformation-dependent disaggregation in a reconstituted yeast prion system. Nat Chem Biol. 18(3) 321-331 doi: 10.1038/s41589-021-00951-y
• Fujita T, Yokoyama T, Shirouzu M, Taguchi H, Ito T, *Iwasaki S (2022) The landscape of translational stall sites in bacteria revealed by monosome and disome profiling. RNA 2022 Mar;28(3):290-302 doi: 10.1261/rna.078188.120
• Tsushima M, Sato S*, Miura K, Niwa T, Taguchi H, Hiroyuki Nakamura* (2022) Intracellular photocatalytic-proximity labeling for profiling protein-protein interactions in microenvironments. Chem. Commun. (Camb.) 58(12) 1926-1929 doi: 10.1039/d1cc05764b.
• Murakawa, T., Nakamura, T., Kawaguchi, K., Murayama, F., Zhao, N., Stasevich, T., Kimura, H., and Fujita, N*. A Drosophila Toolkit for HA-tagged Proteins Unveiled a Block in Autophagy Flux in the Last Instar Larval Fat Body. Development (2022) 149 (6): dev200243. Selected as the cover of Development vol.149 (6).

2021

• Maruyama T, Alam JM, Fukuda T, Kageyama S, Kirisako H, Ishii Y, Shimada I, OhsumiY, Komatsu M, Kanki T, Nakatogawa H, Noda NN. Membrane perturbation by lipidated Atg8 underlies autophagosome biogenesis. Nat Struct Mol Biol. 2021 Jul;28(7):583-593.
• Palihati M, Tsubouchi H*, Argunhan B, Kajitani R, Bakenova O, Han Y.-W, Murayama Y, Itoh T, Iwasaki H* (2021) Homology length dictates the requirement for Rad51 and Rad52 in gene targeting in the Basidiomycota yeast Naganishia liquefaciens. Curr. Genet. 67, 919-936. doi: 10.1007/s00294-021-01201-3.
• Muraszko J, Kramarz K, Argunhan Bilge, Ito K, Baranowska G, Kurokawa Y, Murayama Y, Tsubouchi H, Lambert S, Iwasaki H*, Dziadkowiec D* (2021) Rrp1 translocase and ubiquitin ligase activities restrict the genome destabilising effects of Rad51 in fission yeast. Nucleic Acids Res. 49, 6822-6848. doi.org/10.1093/nar/gkab511.
• Noguchi Y, Kano F, Maiya N, Iwamoto C, Yamasaki S, Otsubo Y, Nakatsu D, Kunishige R, Murata M* (2021) Microscopic image-based covariation network analysis for actin scaffold-modified insulin signaling. iScience 4(7):102724. doi: 10.1016/j.isci.2021.102724
• Matsumura Y, Ito R, Yajima A, Yamaguchi R, Tanaka T, Kawamura T, Magoori K, Abe Y, Uchida A, Yoneshiro T, Hirakawa H, Zhang J, Arai M, Yang C, Yang G, Takahashi H, Fujihashi H, Nakaki R, Yamamoto S, Ota S, Tsutsumi S, Inoue SI, Kimura H, Wada Y, Kodama T, Inagaki T, Osborne TF, Aburatani H, Node K, *Sakai J. Spatiotemporal dynamics of SETD5-containing NCoR-HDAC3 complex determines enhancer activation for adipogenesis. Nat Commun 12, 7045 (2021) doi: 10.1038/s41467-021-27321-5.
• *Hayashi-Takanaka Y, Hayashi Y, Hirano Y, Miyawaki-Kuwakado A, Ohkawa Y, Obuse C, Kimura H, Haraguchi T, *Hiraoka Y. Chromatin loading of MCM hexamers is associated with di-/tri-methylation of histone H4K20 toward S phase entry. Nucleic Acids Res 49, 12152-12166 (2021). doi: 10.1093/nar/gkab1068.
• Bartlett DA, Dileep V, Handa T, Ohkawa Y, Kimura H, Henikoff S, *Gilbert DM. High-throughput single-cell epigenomic profiling by targeted insertion of promoters (TIP-seq). J Cell Biol 220, e202103078 (2021) doi: 10.1083/jcb.202103078.
• Maehara K, Tomimatsu K, Harada A, Tanaka K, Sato S, Fukuoka M, Okada S, Handa T, Kurumizaka H, Saitoh N, Kimura H, *Ohkawa Y. Modeling population size independent tissue epigenomes by ChIL-seq with single thin sections. Mol Syst Biol 17, e10323 (2021) doi: 10.15252/msb.202110323.
• Liu Y, Zhao N, Kanemaki MT, Yamamoto Y, Sadamura Y, Ito Y, Tokunaga M, *Stasevich TJ, *Kimura H. Visualizing looping of two endogenous genomic loci using synthetic zinc-finger proteins with anti-FLAG and anti-HA frankenbodies in living cells. Genes Cells 26, 905-926 (2021), doi:10.1111/gtc.12893.
• Forero-Quintero LS, Raymond W, Handa T, Saxton MN, Morisaki T, Kimura H, Bertrand E, Munsky B, *Stasevich TJ. Live-cell imaging reveals the spatiotemporal organization of endogenous RNA polymerase II phosphorylation at a single gene. Nat Commun 12, 3158 (2021) doi: 10.1038/s41467-021-23417-0.
• Shibuta MK, Sakamoto T, Yamaoka T, Yoshikawa M, Kasamatsu S, Yagi N, Fujimoto S, Suzuki T, Uchino S, Sato Y, Kimura H, *Matsunaga S. A live imaging system to analyze spatiotemporal dynamics of RNA polymerase II modification in Arabidopsis thaliana. Commun Biol 4, 580 (2021) doi: 10.1038/s42003-021-02106-0.
• Zhang J, Matsumura Y, Kano Y, Yoshida A, Kawamura T, Hirakawa H, Inagaki T, Tanaka T, Kimura H, Yanagi S, Fukami K, Doi T, Osborne TF, Kodama T, Aburatani H, *Sakai J. Ubiquitination-dependent and -independent repression of target genes by SETDB1 reveal a context-dependent role for its methyltransferase activity during adipogenesis. Genes Cells 26, 513-529 (2021). doi: 10.1111/gtc.12868.
• Tachiwana H, Dacher M, Maehara K, Harada A, Seto Y, Katayama R, Ohkawa Y, Kimura H, Kurumizaka H, *Saitoh N. Chromatin structure-dependent histone incorporation revealed by a genome-wide deposition assay. Elife 10, e66290 (2021) doi: 10.7554/eLife.66290.
• Muraoka Y, Nikaido A, Kowada R, Kimura H, Yamaguchi M, *Yoshida H. Identification of Rpd3 as a novel epigenetic regulator of Drosophila FIG 4, a Charcot-Marie-Tooth disease-causing gene. Neuroreport 32, 562-568 (2021) doi: 10.1097/WNR.0000000000001636.
• Ohmuro-Matsuyama Y, Kitaguchi T, Kimura H, *Ueda H. Simple Fluorogenic Cellular Assay for Histone Deacetylase Inhibitors Based on Split-Yellow Fluorescent Protein and Intrabodies. ACS Omega 6, 10039-10046 (2021) doi: 10.1021/acsomega.0c06281.
• Grigoryan A, Pospiech J, Krämer S, Lipka D, Liehr T, Geiger H, Kimura H, Mulaw MA, *Florian MC. Attrition of X Chromosome Inactivation in Aged Hematopoietic Stem Cells. Stem Cell Reports 16, 708-716 (2021) doi: 10.1016/j.stemcr.2021.03.007.
• *Ohhata T, Yamazawa K, Miura-Kamio A, Takahashi S, Sakai S, Tamura Y, Uchida C, Kitagawa K, Niida H, Hiratani I, Kobayashi H, Kimura H, Wutz A, *Kitagawa M. Dynamics of transcription-mediated conversion from euchromatin to facultative heterochromatin at the Xist promoter by Tsix. Cell Rep 34, 108912 (2021) doi: 10.1016/j.celrep.2021.
• Sousa-Luís R, Dujardin G, Zukher I, Kimura H, Weldon C, Carmo-Fonseca M, *Proudfoot NJ, *Nojima T. POINT technology illuminates the processing of polymerase-associated intact nascent transcripts. Mol Cell 81, 1935-1950.e6 (2020) doi: 10.1016/j.molcel.2021.02.034.
• *Hieda M, Matsumoto T, Isobe M, Kurono S, Yuka K, Kametaka S, Wang JY, Chi YH, Kameda K, Kimura H, Matsuura N, Matsuura S. The SUN2-nesprin-2 LINC complex and KIF20A function in the Golgi dispersal. Sci Rep 11, 5358 (2021) doi: 10.1038/s41598-021-84750-4.
