2012

Hatakeyama, S. (2012) Ubiquitin-mediated regulation of JAK-STAT signaling in embryonic stem cells. JAK-STAT 1, 168-175.

Nojima, T., Konno, H., Kodera, N., Seio, K., Taguchi, H., and Yoshida, M. (2012) Nano-scale alignment of proteins on a flexible DNA backbone. PLoS One, doi:10.1371/journal.pone.0052534

Sato, K., Sundaramoorthy, E., Rajendra, E., Hattori, H., Jeyasekharan, A.D., Ayoub, N., Schiess, R., Aebersold, R., Nishikawa, H., Sedukhina, A.S., Wada, H., Ohta, T., and Venkitaraman, A.R. (2012) A DNA-damage selective role for BRCA1 E3 ligase in claspin ubiquitylation, CHK1 activation, and DNA repair. Curr. Biol. 22, 1659-1666

2013

Chiba, Y., Mineta, K., Hirai, M.Y., Suzuki, S., Kanaya, S., Takahashi, H., Onouchi, H., Yamaguchi, J., and Naito, S. (2013) Changes in mRNA stability associated with cold stress in Arabidopsis cells. Plant Cell Physiol. 54, 180-194

Fujita, N., Morita, E., Itoh, T., Tanaka, A., Nakaoka, M., Osada, Y., Umemoto, T., Saitoh, T., Nakatogawa, H., Kobayashi, S., Haraguchi, T., Guan, J.L., Iwai, K., Tokunaga, F., Saito, K., Ishibashi, K., Akira, S., Fukuda, M., Noda, T., and Yoshimori, T. (2013) Recruitment of the autophagic machinery to endosomes during infection is mediated by ubiquitin. J. Cell Biol. 203, 115-128

Hisabori, T., Sunamura, E.I., Kim, Y., and Konno, H. (2013) The chloroplast ATP synthase features the characteristic redox regulation machinery. Antioxid. Redox. Signal., doi:10.1089/ars.2012.5044

Ichimura, T., Taoka, M., Shoji, I., Kato, H., Sato, T., Hatakeyama, S., Isobe, T., and Hachiya, N. (2013) 14-3-3 proteins sequester a pool of soluble TRIM32 ubiquitin ligase to repress autoubiquitination and cytoplasmic body formation. J. Cell Sci. 126, 2014-2026

Ichimura, Y., Waguri, S., Sou, Y., Kageyama, S., Hasegawa, J., Ishimura, R., Saito, T., Yang, Y., Kouno, T., Fukutomi, T., Hoshii, T., Hirao, A., Takagi, K., Mizushima, T., Motohashi, H., Lee, M., Yoshimori, T., Tanaka, K., Yamamoto, M., and Komatsu, M. (2013) Phosphorylation of p62 activates the Keap1-Nrf2 pathway during selective autophagy. Mol. Cell 51, 618-631

Iguchi, M., Kujuro, Y., Okatsu, K., Koyano, F., Kimura, M., Suzuki, N., Uchiyama, S., Tanaka, K., and Matsuda, N. (2013) Parkin catalyzed ubiquitin-ester transfer is triggered by PINK1-dependent phosphorylation. J. Biol. Chem. 288, 22019-22032

Kawahara, H., Minami, R., and Yokota, N. (2013) BAG6/BAT3: Emerging roles in quality control for nascent polypeptides. J. Biochem. 153, 147-160

Kimura, Y., Fukushi, J., Hori, S., Matsuda, N., Okatsu, K., Kakiyama, Y., Kawawaki, J., Kakizuka, A., and Tanaka, K. (2013) Different dynamic movements of wild-type and pathogenic VCPs and their cofactors to damaged mitochondria in a Parkin-mediated mitochondrial quality control system. Genes Cells 18, 1131-1143

Kishikawa, J., Ibuki, T., Nakamura, S., Nakanishi, A., Minamino, T., Miyata, T., Namba, K., Konno, H., Ueno, H., Imada, K., and Yokoyama, K. (2013) Common evolutionary origin for the rotor domain of rotary ATPases and flagellar protein export apparatus. PLoS One, doi:10.1371/journal.pone.0064695