• Fujiwara Y, Yamanashi Y, Fujimura A, Sato Y, Kujirai T, Kurumizaka H, Kimura H, Yamatsugu K, *Kawashima SA, *Kanai M. Live-cell epigenome manipulation by synthetic histone acetylation catalyst system. Proc Natl Acad Sci USA 118, e2019554118 (2021) doi: 10.1073/pnas.2019554118.
• Béziat V*, Rapaport F, Hu J, Titeux M, Bonnet des Claustres M, Bourgey M, Griffin H, Bandet É, Ma CS, Sherkat R, Rokni-Zadeh H, Louis DM, Changi-Ashtiani M, Delmonte OM, Fukushima T, Habib T, Guennoun A, Khan T, Bender N, Rahman M, About F, Yang R, Rao G, Rouzaud C, Li J, Shearer D, Balogh K, Al Ali F, Ata M, Dabiri S, Momenilandi M, Nammour J, Alyanakian MA, Leruez-Ville M, Guenat D, Materna M, Marcot L, Vladikine N, Soret C, Vahidnezhad H, Youssefian L, Saeidian AH, Uitto J, Catherinot É, Navabi SS, Zarhrate M, Woodley DT, Jeljeli M, Abraham T, Belkaya S, Lorenzo L, Rosain J, Bayat M, Lanternier F, Lortholary O, Zakavi F, Gros P, Orth G, Abel L, Prétet JL, Fraitag S, Jouanguy E, Davis MM, Tangye SG, Notarangelo LD, Marr N, Waterboer T, Langlais D, Doorbar J, Hovnanian A, Christensen N, Bossuyt X, Shahrooei M, Casanova JL* (2021) Humans with inherited T cell CD28 deficiency are susceptible to skin papillomaviruses but are otherwise healthy. Cell 184(14): 3812-3828. doi: 10.1016/j.cell.2021.06.004.
• Kakihara K, Asamizu K, Moritsugu K, Kubo M, Kitaguchi T, Endo A, Kidera A, Ikeguchi M, Kato A, Komada M*, Fukushima T* (2021) Molecular basis of ubiquitin-specific protease 8 autoinhibition by the WW-like domain. Commun. Biol. 4(1): 1272. doi: 10.1038/s42003-021-02802-x.
• Chadani Y*, Sugata N, Niwa T, Ito Y, Iwasaki S, Taguchi H* (2021) Nascent polypeptide within the exit tunnel stabilizes the ribosome to counteract risky translation. EMBO J. 40(23) e108299 doi: 10.15252/embj.2021108299.
• Nanaura H, Kawamukai H, Fujiwara A, Uehara T, Aiba Y, Nakanishi M, Shiota T, Hibino M, Wiriyasermkul P, Kikuchi S, Nagata R, Matsubayashi M, Shinkai Y, Niwa T, Mannen T, Morikawa N, Naohiko Iguchi, Takao Kiriyama, Ken Morishima, Rintaro Inoue, Masaaki Sugiyama, Oda T, Kodera N, Toma-Fukai S, Sato M, Taguchi H, Nagamori S, Shoji O, Ishimori K, Matsumura H, Sugie K, Saio T*, Yoshizawa T*, Mori E* (2021) C9orf72-derived arginine-rich poly-dipeptides impede phase modifiers. Nature Commun. 12(1) 5301-5301 doi: 10.1038/s41467-021-25560-0.
• Shimada T, Nakazawa K, Tachikawa T, Saito N, Niwa T, Taguchi H, Tanaka K* (2021) Acetate overflow metabolism regulates a major metabolic shift after glucose depletion in Escherichia coli. FEBS lett. 595(15) 2047-2056 doi: 10.1002/1873-3468.14151.
• Nakane K, Sato S, Niwa T, Tsushima M, Tomoshige S, Taguchi H, Ishikawa M, Nakamura H (2021) Proximity Histidine Labeling by Umpolung Strategy Using Singlet Oxygen. J. Am. Chem. Soc. 143(20) 7726-7731 doi: 10.1021/jacs.1c01626.
• Deyama T, Matsui Y, Chadani Y, Sekine Y, Doi N, Fujiwara K* (2021) Transcription-translation of the Escherichia coli genome within artificial cells. Chem. Commun. (Camb.) 57:10367-10370.
• Trinh MDL, Miyazaki D, Ono S, Nomata J, Kono M, Mino H, Niwa T, Okegawa Y, Motohashi K, Taguchi H, Hisabori T, Masuda S* (2021) The evolutionary conserved iron-sulfur protein TCR controls P700 oxidation in photosystem I. iScience 24(2) 102059-102059 doi: 10.1016/j.isci.2021.102059.
• Sugimoto S*, Yamanaka K, Niwa T, Terasawa Y, Kinjo Y, Mizunoe Y, Ogura T (2021) Hierarchical Model for the Role of J-Domain Proteins in Distinct Cellular Functions. J. Mol. Biol. 433(3) 166750-166750 doi: 10.1016/j.jmb.2020.166750.
• Makino S, Kawamata T, Iwasaki S, Ohsumi Y. Selectivity of mRNA degradation by autophagy in yeast Nat. commun. 2021, 12:2316
• Imada T, Shimi T, Kaiho A, Saeki Y, Kimura H. RNA polymerase II condensate formation and association with Cajal and histone locus bodies in living human cells. Genes Cells 2021, in press.
• Sousa-Luís R, Dujardin G, Zukher I, Kimura H, Weldon C, Carmo-Fonseca M, Proudfoot NJ, Nojima T. POINT technology illuminates the processing of polymerase-associated intact nascent transcripts. Mol. cell 2021, in press.
• Zdravković A, Daley JM, Dutta A, Niwa T, Murayama Y, Kanamaru S, Ito K, Maki T, Argunhan B, Takahashi M, Tsubouchi H, Sung P, Iwasaki H. A conserved Ctp1/CtIP C-terminal peptide stimulates Mre11 endonuclease activity. PNAS 2021, 118(11): e2016287118.
• Hilbert L, Sato Y, Kuznetsova K, Bianucci T, Kimura H, Jülicher F, Honigmann A, Zaburdaev V, Vastenhouw NL. Transcription organizes euchromatin via microphase separation. Nat. Commun. 2021, 12:1360.
• Tjalsma SJD, Hori M, Sato Y, Bousard A, Ohi A, Raposo AC, Roensch J, Le Saux A, Nogami J, Maehara K, Kujirai T, Handa T, Bagés-Arnal S, Ohkawa Y, Kurumizaka H, da Rocha ST, Żylicz JJ, Kimura H, Heard E. H4K20me1 and H3K27me3 are concurrently loaded onto the inactive X chromosome but dispensable for inducing gene silencing. EMBO Rep. 2021, 22: e51989.
• Deschoenmaeker F, Mihara S, Niwa T, Taguchi H, Wakabayashi KI, Toyoshima M, Shimizu H, Hisabori T.J Biochem. Thioredoxin pathway in anabaena sp. PCC 7120: activity of NADPH-thioredoxin reductase C. J. Biochem. 2021, mvab014.
• Luu Trinh MD, Miyazaki D, Ono S, Nomata J, Kono M, Mino H, Niwa T, Okegawa Y, Motohashi K, Taguchi H, Hisabori T, Masuda S. The evolutionary conserved iron-sulfur protein TCR controls P700 oxidation in photosystem I. iScience 2021, 24(2): 102059.
• Sonoda Y, Kano F, Murata M. Applications of cell resealing to reconstitute microRNA loading to extracellular vesicles. Sci. Rep. 2021, 11:2900.
• Afshar N, Argunhan B, Palihati M, Taniguchi G, Tsubouchi H, Iwasaki H. A novel motif of Rad51 serves as an interaction hub for recombination auxiliary factors. eLife. 2021, 10: e64131.
• Kittisopikul M, Shimi T, Tatli M, Tran JR, Zheng Y, Medalia O, Jaqaman K, Adam SA, Goldman RD. Computational analyses reveal spatial relationships between nuclear pore complexes and specific lamins. J. Cell Biol. 2021, 220(4): e202007082.
• Ishida K, Naruse K, Mizouchi Y, Ogawa Y, Matsushita M, Shimi T, Kimura H, Fujiyoshi S. Variable immersion microscopy with a high numerical aperture. Opt. Lett. 2021, 46(4): 856-859.
• 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(4): e202000919.
• Tada M, Hayashi A, Asano Y, Kubiura-Ichimaru M, Ito T, Yoshii M, Kimura H, Matsuda Y, Oshimura M. Evidence for divergence of DNA methylation maintenance and a conserved inhibitory mechanism from DNA demethylation in chickens and mammals. Genes Genomics 2021, 43:269-280.
• Fujiwara Y, Yamanashi Y, Fujimura A, Sato Y, Kujirai T, Kurumizaka H, Kimura H, Yamatsugu K, Kawashima SA, Kanai M. Live-cell epigenome manipulation by synthetic histone acetylation catalyst system. PNAS 2021, 118(4): e2019554118.
• Miwa T, Chadani Y, Taguchi H. Escherichia coli small heat shock protein IbpA is an aggregation-sensor that self-regulates its own expression at post-transcriptional levels. Mol. Microbiol. 2021, 115(1): 142-156.

2020

• Kittisopikul M, Vahabikashi A, Shimi T, Goldman RD, Jaqaman K. Adaptive multiorientation resolution analysis of complex filamentous network images. Bioinformatics 2020, 36(20): 5093-5103.
• Sakamoto Y, Sato M, Sato Y, Harada A, Suzuki T, Goto C, Tamura K, Toyooka K, Kimura H, Ohkawa Y, Hara-Nishimura I, Takagi S, Matsunaga S. Subnuclear gene positioning through lamina association affects copper tolerance. Nat. Commun. 2020, 11:5914.
• Matsuda T, Hiyama TY, Kobayashi K, Kobayashi K, Noda M. Distinct CCK-positive SFO neurons are involved in persistent or transient suppression of water intake. Nat. Commun. 2020, 11:5692.
• Matoba K, Kotani T, Tsutsumi A, Tsuji T, Mori T, Noshiro D, Sugita Y, Nomura N, Iwata S, Ohsumi Y, Fujimoto T, Nakatogawa H, Kikkawa M, Noda NN. Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion. Nat. Struct. Mol. Biol. 2020, 27: 1185-1193.
• Gruszka　DT, Xie S, Kimura H, Yardimci H. Single-molecule imaging reveals control of parental histone recycling by free histones during DNA replication. Sci. Advances 2020, 6(38): eabc0330.
• Murakawa T, Kinger AA, Sakamaki Y, Fukuda M, Fujita N. An autophagy-dependent tubular lysosomal network synchronizes degradative activity required for muscle remodeling. J. Cell Sci. 2020, 133: jcs248336.
• Fushimi K, Hoshino H, Shinozaki-Narikawa N, Kuwasaki Y, Miyake K, Nakajima T, Sato M, Kano F, Narikawa R. The Cruciality of Single Amino Acid Replacement for the Spectral Tuning of Biliverdin-Binding Cyanobacteriochromes. Int. J. Mol. Sci. 2020, 21(17): 6278.
• May AI, Prescott M, Ohsumi Y. Autophagy facilitates adaptation of budding yeast to respiratory growth by recycling serine for one-carbon metabolism. Nat. Commun. 2020, 11:5052.
• Handa T, Harada A, Maehara K, Sato S, Nakao M, Goto N, Kurumizaka H, Ohkawa Y, Kimura H. Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input. Nat. Protoc. 2020, 15:3334?3360.
• Perera SN, Williams RM, Lyne R, Stubbs O, Buehler DP, Sauka-Spengler T, Noda M, Micklem G, Southard-Smith EM, Baker CVH. Insights into olfactory ensheathing cell development from a laser-microdissection and transcriptome-profiling approach. Glia 2020, 68(12): 2550-2584.
• Kashiwagi D, Shen HK, Sim S, Sano K, Ishida Y, Kimura A, Niwa T, Taguchi H, Aida T. Molecularly Engineered “Janus GroEL”: Application to Supramolecular Copolymerization with a Higher Level of Sequence Control. J. Am. Chem. Soc. 2020, 142(31): 13310-13315.
• Martins NMC, Cisneros-Soberanis F, Pesenti E, Kochanova NY, Shang WH, Hori T, Nagase T, Kimura H, Larionov V, Masumoto H, Fukagawa T, Earnshaw WC. H3K9me3 maintenance on a Human Artificial Chromosome is required for segregation but not centromere epigenetic memory. J. Cell Sci. 2020, 133: jcs242610.
• Hayashi-Takanaka Y, Kina Y, Nakamura F, Becking LE, Nakao Y, Nagase T, Nozaki N, Kimura H. Histone modification dynamics as revealed by a multicolor immunofluorescence-based single-cell analysis. J. Cell Sci. 2020, 133: jcs243444.
• Ideno H, Nakashima K, Komatsu K, Araki R, Abe M, Arai Y, Kimura H, Shinkai Y, Tachibana M, Nifuji A. G9a is involved in the regulation of cranial bone formation through activation of Runx2 function during development. Bone 2020, 137:115332.
• Ochiai H, Hayashi T, Umeda M, Yoshimura M, Harada A, Shimizu Y, Nakano K, Saitoh N, Liu Z, Yamamoto T, Okamura T, Ohkawa Y, Kimura H, Nikaido I. Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells. Sci. Advances 2020, 6(25): eaaz6699.
• Watson NA, Cartwright TN, Lawless C, Camara-Donoso M, Sen O, Sako K, Hirota T, Kimura H, Higgins JMG. Kinase inhibition profiles as a tool to identify kinases for specific phosphorylation sites. Nat. Commun. 2020, 11:1684.
• Golfier S, Quail T, Kimura H, Brugues J. Cohesin and condensin extrude DNA loops in a cell cycle-dependent manner. eLife 2020, 9: e53885.
• Onaka AT, Su J, Katahira Y, Tang C, Zafar F, Aoki K, Kagawa W, Niki H, Iwasaki H, Nakagawa T. DNA replication machinery prevents Rad52-dependent single-strand annealing that leads to gross chromosomal rearrangements at centromeres. Commun. Biol. 2020, 3:202.
• Tsubouchi H, Argunhan B, Ito K, Takahashi M, Iwasaki H. Two auxiliary factors promote Dmc1-driven DNA strand exchange via stepwise mechanisms. PNAS 2020, 117(22): 12062-12070.
• Ito K, Murayama Y, Kurokawa Y, Kanamaru S, Kokabu Y, Maki T, Mikawa T, Argunhan B, Tsubouchi H, Ikeguchi M, Takahashi M, Iwasaki H. Real-time tracking reveals catalytic roles for the two DNA binding sites of Rad51. Nat. Commun. 2020, 11:2950.
• Tomioka Y, Kotani T, Kirisako H, Oikawa Y, Kimura Y, Hirano H, Ohsumi Y, Nakatogawa H. TORC1 inactivation stimulates autophagy of nucleoporin and nuclear pore complexes. J. Cell Biol. 2020, 219(7): e201910063.
• Yamasaki A, Jin Y, Ohsumi Y. Mitotic phosphorylation of the ULK complex regulates cell cycle progression. PLoS Biol. 2020, 18(6): e3000718.
• Sakuta H, Lin CH, Yamada M, Kita Y, Tokuoka SM, Shimizu T, Noda M. Na_x-positive glial cells in the organum vasculosum laminae terminalis produce epoxyeicosatrienoic acids to induce water intake in response to increases in [Na⁺] in body fluids. Neurosci. Res. 2020, 154: 45-51.
• Sakuta H, Lin CH, Hiyama TY, Matsuda T, Yamaguchi K, Shigenobu S, Kobayashi K, Noda M. SLC9A4 in the organum vasculosum of the lamina terminalis is a [Na⁺] sensor for the control of water intake. Eur. J. Phys. 2020, 472: 609-624.
• Argunhan B, Sakakura M, Afshar N, Kurihara M, Ito K, Maki T, Kanamaru S, Murayama Y, Tsubouchi H, Takahashi M, Takahashi H, Iwasaki H. Cooperative interactions facilitate stimulation of Rad51 by the Swi5-Sfr1 auxiliary factor complex. eLife 2020, 9: e52566.
• Konno H, Watanabe-Nakayama T, Uchihashi T, Okuda M, Zhu L, Kodera N, Kikuchi Y, Ando T, Taguchi H. Dynamics of oligomer and amyloid fibril formation by yeast prion Sup35 observed by high-speed atomic force microscopy. PNAS 2020, 117 (14): 7831-7836.
• Muta M, Iizuka R, Niwa T, Guo Y, Taguchi H, Funatsu T. Nascent SecM chain interacts with outer ribosomal surface to stabilize translation arrest. Biochemical J. 2020, 477(2) 557-566.
• Naito S, Fukushima T, Endo A, Denda K, Komada M. Nik-related kinase is targeted for proteasomal degradation by the chaperone-dependent ubiquitin ligase CHIP. FEBS PRESS 2020, 594(11): 1778-1786.
• Higashijima Y, Matsui Y, Shimamura T, Nakaki R, Nagai N, Tsutsumi S, Abe Y, Link VM, Osaka M, Yoshida M, Watanabe R, Tanaka T, Taguchi A, Miura M, Ruan X, Li G, Inoue T, Nangaku M, Kimura H, Furukawa T, Aburatani H, Wada Y, Ruan Y, Glass CK, Kanki Y. Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells. EMBO J. 2020, e103949.