Kobayashi, E., Suzuki, T., and Yamamoto, M. (2013) Roles Nrf2 plays in myeloid cells and related disorders. Oxid. Med. Cell. Longev., doi:10.1155/2013/529219

Koyano, F., Okatsu, K., Ishigaki, S., Fujioka, Y., Kimura, M., Sobue, G., Tanaka, K., and Matsuda, N. (2013) The principal PINK1 and Parkin cellular events triggered in response to dissipation of mitochondrial membrane potential occur in primary neurons. Genes Cells 18, 672-681

Li, X., Bian, Y., Takizawa, Y., Hashimoto, T., Ikoma, T., Tanaka, J., Kitamura, N., Inagaki, Y., Komada, M., and Tanaka, T. (2013) ERK-dependent downregulation of Skp2 reduces Myc activity with HGF, leading to inhibition of cell proliferation through a decrease in Id1 expression. Mol. Cancer Res. 11, 1437-1447

Maruyama, Y., Yamoto, N., Suzuki, Y., Chiba, Y., Yamazaki, K., Sato, T., and Yamaguchi, J. (2013) Arabidopsis transcriptional repressor ERF9 participates in resistance against necrotrophic fungi. Plant Sci. 213, 79-87

Nakatsukasa, K., Brodsky, J.L., and Kamura, T. (2013) A stalled retrotranslocation complex reveals physical linkage between substrate recognition and proteasomal degradation during ER associated degradation. Mol. Biol. Cell 24, 1765-1775

Nishide, A., Kim, M., Takagi, K., Himeno, A., Sanada, T., Sasakawa, C., and Mizushima, T., (2013) Structural basis for the recognition of Ubc13 by the Shigella flexneri effector OspI. J. Mol. Biol. 425, 2623-2631

Okatsu, K., Uno, M., Koyano, F., Go, E., Kimura, M., Oka, T., Tanaka, K., and Matsuda, N. (2013) A dyadic PINK1-containing complex on depolarized mitochondria stimulates Parkin recruitment. J. Biol. Chem. 288, 36372-36384

Okuhira, K., Demizu, Y., Hattori, T., Ohoka, N., Shibata, N., Nishimaki-Mogami, T., Okuda, H., Kurihara, M., and Naito, M. (2013) Development of hybrid small molecules that induce degradation of estrogen receptor-alpha and necrotic cell death in breast cancer cells. Cancer Sci. 104, 1492-1498

Okumura, F., Okumura, A.J., Uematsu, K., Hatakeyama, S., Zhang, D.E., and Kamura, T. (2013) Activation of Double-stranded RNA-activated Protein Kinase (PKR) by Interferon-stimulated Gene 15 (ISG15) Modification Down-regulates Protein Translation. J. Biol. Chem. 288, 2839-2847

Sasaki, Y., Sano, S., Nakahara, M., Murata, S., Kometani, K., Aiba, Y., Sakamoto, S., Watanabe, Y., Tanaka, K., Kurosaki, K., and Iwai, K. (2013) Defective immune responses in mice lacking LUBAC-mediated linear ubiquitination in B cells. EMBO J. 32, 2463- 2476

Sato, T., Sako, K., and Yamaguchi, J. (2013) Chapter 45 Assay for proteasome-dependent protein degradation and ubiquitinated proteins in “Plant Proteomics: Methods and Protocols Second Edition" (edited by J V Jorrín Novo, S Komatsu, W Weckwerth, S Wienkoop), Methods in Molecular Biology, vol. 1072, Springer Protocol, Humana Press, pp. 655-663　DOI:10.1007/978-1-62703-631-3_45

Sato, Y., Yoshizato, T., Shiraishi, Y., Maekawa, S., Okuno, Y., Kamura, T., Shimamura, T., Sato-Otsubo, A., Nagae, G., Suzuki, H., Nagata, Y., Yoshida, K., Kon, A., Suzuki, Y., Chiba, K., Tanaka, H., Niida, A., Fujimoto, A., Tsunoda, T., Morikawa, T., Maeda, D., Kume, H., Sugano, S., Fukayama, M., Aburatani, H., Sanada, M., Miyano, S., Homma, Y., and Ogawa, S. (2013) Integrated molecular analysis of clear-cell renal cell carcinoma. Nat. Genet. 45:860-867