• Fujioka Y, Alam JM, Noshiro D, Mouri K, Ando T, Okada Y, May AI, Knorr RL, Suzuki K, Ohsumi Y, Noda NN. Phase separation organizes the site of autophagosome formation. Nature 2020, 578:301-305.
• Yamasaki A, Alam JM, Noshiro D, Hirata E, Fujioka Y, Suzuki K, Ohsumi Y, Noda NN. Liquidity Is a Critical Determinant for Selective Autophagy of Protein Condensates. Mol. Cell 2020, 77(6): 1163-1175.
• Shinozaki D, Merkulova EA, Naya L, Horie T, Kanno Y, Seo M, Ohsumi Y, Masclaux Daubresse C, Yoshimoto K. Autophagy Increases Zinc Bioavailability to Avoid Light-Mediated ROS Production under Zn Deficiency. Plant. Physiol. 2020, 182: 1284-1296.
• Mattioni A, Boldt K, Auciello G, Komada M, Rappoport JZ, Ueffing M, Castagnoli L, Cesareni G, Santonico E. Ring Finger Protein 11 (RNF11) acts on ligand-activated EGFR via the direct interaction with the UIM region of ANKRD13 protein family. FEBS J. 2020, https://doi.org/10.1111/febs.15226.

2019

• Denda K, Ida K, Tanno M, Nakao-Wakabayashi K, Komada M, Hayashi N. Proteomic analysis of Nrk gene-disrupted placental tissue cells explains physiological significance of NRK. BMC Res. Notes 2019, 12:785.
• Nakato R, Wada Y, Nakaki R, Nagae G, Katou Y, Tsutsumi S, Nakajima N, Fukuhara H, Iguchi A, Kohro T, Kanki Y, Saito Y, Kobayashi M, Izumi-Taguchi A, Osato N, Tatsuno K, Kamio A, Hayashi-Takanaka Y, Wada H, Ohta S, Aikawa M, Nakajima H, Nakamura M, McGee RC, Heppner KW, Kawakatsu T, Genno M, Yanase H, Kume H, Senbonmatsu T, Homma Y, Nishimura S, Mitsuyama T, Aburatani H, Kimura H, Shirahige K. Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells. Epigenetics & Chromatin 2019, 12:77.
• Nakamura S, Hira S, Fujiwara M, Miyagata N, Tsuji T, Kondo A, Kimura H, Shinozuka Y, Hayashi M, Kobayashi S, Mukai M. A truncated form of a transcription factor Mamo activates vasa in Drosophila embryos. Commun. Biol. 2019, 2:422.
• Liu C, Kobashigawa Y, Yamauchi S, Toyota Y, Teramoto M, Ikeguchi Y, Fukuda N, Sato T, Sato Y, Kimura H, Morioka H. Preparation of single-chain Fv antibodies in the cytoplasm of Escherichia coli by simplified and systematic chaperone optimization. J. Biol. Chem. 2019, 166(6): 455-462.
• Dacher M, Tachiwana H, Horikoshi N, Kujirai T, Taguchi H, Kimura H, Kurumizaka H. Incorporation and influence of Leishmania histone H3 in chromatin. Nucleic Acids Res. 2019, 47(22): 16637-11648.
• Suda K, Muraoka Y, Ortega-Yanez A, Yoshida H, Kizu F, Hochin T, Kimura H, Yamaguchi M. Reduction of Rpd3 suppresses defects in locomotive ability and neuronal morphology induced by the knockdown of Drosophila SLC25A46 via an epigenetic pathway. Exp. Cell Res. 2019, 385(2): 111673.
• Karoutas A, Szymanski W, Rausch T, Guhathakurta S, Rog-Zielinska EA, Peyronnet R, Seyfferth J, Chen HR, de Leeuw R, Herquel B, Kimura H, Mittler G, Kohl P, Medalia O, Korbel JO, Akhtar A. The NSL complex maintains nuclear architecture stability via lamin A/C acetylation. Nat. Cell Bioligy 2019, 21:1248-1260.
• Ohka F, Shinjo K, Deguchi S, Matsui Y, Okuno Y, Katsushima K, Suzuki M, Kato A, Ogiso N, Yamamichi A, Aoki K, Suzuki H, Sato S, Arul Rayan N, Prabhakar S, Goke J, Shimamura T, Maruyama R, Takahashi S, Suzumura A, Kimura H, Wakabayashi T, Zong H, Natsume A, Kondo Y. Pathogenic Epigenetic Consequences of Genetic Alterations in IDH-Wild-Type Diffuse Astrocytic Gliomas. Cancer Res. 2019, 79(19): 4814.
• Yamauchi S, Kobashigawa Y, Fukuda N, Teramoto M, Toyota Y, Liu C, Ikeguchi Y, Sato T, Sato Y, Kimura H, Masuda T, Ohtsuki S, Noi K, Ogura T, Morioka H. Cyclization of Single-Chain Fv Antibodies Markedly Suppressed Their Characteristic Aggregation Mediated by Inter-Chain VH-VL Interactions. Molecules 2019, 24(14): 2620.
• Tsushima M, Sato S, Niwa T, Taguchi H, Nakamura H. Catalyst-proximity protein chemical labelling on affinity beads targeting endogenous lectins. Chemical Commun. 2019, 55(88): 13275-13278.
• Fukuura K, Inoue Y, Miyajima C, Watanabe S, Tokugawa M, Morishita D, Ohoka N, Komada M, Hayashi H. The ubiquitin-specific protease USP17 prevents cellular senescence by stabilizing the methyltransferase SET8 and transcriptionally repressing p21. J. Biol. Chem. 2019, 294(44): 16429-16439.
• Nakatsu D, Kano F, Shinozaki-Narikawa N, Murata M. Pyk2-dependent phosphorylation of LSR enhances localization of LSR and tricellulin at tricellular tight junctions. PLoS One 2019, 14(10): e0223300.
• Kano F, Murata M. Semi-Intact Cell System for Reconstituting and Analyzing Cellular Golgi Dynamics. The Golgi Apparatus and Centriole 2019, 67: 233-250.
• Fukuda T, Kawai-Noma S, Pack CG, Taguchi H. Large-scale analysis of diffusional dynamics of proteins in living yeast cells using fluorescence correlation spectroscopy. Biochem. Biophys. Res. Commun. 2019, 520(2): 237-242.
• Sato Y, Hilbert L, Oda H, Wan Y, Heddleston JM, Chew TL, Zaburdaev V, Keller P, Lionnet T, Vastenhouw N, Kimura H. Histone H3K27 acetylation precedes active transcription during zebrafish zygotic genome activation as revealed by live-cell analysis. Development 2019, 146: dev179127.
• Winkelman BHJ, Howlett MHC, Holzel MB, Joling C, Fransen KH, Pangeni G, Kamermans S, Sakuta H, Noda M, Simonsz HJ, McCall MA, De Zeeuw CI, Kamermans M. Nystagmus in patients with congenital stationary night blindness (CSNB) originates from synchronously firing retinal ganglion cells PLoS Biol. 2019, 17(9): e3000174.
• Fujikawa, A, Sugawara H, Tanga N, Ishii K, Kuboyama K, Uchiyama S, Suszuki R, Noda M. A head-to-toe dimerization has physiological relevance for ligand-induced inactivation of protein tyrosine receptor type Z. J. Biol. Chem. 2019, 294(41): 14953-14965.
• Fujikawa A, Noda Y, Yamamoto H, Tanga N, Sakaguchi G, Hattori S, Song WJ, Sora I, Nabeshima T, Katsuura G, Noda M. Mice deficient in protein tyrosine phosphatase receptor type Z (PTPRZ) show reduced responsivity to methamphetamine despite an enhanced response to novelty. PLoS One 2019, 14(8): e0221205.
• Sakuta H, Lin CH, Yamada M, Kita Y, Tokuoka SM, Shimizu T, Noda M. Na_x-positive glial cells in the organum vasculosum laminae terminalis produce epoxyeicosatrienoic acids to induce water intake in response to increases in [Na⁺] in body fluids. Neurosci. Res. 2019, pii: S0168-0102(19)30068-9.
• Chung CI, Sato Y, Ohmuro-Mutsuyama Y, Machida S, Kurumizaka H, Kimura H, Ueda H. Intrabody-based FRET probe to visualize endogenous histone acetylation. Sci. Rep. 2019, 9:10188.
• Horikoshi N, Kujirai T, Sato K, Kimura H, Kurumizaka H. Structure-based design of an H2A.Z.1 mutant stabilizing a nucleosome in vitro and in vivo. Biochem. Biophys. Res. Commun. 2019, 515(4): 719-724.
• Zhao N, Kamijo K, Fox PD, Oda H, Morisaki T, Sato Y, Kimura H, Stasevich TJ. A genetically encoded probe for imaging nascent and mature HA-tagged proteins in vivo. Nat. Commun. 2019, 10(1): 2947.
• Tanga N, Kuboyama K, Kishimoto A, Kihara M, Kiyonari H, Watanabe T, Fujikawa A, Noda M. Behavioral and neurological analyses of adult mice carrying null and distinct loss-of-receptor function mutation in protein tyrosine phosphatase receptor type Z (PTPRZ). PLoS One 2019, 14(6): e0217880.
• Tanga N, Kuboyama K, Kishimoto A, Kiyonari H, Shiraishi A, Suzuki R, Watanabe T, Fujikawa A, Noda M. The PTN-PTPRZ signal activates the AFAP1L2-dependent PI3K-AKT pathway for oligodendrocyte differentiation: Targeted inactivation of PTPRZ activity in mice. Glia 2019, 67, 967-984.
• Hayashi-Takanaka Y, Kina Y, Nakamura F, Yamazaki S, Harata M, Soest RWMV, Kimura H, Nakao Y. Effect of mycalolides isolated from a marine sponge Mycale aff. nullarosette on actin in living cells. Sci. Rep. 2019, 9:7540.
• Iwama R, Ohsumi Y. Analysis of autophagy activated during changes in carbon source availability in yeast cells. J. Biol. Chem. 2019, 294(14): 5590-5603.
• Homma Y, Kinoshita R, Kuchitsu Y, Wawro PS, Marubashi S, Oguchi ME, Ishida M, Fujita N, Fukuda M. Comprehensive knockout analysis of the Rab family GTPases in epithelial cells. J. Cell Biol. 2019, 218(6): 2035.
• Deschoenmaeker F, Mihara S, Niwa T, Taguchi H, Nomata J, Wakabayashi K, Hisabori T. Disruption of the Gene trx-m1 Impedes the Growth of Anabaena sp. PCC 7120 under Nitrogen Starvation. Plant Cell Physiol. 2019, 60(7): 1504-1513.
• Niwa T, Uemura E, Matsuno Y, Taguchi H. Translation‐coupled protein folding assay using a protease to monitor the folding status. Protein Sci. 2019, 03 May.
• Nojima T, Niwa T, Taguchi H. Proteome Analysis of Phase-Separated Condensed Proteins with Ionic Surfactants Revealed Versatile Formation of Artificial Biomolecular Condensates. Biomacromolecules 2019, 20(1): 539-545.
• Furuki T, Niwa T, Taguchi H, Hatanaka R, Kikawada T, Sakurai M. A LEA model peptide protects the function of a red fluorescent protein in the dry state. Biochem. Biophys. Rep. 2019, 17:27-31.
• Osawa T, Kotani T, Kawaoka T, Hirata E, Suzuki K, Nakatogawa H, Ohsumi Y, Noda NN. Atg2 mediates direct lipid transfer between membranes for autophagosome formation. Nat. Struct. Mol. Biol. 2019, 26(4): 281-288.
• Harada K, Kotani T, Kirisako H, Sakoh-Nakatogawa M, Oikawa Y, Kimura Y, Hirano H, Yamamoto H, Ohsumi Y, Nakatogawa H. Two distinct mechanisms target the autophagy-related E3 complex to the pre-autophagosomal structure. eLife 2019, 8: e43088.
• Nagashima R, Hibino K, Ashwin SS, Babokhov M, Fujishiro S, Imai R, Nozaki T, Tamura S, Tani T, Kimura H, Shribak M, Kanemaki MT, Sasai M, Maeshima K. Single nucleosome imaging reveals loose genome chromatin networks via active RNA polymerase II. J. Cell Biol. 2019, 218(5): 1511.
• Matsuda T, Irie T, Katsurabayashi S, Hayashi Y, Nagai T, Hamazaki N, Adefuin AMD, Miura F, Ito T, Kimura H, Shirahige K, Takeda T, Iwasaki K, Imamura T, Nakashima K. Pioneer Factor NeuroD1 Rearranges Transcriptional and Epigenetic Profiles to Execute Microglia-Neuron Conversion. NEURON 2019, 101(3): 472-485.e7.
• Murashima A, Shinjo K, Katsushima K, Onuki T, Kondoh Y, Osada H, Kagaya N, Shin-ya K, Kimura H, Yoshida M, Murakami S, Kondo Y. Identification of a chemical modulator of EZH2-mediated silencing by cell-based high-throughput screening assay. J. Biochemistry 2019, 166(1): 41-50.
• Arimura Y, Tachiwana H, Takagi H, Hori T, Kimura H, Fukagawa T, Kurumizaka H. The CENP-A centromere targeting domain facilitates H4K20 monomethylation in the nucleosome by structural polymorphism. Nat. Commun. 2019, 10:576.
• Shimi T, Kimura H. A mosaic of old and young nucleoporins. J. Cell Biol. 2019, 218(2): 385.
• Ito K, Argunhan B, Tsubouchi H, Iwasaki H. Real-time Observation of the DNA Strand Exchange Reaction Mediated by Rad51. J. Vis. Exp. 2019, Feb 13; (144).
• Thon G, Maki T, Haber JE, Iwasaki H. Mating-type switching by homology-directed recombinational repair: a matter of choice. Curr. Genet. 2019, 65(2): 351-362.
• Kunishige R, Kano F, Murata M. The cell resealing technique for manipulating, visualizing, and elucidating molecular functions in living cells. BBA Gen. Subj. 2019, S0304-4165 (19): 30071-30076.
• Kano F, Murata M. Phosphatidylinositol-3-phosphate-mediated actin domain formation linked to DNA synthesis upon insulin treatment in rat hepatoma-derived H4IIEC3 cells. BBA Mol. Cell Res. 2019, 1866 (5): 793-805.
• Ogasawara F, Kano F, Murata M, Kimura Y, Kioka N, Ueda K. Changes in the asymmetric distribution of cholesterol in the plasma membrane influence streptolysin O pore formation. Sci. Rep. 2019, 9:4548.
• Chan WH, Komada M, Fukushima T, Southard-Smith EM, Anderson CR, Wakefield MJ. RNA-seq of Isolated Chromaffin Cells Highlights the Role of Sex-Linked and Imprinted Genes in Adrenal Medulla Development. Sci. Rep. 2019, 9:3929.
• Sakai R, Fukuda R, Unida S, Aki M, Ono Y, Endo A, Kusumi S, Koga D, Fukushima T, Komada M, Okiyoneda T. The integral function of the endocytic recycling compartment is regulated by RFFL-mediated ubiquitylation of Rab11 effectors. J. Cell. Sci. 2019, 132: jcs228007.
• Yamagata K, Nagai K, Miyamoto H, Anzai M, Kato H, Miyamoto K, Kurosaka S, Azuma R, Kolodeznikov II, Protopopov AV, Plotnikov VV, Kobayashi H, Kawahara-Miki R, Kono T, Uchida M, Shibata Y, Handa T, Kimura H, Hosoi Y, Mitani T, Matsumoto K, Iritani A. Signs of biological activities of 28,000-year-old mammoth nuclei in mouse oocytes visualized by live-cell imaging. Sci. Rep. 2019, 9:4050.
• Okita AK, Zafar F, Su J, Weerasekara D, Kajitani T, Takahashi TS, Kimura H, Murakami Y, Masukata H, Nakagawa T. Heterochromatin suppresses gross chromosomal rearrangements at centromeres by repressing Tfs1/TFIIS-dependent transcription. Commun. Biol. 2019, 2:17.
• Harada A, Maehara K, Handa T, Arimura Y, Nogami J, Hayashi-Takanaka Y, Shirahige K, Kurumizaka H, Kimura H, Ohkawa Y. A chromatin integration labelling method enables epigenomic profiling with lower input. Nat. Cell Biology 2019, 21:287-296.

2018

• Nomura K, Hiyama TY, Sakuta H, Matsuda T, Lin CH, Kobayashi K, Kobayashi K, Kuwaki T, Takahashi K, Matsui S, Noda M. [Na⁺] increases in body fluids sensed by central Na_x induce sympathetically mediated blood pressure elevations via H⁺-dependent activation of ASIC1a. Neuron 2018, 101, 60-75.
• Sugita S, Watanabe K, Hashimoto K, Niwa T, Uemura E, Taguchi H, Watanabe YH. Electrostatic interactions between middle domain motif-1 and the AAA1 module of the bacterial ClpB chaperone are essential for protein disaggregation. J. Biol. Chem. 2018, 293(50): 19228-19239.