Sun, H.H., Fukao, Y., Ishida, S., Yamamoto, H., Maekawa, S., Fujiwara, M., Sato, T., and Yamaguchi, J. (2013) Proteomics analysis reveals a highly heterogenous proteasome composition and the post-translational regulation of peptidase activity under pathogen signaling in plants. J. Proteome Res. 12, 5084-5095

Suzuki, T., Motohashi, H., and Yamamoto, M. (2013) Toward clinical application of the Keap1-Nrf2 pathway. Trends Pharmacol. Sci. 34, 340-346

Suzuki, S., Ohashi, N., and Kitagawa, M. (2013) Roles of the Skp2/p27 axis in the progression of chronic nephropathy. Cell. Mol. Life Sci. 70, 3277-3289

Suzuki, T., Shibata, T., Takaya, K., Shiraishi, K., Kohno, T., Kunitoh, H., Tsuta, K., Furuta, K., Goto, K., Hosoda, F., Sakamoto, H., Motohashi, H., and Yamamoto, M. (2013) Regulatory nexus of synthesis and degradation deciphers cellular Nrf2 expression levels. Mol. Cell. Biol. 33, 2402-2412

Tanno, H. and Komada, M. (2013) The ubiquitin code and its decoding machinery in the endocytic pathway. J. Biochem. 153, 497-504

Tsuchiya, H., Arai, N., Tanaka, K., and Saeki, Y. (2013) Cytoplasmic proteasomes are not indispensable for cell growth in Saccharomyces cerevisiae. Biochem. Biophys. Res. Commun. 436, 372--376

Tsuchiya, H., Tanaka, K., and Saeki, Y. (2013) The parallel reaction monitoring method contributes to a highly sensitive polyubiquitin chain quantification. Biochem. Biophys. Res. Commun. 436, 223-229

Watanabe, Y., Maeda, I., Oikawa, R., Wu, W., Tsuchiya, K., Miyoshi, Y., Itoh, F., Tsugawa, K.I, and Ohta, T. (2013) Aberrant DNA methylation status of DNA repair genes in breast cancer treated with neoadjuvant chemotherapy. Genes Cells 18, 1120-1130

2014

Ai, L., Kim, W.-J., Alpay, M., Tang, M., Pardo, C.E., Hatakeyama, S., May, W.S., Kladde, M.P., Heldermon, C.D., Siegel, E.M., and Brown, K.D. (2014) TRIM29 suppresses TWIST1 and invasive breast cancer behavior. Cancer Res. 74, 4875-4887.

Aoyama, S., Huarancca Reyes, T., Guglielminetti, L., Yu, L., Morita, Y., Sato, T., and Yamaguchi, J. (2014) Ubiquitin ligase ATL31 functions in leaf senescence in response to the balance between atmospheric CO2 and nitrogen availability in Arabidopsis. Plant Cell Physiol. 55, 293-305.

Aoyama, S., Lu, Y., Yamaguchi, J., and Sato, T. (2014) Regulation of senescence under elevated atmospheric CO2 via ubiquitin modification. Plant Signal. Behav. ,9, e28839.

Ashida, H., Kim, M., and Sasakawa, C. (2014) Exploitation of the host ubiquitin system by human bacterial pathogens. Nat. Rev. Microbiol., 12, 399-413.

Fujita, H., Rahighi, S., Akita, M., Kato, R., Sasaki, Y., Wakatsuki, S., and Iwai, K. (2014) Mechanism underlying IKK activation mediated by the linear ubiquitin chain assembly complex (LUBAC). Mol. Cell. Biol. 34, 1322-1335.

Fukasawa, H., Furuya, R., Yasuda, H., Fujigaki Y., Yamamato, T., Hishida, A., and Kitagawa, M. (2014) Anti-cancer agent-induced nephrotoxicity. Anticancer Agents Med. Chem. 14, 921-927.

Fukutomi, T., Takagi, K., Mizushima, T., Ohuchi, N., and Yamamoto, M. (2014) Kinetic, Thermodynamic and Structural Characterizations of Association between Nrf2-DLGex Degron and Keap1. Mol. Cell. Biol. 34, 832-846.

Gossan, N., Zhang, F., Guo, B., Jin, D., Yoshitane, H., Yao, A., Glossop, N., Zhang, Y. Q., Fukada, Y., and Meng, Q. J. (2014) The E3 ubiquitin ligase UBE3A is an integral component of the molecular circadian clock through regulating the BMAL1 transcription factor. Nucleic Acids Res. 42, 5765-5775.

Harada, M., Kotake, Y., Ohhata, T., Kitagawa, K., Niida, H., Matsuura, S., Funai, K., Sugimura, H., Suda, T., and Kitagawa, M. (2014) YB-1 promotes transcription of cyclin D1 in human non-small-cell lung cancers. Genes Cells 19, 504-516.

Harima, Y., Imayoshi, I., Shimojo, H., Kobayashi, T., and Kageyama, R. (2014) The roles and mechanism of ultradian oscillatory expression of the mouse Hes genes. Semin. Cell. Dev. Biol. 34, 85-90.

Hirano, A., Kurabayashi, N., Nakagawa, T., Shioi, G., Todo, T., Hirota, T., and Fukada, Y. (2014) In vivo role of phosphorylation of cryptochrome 2 in the mouse circadian clock. Mol. Cell. Biol. 34, 4464-4473.

Iwai, K., Fujita, H., and Sasaki, Y. (2014) Linear ubiquitin chains: NF-κB signalling, cell death, and beyond. Nat. Rev. Mol. Cell Biol. 15, 503-508.

Iwai, K. and Tanaka, K. (2014) Ubiquitin chain elongation: An intriguing strategy. Mol. Cell 56, 189‒191.

Kanno, Y., Watanabe, M., Kimura, T., Nonomura, K., Tanaka, S., and Hatakeyama, S. (2014) TRIM29 as a novel prostate basal cell marker for diagnosis of prostate cancer. Acta Histochem. 116, 708-712.

Kikuchi, R., Ohata, H., Ohoka, N., Kawabata, A., and Naito, M. (2014) APOLLON protein promotes early mitotic CYCLIN A degradation independent of the spindle assembly checkpoint. J. Biol. Chem. 289, 3457-3467.

Kim, M., Otsubo, R., Morikawa, H., Nishide, A., Takagi, K., Sasakawa, C., and Mizushima, T. (2014) Bacterial effectors and their functions in the ubiquitin-proteasome system: insight from the modes of substrate recognition. Cells 3, 848-864.

Kimura, T., Tsutsumi, N., Arita, K., Ariyoshi, M., Ohnishi, H., Kondo, N., Shirakawa, M., Kato, Z., and Tochio, H. (2014) Purification, crystallization and preliminary X-ray crystallographic analysis of human IL-18 and its extracellular complexes. Acta Crystallogr. F Struct. Biol. Commun. 70, 1351-1356.

Kitagawa, K., Shibata, K., Matsumoto, A., Matsumoto, M., Ohhata, T., Nakayama, KI., Niida, H., and Kitagawa, M. (2014) Fbw7 targets GATA3 through CDK2-dependent proteolysis and contributes to regulation of T-cell development. Mol. Cell. Biol. 34, 2732-2744.

Kobayashi, T. and Kageyama, R. (2014) Expression dynamics and functions of Hes genes in development and diseases. Curr. Top. Dev. Biol. 110, 263-283.

Koyano, F., Okatsu, K., Kosako, H., Tamura, Y., Go, E., Kimura, M., Kimura, Y., Tsuchiya, H, Yoshihara, H., Hirokawa, T., Endo, T., Fon, E.A., Trempe, J., Saeki, Y., Tanaka, K., and Matsuda, N. (2014) Ubiquitin is phosphorylated by PINK1 to activate parkin. Nature 510, 162-166.

Maekawa, S., Inada, N., Yasuda, S., Fukao, Y., Fujiwara, M., Sato, T., and Yamaguchi, J. (2014) The carbon/nitrogen regulator ATL31 controls papilla formation in response to powdery mildew fungi penetration by interacting with SYP121 in Arabidopsis. Plant Physiol. 164, 879-887.

Miyazaki, S., Kikuchi, H., Iino I., Uehara, T, Setoguchi, T., Fujita, T., Hiramatsu, Y., Ohta, M., Kamiya, K., Kitagawa, K., Kitagawa, M., Baba, S., and Konno, K. (2014) Anti-VEGF antibody therapy induces tumor hypoxia and stanniocalcin 2 expression and potentiates growth of human colon cancer xenografts. Int. J. Cancer 135, 295-307.