• Deschoenmaeker F, Mihara S, Niwa T, Taguchi H, Wakabayashi K, Hisabori T. The Absence of Thioredoxin m1 and Thioredoxin C in Anabaena sp. PCC 7120 Leads to Oxidative Stress. Plant Cell Physiol. 2018, 59(12): 2432-2441.
• Liu XM, Yamasaki A, Du XM, Coffman VC, Ohsumi Y, Nakatogawa H, Wu JQ, Noda NN. Lipidation-independent vacuolar functions of Atg8 rely on its noncanonical interaction with a vacuole membrane protein. eLife 2018, 7: e41237.
• Watanabe-Takahashi M, Yamasaki S, Murata M, Kano F, Motoyama J, Yamate J, Omi J, Sato W, Ukai H, Shimasaki K, Ikegawa M, Tamura-Nakano M, Yanoshita R, Nishino Y, Miyazawa A, Natori Y, Toyama-Sorimachi N, Nishikawa K. Exosome-associated Shiga toxin 2 is released from cells and causes severe toxicity in mice. Sci. Rep. 2018, 17:10776.
• Lu CH, Yeh HY, Su GC, Ito K, Kurosawa Y, Iwasaki H, Chi P, Li HW. Swi5-Sfr1 stimulates Rad51 recombinase filament assembly by modulating Rad51 dissociation. Proc. Natl. Acad. Sci. USA. 2018, 115(43): E10059-E10068.
• Kotani T, Kirisako H, Koizumi M, Ohsumi Y, Nakatogawa H. The Atg2-Atg18 complex tethers pre-autophagosomal membranes to the endoplasmic reticulum for autophagosome formation. Proc. Natl. Acad. Sci. USA. 2018, 115(41): 10363-10368.
• Yoshimoto K, Ohsumi Y. Unveiling the Molecular Mechanisms of Plant Autophagy?From Autophagosomes to Vacuoles in Plants. Plant Cell Physiol. 2018, 59(7): 1337-1344.
• Sato Y, Stasevich TJ, Kimura H. Visualizing the Dynamics of Inactive X Chromosomes in Living Cells Using Antibody-Based Fluorescent Probes. X-Chromosome Inactivation 2018, 91-102.
• Azuma Y, Imai H, Kawaguchi Y, Nakase I, Kimura H, Futaki S. Modular Redesign of a Cationic Lytic Peptide To Promote the Endosomal Escape of Biomacromolecules. Angewandte Chemie 2018, 57(39): 12771-12774.
• Handoko L, Kaczkowski B, Hon CC, Lizio M, Wakamori M, Matsuda T, Ito T, Jeyamohan P, Sato Y, Sakamoto K, Yokoyama S, Kimura H, Minoda A, Umehara T. JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states. Epigenetics 2018, 13, 4:410-431.
• 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(19): 10007-10018.
• Arai E, Miura F, Totoki Y, Yamashita S, Tian Y, Gotoh M, Ojima H, Nakagawa H, Takahashi Y, Nakamura H, Hama N, Kato M, Kimura H, Suzuki Y, Ito T, Shibata T, Kanai Y. Epigenome mapping of human normal purified hepatocytes: personal epigenome variation and genome-epigenome correlation. Epigenomics 2018, 10, 7.
• 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, 71:14-41.
• Takeuchi A, Iida K, Tsubota T, Hosokawa M, Denawa M, Brown JB, Ninomiya K, Ito M, Kimura H, Abe T, Kiyonari H, Ohno K, Hagiwara M. Loss of Sfpq Causes Long-Gene Transcriptopathy in the Brain. Cell Rep. 2018, 23(5): 1326-1341.
• Abe Y, Fujiwara Y, Takahashi H, Matsumura Y, Sawada T, Jiang S, Nakaki R, Uchida A, Nagao N, Naito M, Kajimura S, Kimura H, Osborne TF, Aburatani H, Kodama T, Inagaki T, Sakai J. Histone demethylase JMJD1A coordinates acute and chronic adaptation to cold stress via thermogenic phospho-switch. Nat. Commun. 2018, 9:1566.
• Maki T, Ogura N, Haber JE, Iwasaki H, Thon G. New insights into donor directionality of mating-type switching in Schizosaccharomyces pombe. PLoS Genetics 2018, 14(5): e1007424.
• Kawaguchi K, Endo A, Fukushima T, Madoka Y, Tanaka T, Komada M. Ubiquitin-specific protease 8 deubiquitinates Sec31A and decreases large COPII carriers and collagen IV secretion. Biochem. Biophys. Res. Commun. 2018, 499(3): 635-641.
• 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, Ohkawa Y. Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration. Nat. Commun. 2018, 9(1):1400.
• Kuroki S, Nakai Y, Maeda R, Okashita N, Akiyoshi M, Yamaguchi Y, Kitano S, Miyachi H, Nakato R, Ichiyanagi K, Shirahige K, Kimura H, Shinkai Y, Tachibana M. Combined Loss of JMJD1A and JMJD1B Reveals Critical Roles for H3K9 Demethylation in the Maintenance of Embryonic Stem Cells and Early Embryogenesis. Stem Cell Reports 2018, 10(4): 1340-1354.
• Ruppert JG, Samejima K, Platani M, Molina O, Kimura H, Jeyaprakash AA, Ohta S, Earnshaw WC. HP1α targets the chromosomal passenger complex for activation at heterochromatin before mitotic entry. EMBO J. 2018, 37(6): e97677.
• Jenness C, Giunta S, Muller MM, Kimura H, Muir TW, Funabiki H. HELLS and CDCA7 comprise a bipartite nucleosome remodeling complex defective in ICF syndrome. Proc. Natl. Acad. Sci. USA 2018, 115(5): E876-E885.
• Chen CCL, Goyal P, Karimi MM, Abildgaard MH, Kimura H, Lorincz MC. H3S10ph broadly marks early-replicating domains in interphase ESCs and shows reciprocal antagonism with H3K9me2. Genome Res. 2018, 28(1): 37-51.
• Shiraishi K, Shindo A, Harada A, Kurumizaka H, Kimura H, Ohkawa Y, Matsuyama H. Roles of histone H3.5 in human spermatogenesis and spermatogenic disorders. Andrology 2018, 6(1): 158-165.
• Yamaguchi M, Satoo K, Suzuki H, Fujioka Y, Ohsumi Y, Inagaki F, Noda NN. Atg7 Activates an Autophagy-Essential Ubiquitin-like Protein Atg8 through Multi-Step Recognition. J. Mol. Biol. 2018, 430(3): 249-257.
• Kim R, Kanamaru S, Mikawa T, Prevost C, Ishii K, Ito K, Uchiyama S, Oda M, Iwasaki H, Kim SK, Takahashi M. RecA requires two molecules of Mg2+ ions for its optimal strand exchange activity in vitro. Nucleic Acids Res. 2018, 46:2548-2559.
• Murayama Y, Samora CP, Kurokawa Y, Iwasaki H, Uhlmann F. Establishment of DNA-DNA interactions by the cohesin ring. Cell 2018, 172:465-477.
• Ito K, Murayama Y, Takahashi M, Iwasaki H. Two three-strand intermediates are processed during Rad51-driven DNA strand exchange. Nat. Struct. Mol. Biol. 2018, 25:29-36.
• Murakami M, Kano F, Murata M. LLO-mediated cell resealing system for analyzing intracellular activity of membrane-impermeable biopharmaceuticals of mid-sized molecular weight. Sci. Rep. 2018, 8(1): 1946.
• Yamaoki Y, Kiyoishi A, Miyake M, Kano F, Murata M, Nagata T, Katahira M. The first successful observation of in-cell NMR signals of DNA and RNA in living human cells. Phys. Chem. Chem. Phys. 2018, 20(5): 2982-2985.
• Xie X, Matsumoto S, Endo A, Fukushima T, Kawahara H, Saeki Y, Komada M. Deubiquitinases USP5 and USP13 are recruited to and regulate heat-induced stress granules by deubiquitinating activities. J. Cell Sci. 2018, 131: jcs210856.
• Tsuchiya H, Burana D, Ohtake F, Arai N, Kaiho A, Komada M, Tanaka K, Saeki Y. Ub-ProT reveals global length and composition of protein ubiquitylation in cells. Nat. Commun. 2018, 9(1): 524.
• Uemura E, Niwa T, Minami S, Takemoto K, Fukuchi S, Machida K, Imataka H, Ueda T, Ota M, Taguchi, H. Large-scale aggregation analysis of eukaryotic proteins reveals an involvement of intrinsically disordered regions in protein folding. Sci. Rep. 2018, 8:678.
• Kashiwagi D, Sim S, Niwa T, Taguchi H, Aida T. Protein Nanotube Selectively Cleavable with DNA: Supramolecular Polymerization of "DNA-Appended Molecular Chaperones. J. Am. Chem. Soc. 2018, 140:26-29.