Miyazaki, Y., Shimizu, A., Pastan, I., Taguchi, K., Naganuma, E., Suzuki, T., Hosoya, T., Yokoo, T., Saito, A., Miyata, T., Yamamoto, M., and Matsusaka, T. (2014) Keap1 inhibition attenuates glomeruloscerosis. Nephrol. Dial. Transplant. 29, 783-791.

Moroishi, T., Yamauchi, T., Nishiyama, M., and Nakayama, K.I. (2014) HERC2 targets the iron regulator FBXL5 for degradation and modulates iron metabolism. J. Biol. Chem. 289, 16430-16441.

Nagashima, F., Suzuki, I.K., Shitamukai, A., Sakaguchi, H., Iwashita, M., Kobayashi, T., Tone, S., Toida, K., Vanderhaeghen, P., and Kosodo, Y. (2014) Novel and robust transplantation reveals the acquisition of polarized processes by cortical cells derived from mouse and human pluripotent stem cells. Stem. Cells. Dev. 23, 2129-2142.

Nakatsukasa, K., Kanada, A., Matsuzaki, M., Byrne, S.D., Okumura, F., and Kamura, T. (2014) The nutrient stress-induced small GTPase Rab5 contributes to the activation of vesicle trafficking and vacuolar activity. J. Biol. Chem. 289, 20970-20978.

Nakatsukasa, K., Kamura T., and Brodsky, J.L. (2014) Recent technical developments in the study of ER-associated degradation. Curr. Opin. Cell Biol. 29, 82-91.

Ohoka, N., Nagai, K., Hattori, T., Okuhira, K., Shibata, N., Cho, N., and Naito, M. (2014) Cancer cell death induced by novel small molecules degrading the TACC3 protein via the ubiquitin-proteasome pathway. Cell Death Dis. 5, e1513.

Ohtake, F., Saeki, Y., Sakamoto, K., Ohtake, K., Nishikawa, H., Tsuchiya, H., Ohta, T., Tanaka, K., and Kanno, J. (2014) Ubiquitin acetylation inhibits polyubiquitin chain elongation. EMBO Rep. 16, 192-201.

Pack, C.G., Yukii, H., Toh-E, A., Kudo, T., Tsuchiya, H., Kaiho, A., Sakata, E., Murata, S., Yokosawa, H., Sako, Y., Baumeister, W., Tanaka, K., and Saeki Y. (2014) Quantitative live-cell imaging reveals spatio-temporal dynamics and cytoplasmic assembly of the 26S proteasome. Nat. Commun. 5, 3396.

Pekovic-Vaughan,V., Gibbs, J., Yoshitane, H., Yang, N., Pathiranage, D., Guo, B., Sagami, A., Taguchi, K., Bechtold, D., Loudon, A., Yamamoto, M., Chan, J., van der Horst, G.T.J., Fukada, Y., and Meng, Q.J. (2014) The circadian clock regulates rhythmic activation of the NRF2/glutathione-mediated antioxidant defense pathway to modulate pulmonary fibrosis. Genes Dev. 28, 548-560.

Queisser, M.A., Dada, L.A., Deiss-Yehiely, N., Angulo, M., Zhou, G., Kouri, F.M., Knab, L.M., Liu, J., Stegh, A.H., DeCamp, M.M., Budinger, G.R., Chandel, N.S., Ciechanover, A., Iwai, K., and Sznajder, J.I. (2014) HOIL-1L functions as the PKCζ ubiquitin ligase to promote lung tumor growth. Am. J. Respir. Crit. Care Med. 190, 688-698.

Rodgers, M.A., Bowman, J., Fujita, H., Orazio, N., Shi, M., Liang, Q., Amatya, R., Kelly, T.J., Iwai, K., Ting, J., and Jung, J.U. (2014) The linear ubiquitin assembly complex (LUBAC) is essential for NLRP3 inflammasome activation. J. Exp. Med. 211, 1333-1347.

Sakamoto, H., Egashira, S., Saito, N., Kirisako, T., Miller, S., Sasaki, Y., Matsumoto, T., Shimonishi, M., Komatsu, T., Terai, T., Ueno, T., Hanaoka, K., Kojima, H., Okabe, T., Wakatsuki, S., Iwai, K. (corresponding author), and Nagano, T. (2014) Gliotoxin suppresses NF-κB activation by selectively inhibiting linear ubiquitin chain assembly complex (LUBAC). ACS Chem. Biol. 10, 675-681.

Sako, K., Yanagawa, Y., Kanai, T., Sato, T., Seki, M., Fujiwara, M., Fukao, Y., and Yamaguchi, J. (2014) Proteomic analysis of 26S proteasome reveals its direct interaction with transit peptides of plastid protein precursors for their degradation. J. Proteome Res. 13, 3223-3230.

Sato, T., Takahashi, H., Hatakeyama, S., Iguchi, A., and Ariga, T. (2014) The TRIM-FLMN protein TRIM45 directly interacts with RACK1 and negatively regulates PKC-mediated signaling pathway. Oncogene 34, 1280-1291.

Satoh, T., Saeki, Y., Hiromoto, T., Wang, Y., Uekusa, Y., Yagi, H., Yoshihara, H., Yagi-Utsumi, M., Mizushima, T., Tanaka, K., and Kato, K. (2014) Structural basis of proteasome formation controlled by an assembly chaperone Nas2. Structure 22, 731-743.

Shoda, T., Okuhira, K., Kato, M., Demizu, Y., Inoue, H., Naito, M., and Kurihara, M. (2014) Design and synthesis of tamoxifen derivatives as a selective estrogen receptor down- regulator. Bioorg. Med. Chem. Lett. 24, 87-89.

Suzuki, S., Mimuro, H., Kim, M., Ogawa, M., Ashida, H., Toyotome, T., Franchi, L., Suzuki, M., Sanada, T., Suzuki, T., Tsutsui, H., Nunez, G., and Sasakawa, C. (2014) Shigella IpaH7.8 E3 ligase targets glomulin and activates inflammasomes to demolish macrophages. Proc. Natl. Acad. Sci. USA 111, E4254-E4263.

Takagi, K., Saeki, Y., Yashiroda, H., Yagi, H., Kaiho, A., Murata, S., Yamane, T., Tanaka, K., Mizushima, T., and Kato, K. (2014) Pba3-Pba4 heterodimer acts as a molecular matchmaker in proteasome α-ring formation. Biochem. Biophys. Res. Commun. 450, 1110-1114.

Takiuchi, T., Nakagawa, T., Tamiya, H., Fujita, H., Sasaki, Y., Saeki, Y., Takeda, H., Sawasaki, T., Buchberger, A., Kimura, T., and Iwai, K. (2014) Suppression of LUBAC-mediated linear ubiquitination by a specific interaction between LUBAC and the deubiquitinases CYLD and OTULIN. Genes Cells 19, 254-272.

Tamiya, H., Terao, M., Takiuchi, T., Nakahara, M., Sasaki, Y., Katayama, I., Yoshikawa, H., and Iwai K. (2014) IFN-γ or IFN-α ameliorates chronic proliferative dermatitis by inducing expression of linear ubiquitin chain assembly complex. J. Immunol. 192, 3793-3804.

Tanno, H., Shigematsu, T., Nishikawa, S., Hayakawa, A., Denda, K., Tanaka, T., and Komada, M. (2014) Ubiquitin-interacting motifs confer full catalytic activity, but not ubiquitin chain substrate specificity, to deubiquitinating enzyme USP37. J. Biol. Chem. 289, 2415-2423.

Tsutsumi, N., Kimura, T,, Arita, K., Ariyoshi, M., Ohnishi, H., Yamamoto, T., Zuo, X., Maenaka, K., Park, E.Y., Kondo, N., Shirakawa, M., Tochio, H., and Kato, Z. (2014) The structural basis for receptor recognition of human interleukin-18. Nat. Commun. 5, 5340.

Uchida, C., Hattori, T., Takahashi, H., Yamamoto, N., Kitagawa, M., and Taya, Y. (2014) Interaction between RB protein and NuMA is required for proper alignment of spindle microtubules. Genes Cells 19, 89-96.