2017

• Adachi A, Koizumi M, Ohsumi Y. Autophagy induction under carbon starvation conditions is negatively regulated by carbon catabolite repression. J. Biol. Chem. 2017, 292(48): 19905-19918.
• Asada R, Umeda M, Adachi A, Senmatsu S, Abe T, Iwasaki H, Ohta K, Hoffman C, Hirota K. Recruitment and delivery of the fission yeast Rst2 transcription factor via a local genome structure counteracts repression by Tup1-family corepressors. Nucleic. Acids Res. 2017, 45:9361-9371.
• Argunhan B, Leung WK, Afshar N, Terentyev Y, Subramanian VV, Murayama Y, Hochwagen A, Iwasaki H, Tsubouchi T, Tsubouchi H. Fundamental cell cycle kinases collaborate to ensure timely destruction of the synaptonemal complex during meiosis. EMBO J. 2017, 36:2488-2509.
• Jo M, Murayama Y, Tsutsui Y, Iwasaki H. In vitro site-specific recombination mediated by the tyrosine recombinase XerA of Thermoplasma acidophilum. Genes Cells 2017, 22:646-661.
• Kobayashi Y, Misumi O, Odahara M, Ishibashi K, Hirono M, Hidaka K, Endo M, Sugiyama H, Iwasaki H, Kuroiwa T, Shikanai T, Nishimura Y. Holliday junction resolvases mediate chloroplast nucleoid segregation. Science 2017, 356:631-634.
• Kano F, Noguchi Y, Murata, M. Establishment and phenotyping of disease model cells created by cell-resealing technique. Sci. Rep. 2017, 7:15167.
• Horiuchi Y, Nakatsu D, Kano F, Murata M. Pyruvate kinase M1 interacts with A-Raf and inhibits endoplasmic reticulum stress-induced apoptosis by activating MEK1/ERK pathway in mouse insulinoma cells. Cell Signal 2017, 38:212-222.
• An PNT, Shimaji K, Tanaka R, Yoshida H, Kimura H, Fukusaki E, Yamaguchi M. Epigenetic regulation of starvation-induced autophagy in Drosophila by histone methyltransferase G9a. Sci. Rep. 2017, 7(1): 7343.
• Arai R, Sugawara T, Sato Y, Minakuchi Y, Toyoda A, Nabeshima K, Kimura H, Kimura A. Reduction in chromosome mobility accompanies nuclear organization during early embryogenesis in Caenorhabditis elegans. Sci. Rep. 2017, 7(1): 3631.
• Imre L, Simándi Z, Horváth A, Fenyöfalvi G, Nánási P, Niaki EF, Hegedus É, Bacsó Z, Weyemi U, Mauser R, Ausio J, Jeltsch A, Bonner W, Nagy L, Kimura H, Szabó G. Nucleosome stability measured in situ by automated quantitative imaging. Sci. Rep. 2017, 7(1):12734.
• Isobe SY, Nagao K, Nozaki N, Kimura H, Obuse C. Inhibition of RIF1 by SCAI Allows BRCA1-Mediated Repair. Cell Rep. 2017, 20(2): 297-307.
• Kajitani T, Kato H, Chikashige Y, Tsutsumi C, Hiraoka Y, Kimura H, Ohkawa Y, Obuse C, Hermand D, Murakami Y. Ser7 of RNAPII-CTD facilitates heterochromatin formation by linking ncRNA to RNAi. Proc. Natl. Acad. Sci. USA 2017, 114(52): E11208-E11217.
• 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(3): 310-327.
• Kamiunten T, Ideno H, Shimada A, Arai Y, Terashima T, Tomooka Y, Nakamura Y, Nakashima K, Kimura H, Shinkai Y, Tachibana M, Nifuji A. Essential roles of G9a in cell proliferation and differentiation during tooth development. Exp. Cell Res. 2017, 357(2): 202-210.
• Kurita K, Sakamoto T, Yagi N, Sakamoto Y, Ito A, Nishino N, Sako K, Yoshida M, Kimura H, Seki M, Matsunaga S. Live imaging of H3K9 acetylation in plant cells. Sci. Rep. 2017, 7:45894.
• Partolina M, Thoms HC, MacLeod KG, Rodriguez-Blanco G, Clarke MN, Venkatasubramani AV, Beesoo R, Larionov V, Neergheen-Bhujun VS, Serrels B, Kimura H, Carragher NO, Kagansky A. Global histone modification fingerprinting in human cells using epigenetic reverse phase protein array. Cell Death Discov. 2017, 3:16077.
• Sato Y, Kimura H. Semi-quantitative Analysis of H4K20mel Levels in Living Cells Using Mintbody. Bio-protocol 2017, 7(10): e2276.
• Shiomi T, Muto A, Hozumi S, Kimura H, Kikuchi Y. Histone H3 Lysine 27 Trimethylation Leads to Loss of Mesendodermal Competence During Gastrulation in Zebrafish Ectodermal Cells. Zoo Sci. 2017, 34(1): 64-71.
• Shirai A, Kawaguchi T, Shimojo H, Muramatsu D, Ishida-Yonetani M, Nishimura Y, Kimura H, Nakayama JI, Shinkai Y. Impact of nucleic acid and methylated H3K9 binding activities of Suv39h1 on its heterochromatin assembly. eLife 2017, 6: e25317.
• Shishido Y, Baba T, Sato T, Shima Y, Miyabayashi K, Inoue M, Akiyama H, Kimura H, Kanai Y, Ishihara Y, Haraguchi S, Miyazaki A, Rozman D, Yamazaki T, Choi MH, Ohkawa Y, Suyama M, Morohashi KI. Differential lactate and cholesterol synthetic activities in XY and XX Sertoli cells. Sci. Rep. 2017, 7:41912.
• Taguchi H, Xie Y, Horikoshi N, Maehara K, Harada A, Nogami J, Sato K, Arimura Y, Osakabe A, Kujirai T, Iwasaki T, Semba Y, Tachibana T, Kimura H, Ohkawa Y, Kurumizaka H. Crystal Structure and Characterization of Novel Human Histone H3 Variants, H3.6, H3.7, and H3.8. Biochemistry 2017, 56(16): 2184-2196.
• 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. Testis-Specific Histone Variant H3t Gene Is Essential for Entry into Spermatogenesis. Cell Rep. 2017, 18(3): 593-600.
• Yamazaki T, Hatano Y, Handa T, Kato S, Hoida K, Yamamura R, Fukuyama T, Uematsu T, Kobayashi N, Kimura H, Yamagata K. Targeted DNA methylation in pericentromeres with genome editing-based artificial DNA methyltransferase. PLoS One 2017, 12(5): e0177764.
• Pack CG, Inoue Y, Higurashi T, Kawai-Noma S, Hayashi D, Craig E, Taguchi H. Heterogeneous interaction network of yeast prions and remodeling factors detected in live cells. BMB Rep. 2017, 50:478-483.
• Chadani Y, Niwa T, Izumi T, Sugata N, Nagao A, Suzuki T, Chiba S, Ito K, Taguchi H. Intrinsic ribosome destabilization underlies translation and provides an organism with a strategy of environmental sensing. Mol. Cell 2017, 68:528-539.
• Fujiwara K, Sawamura T, Niwa T, Deyama T, Nomura SM, Taguchi H, Doi N. In vitro transcription-translation using bacterial genome as a template to reconstitute intracellular profile. Nucleic Acids Res. 2017, 45:11449-11458.
• Fukushima T, Yoshihara H, Furuta H, Hakuno F, Iemura S, Natsume T, Nakatsu Y, Kamata H, Asano T, Komada M, Takahashi S. USP15 attenuates IGF-I signaling by antagonizing Nedd4-induced IRS-2 ubiquitination. Biochem. Biophys. Res. Commun. 2017, 484(3): 522-528.
• Horie T, Kawamata T, Matsunami M, Ohsumi Y. Recycling of iron via autophagy is critical for the transition from glycolytic to respiratory growth. J. Biol. Chem. 2017, 292(20): 8533-8543.
• Kawaguchi K, Uo K, Tanaka T, Komada M. Tandem UIMs confer Lys48 ubiquitin chain substrate preference to deubiquitinase USP25. Sci. Rep. 2017, 7:45037.
• Kawamata T, Horie T, Matsunami M, Sasaki M, Ohsumi Y. Zinc starvation induces autophagy in yeast. J. Biol. Chem. 2017, 292(20): 8520-8530.
• Horie T, Kawamata T, Ohsumi Y. Recycling of trace metals by the bulk autophagy in the budding yeast, Saccharomyces cerevisiae J. Adv. Nutr. Hum. Metab. 2017, 3, e1602.
• Komada M, Reincke M, Theodoropoulou M. USP8, ubiquitin-specific protease 8. Encyclopedia of Signaling Molecules, 2nd Edition 2017, 1-9.
• Taguchi Y, Horiuchi Y, Kano F, Murata M. Novel prosurvival function of Yip1A in human cervical cancer cells: constitutive activation of the IRE1 and PERK pathways of the unfolded protein response. Cell Death Dis. 2017, 8, e2718.

2016

• Goto M, Toda N, Shimaji K, Suong DN, Vo N, Kimura H, Yoshida H, Inoue YH, Yamaguchi M. Polycomb-dependent nucleolus localization of Jumonji/Jarid2 during Drosophila spermatogenesis. Spermatogenesis 2016, 6(3):e1232023.
• Katsushima K, Natsume A, Ohka F, Shinjo K, Hatanaka A, Ichimura N, Sato S, Takahashi S, Kimura H, Totoki Y, Shibata T, Naito M, Kim HJ, Miyata K, Kataoka K, Kondo Y. Targeting the Notch-regulated non-coding RNA TUG1 for glioma treatment. Nat. Commun. 2016, 7:13616.
• Burana D, Yoshihara, H, Tanno H, Yamamoto A, Saeki Y, Tanaka K, Komada M. Ankrd13 family of ubiquitin-interacting motif-bearing proteins regulates VCP/p97-mediated lysosomal traffic of caveolin-1. J. Biol. Chem. 2016, 291, 6218-6231.
• Chadani Y, Niwa T, Chiba S, Taguchi H, Ito K. Integrated in vivo and in vitro nascent chain profiling reveals widespread translational pausing. Proc. Natl. Acad. Sci. USA 2016, 113, E829-E838.
• Hansel-Hertsch R, Beraldi D, Lensing SV, Mar sico G, Zyner K, Parry A, Di Antonio M, Pike J, Kimura H, Narita M, Tannahill D, Balasubramanian S. G-quadruplex structures mark human regulatory chromatin. Nat. Genet. 2016, 48, 1267-1272.
• Hayashi K, Inoshita N, Kawaguchi K, Ardisasmita AI, Suzuki H, Fukuhara N, Okada M, Nishioka H, Takeuchi Y, Komada M, Takeshita A, Yamada S. The USP8 mutational status may predict drug susceptibility in corticotroph adenomas of Cushing's disease. Eur. J. Endocrinol. 2016, 174, 213-226.
• Kaimori J.Y, Maehara K, Hayashi-Takanaka Y, Harada A, Fukuda M, Yamamoto S, Ichimaru N, Umehara T, Yokoyama S, Matsuda R, Ikura T, Nagao K, Obuse C, Nozaki N, Takahara S, Takao T, Ohkawa Y, Kimura H, Isaka Y. Histone H4 lysine 20 acetylation is associated with gene repression in human cells. Sci. Rep. 2016, 6:24318.
• Kang Y, Wang J, Neff A, Kratzer S, Kimura H, Davis RE. Differential chromosomal localization of centromeric histone CENP-A contributes to nematode programmed DNA Elimination. Cell Rep. 2016, 16(9): 2308-23016.
• Katsushima K, Natsume A, Ohka F, Shinjo K, Hatanaka A, Ichimura N, Sato S, Takahashi S, Kimura H, Totoki Y, Shibata T, Naito M, Kim HJ, Miyata K, Kataoka K, Kondo Y. Targeting the Notch-regulated non-coding RNA TUG1 for glioma treatment. Nat. Commun. 2016, 7, 13616.
• Koide S, Oshima M, Takubo K, Yamazaki S, Nitta E, Saraya A, Aoyama K, Kato Y, Miyagi S, Nakajima-Takagi Y, Chiba T, Matsui H, Arai F, Suzuki Y, Kimura H, Nakauch H, Suda T, Shinkai Y, Iwama A. Setdb1 maintains hematopoietic stem and progenitor cells by restricting the ectopic activation of nonhematopoietic genes. Blood 2016, 128, 638-649.
• Kujirai T, Horikoshi N, Sato K, Maehara K, Machida S, Osakabe A, Kimura H, Ohkawa Y, Kurumizaka H. Structure and function of human histone H3.Y nucleosome. Nucleic Acids Res. 2016, 44, 6127-6141.
• Martins NM, Bergmann JH, Shono N, Kimura H, Larionov H, Masumoto H, Earnshaw WC. Epigenetic engineering shows that a human centromere resists silencing mediated by H3K27me3/K9me3. Mol. Biol. Cell 2016, 27, 177-196.
• Nakajima E, Shimaji K, Umegawachi T, Tomida S, Yoshida H, Yoshimoto N, Izawa S, Kimura H, Yamaguchi M. The histone deacetylase gene Rpd3 is required for starvation stress resistance. PLoS One 2016, 11, e0167554.
• Niwa T, Fujiwara K, Taguchi H. Identification of novel in vivo obligate GroEL/ES substrates based on data from a cell-free proteomics approach. FEBS Lett. 2016, 590, 251-257.
• Ohzeki J, Shono N, Otake K, Martins NM, Kugou K, Kimura H, Nagase T, Larionov V, Earnshaw WC, Masumoto H. KAT7/HBO1/MYST2 regulates CENP-A chromatin assembly by antagonizing Suv39h1-mediated centromere inactivation. Dev. Cell 2016, 37, 413-427.
• Oka M, Mura S, Yamada K, Sangel P, Hirata S, Maehara K, Kawakami K, Tachibana T, Ohkawa Y, Kimura H, Yoneda Y. Chromatin-prebound Crm1 recruits Nup98-HoxA9 fusion to induce aberrant expression of Hox cluster genes. eLife 2016, 5: e09540.
• Sato Y, Kujirai T, Arai R, Asakawa H, Ohtsuki C, Horikoshi N, Yamagata K, Ueda J, Nagase T, Haraguchi T, Hiraoka Y, Kimura A, Kurumizaka H, Kimura H. A genetically encoded probe for live-cell imaging of H4K20 monomethylation. J. Mol. Biol. 2016, 428, 3885-3902.
• Shang WH, Hori T, Westhorpe FG, Godek KM, Toyoda A, Misu S, Monma N, Ikeo K, Carroll CW, Takami Y, Fujiyama A, Kimura H, Straight AF, Fukagawa T. Acetylation of histone H4 lysine 5 and 12 is required for CENP-A deposition into centromeres. Nat. Commun. 2016, 7, 13465.
• Shimaji K, Konishi T, Yoshida H, Kimura H, Yamaguchi M. Genome-wide genetic screen identified the link between dG9a and epidermal growth factor receptor signaling pathway in vivo. Exp. Cell Res. 2016, 346, 53-64.
• Sim SH, Niwa T, Taguchi H, Aida T. Supramolecular nanotube of chaperonin GroEL: length control for cellular uptake using single-ring GroEL mutant as end-capper. J. Am. Chem. Soc. 2016, 138, 11152-11155.
• Suzuki M, Takagi C, Miura S, Sakane Y, Sakuma T, Sakamoto N, Endo T, Kamei Y, Sato Y, Kimura H, Yamamoto T, Ueno N, Suzuki KT. In vivo tracking of histone H3 lysine 9 acetylation in Xenopus laevis during tail regeneration. Genes Cells 2016, 21, 358-369.
• Suzuki S, Kato H, Suzuki Y, Chikashige Y, Hiraoka Y, Kimura H, Nagao K, Obuse C, Takahata S, Murakami Y. Histone H3K36 trimethylation is essential for multiple silencing mechanisms in fission yeast. Nucleic Acids Res. 2016, 44, 4147-4162.
• Urahama T, Harada A, Maehara K, Horikoshi H, Sato K, Sato Y, Shiraishi K, Sugino N, Osakabe A, Tachiwana H, Kagawa W, Kimura H, Ohkawa Y, Kurumizaka H. Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis. Epigenetics Chromatin 2016, 9, 2.
• Yamamoto H, Fujioka Y, Suzuki SW, Noshiro D, Suzuki H, Kondo-Kakuta C, Kimura Y, Hirano H, Ando T, Noda NN, Ohsumi Y. The intrinsically disordered protein Atg13 mediates supramolecular assembly of autophagy initiation complexes. Dev. Cell 2016, 38, 86-99.
• Yamasaki A, Watanabe Y, Adachi W, Suzuki K, Matoba K, Kirisako H, Kumeta H, Nakatogawa H, Ohsumi Y. Inagaki F, Noda NN. Structural basis for receptor-mediated selective autophagy of aminopeptidase I aggregates. Cell Rep. 2016, 16(1): 19-27.
• Yanagawa T, Denda K, Inatani T, Fukushima T, Tanaka T, Kumaki N, Inagaki Y, Komada M. Deficiency of X-linked protein kinase Nrk during pregnancy triggers breast tumor in mice. Am. J. Pathol. 2016, 186, 2751-2760.