Walinda, E., Morimoto, D., Sugase, K., Konuma, T., Tochio, H., and Shirakawa, M. (2014) Solution structure of the ubiquitin-associated (UBA) domain of human autophagy receptor NBR1 and its interaction with ubiquitin and polyubiquitin. J. Biol. Chem. 289, 13890-13902.

Wang, Z., Okuma, Y., Kasuya, D., Mitsuoka, K., Saeki, Y., and Yasunaga, T. (2014) Structural analysis of the 26S proteasome by cryo-electron microscopy and single- particle analysis. Microscopy (Oxf) 63, i32.

Yabe, I., Tanino, M., Yaguchi, H., Takiyama, A., Cai, H., Kanno, H., Takahashi, I., Hayashi, Y., Watanabe, M., Takahashi, H., Hatakeyama, S., Tanaka, S., and Sasaki, H. (2014) Pathology of frontotemporal dementia with limb girdle muscular dystrophy caused by a DNAJB6 mutation. Clin. Neurol. Neurosur. 127, 10-12.

Yaguchi, H., Yabe, I., Takahashi, H., Okumura, F., Takeuchi, A., Horiuchi, K., Kan, T., Kanda, A, Saito, W., Matsumoto, M., Nakayama, K.I., Hatakeyama, S., and Sasaki, H. (2014) Identification of anti-Sez6l2 antibody in a patient with cerebellar ataxia and retinopathy. J. Neurol. 261, 244-246.

Yamamoto, T., Tsutsumi, N., Tochio, H., Ohnishi, H., Kubota, K., Kato, Z., Shirakawa, M., and Kondo, N. (2014) Functional assessment of the mutational effects of human IRAK4 and MyD88 genes. Mol. Immunol. 58, 66-76.

Yamauchi, T., Nishiyama, M., Moroishi, T., Yumimoto, K., and Nakayama, K.I. (2014) MDM2 mediates nonproteolytic polyubiquitylation of the DEAD-box RNA helicase DDX24. Mol. Cell. Biol. 34, 3321-3340.

Yang, Y., Schmitz, R., Mitala, J.J. Jr,, Whiting, A., Xiao, W., Ceribelli, M., Wright, G.W., Zhao, H., Yang, Y., Xu, W., Rosenwald, A., Ott, G., Gascoyne, R.D., Connors, J.M., Rimsza, L.M., Campo, E., Jaffe, E.S., Delabie, J., Smeland, E.B., Braziel, R.M., Tubbs, R.R., Cook, J.R., Weisenburger, D.D., Chan, W.C., Wiestner, A., Kruhlak, M.J., Iwai, K., Bernal, F., and Staudt, L.M. (2014) Essential role of the linear ubiquitin chain assembly complex in lymphoma revealed by rare germline polymorphisms. Cancer Discov. 4, 480-493.

Yasuda, S., Sato, T., Maekawa, S., Aoyama, S., Fukao, Y., and Yamaguchi, J. (2014) Phosphorylation of Arabidopsis ubiquitin ligase ATL31 is critical for plant carbon/nitrogen nutrient balance and controls the stability of 14-3-3 proteins. J. Biol. Chem. 289, 15179-15193.

2015

Bowman, J., Rodgers, M.A., Shi, M., Amatya, R., Hostager, B., Iwai, K., Gao, S.J., and Jung, J.U. (2015) Posttranslational modification of HOIP blocks Toll-like receptor 4-mediated linear-ubiquitin-chain formation. MBio. 6, e01777-15

Buchert, F., Konno. H., and Hisabori, T. (2015) Redox regulation of CF1-ATPase involves interplay between the γ-subunit neck region and the turn region of the βDELSEED-loop. Biochim. Biophys. Acta, doi:10.1016/j.bbabio.2015.01.013

Fukuda, T., Tsuruga, T., Kuroda, T., Takeuchi, J., Wu, W., and Ohta, T. (2015) The BARD1/HP1 interaction: Another clue to heterochromatin involvement in homologous recombination. Mol Cell Oncol., doi:10.1080/23723556.2015.1030535

Fukuda, T., Wu, W., Okada, M., Maeda, I., Kojima, Y., Hayami, R., Miyoshi, Y., Tsugawa, K.I., and Ohta, T. (2015) Class I HDAC inhibitors inhibit the retention of BRCA1 and 53BP1 at the site of DNA damage. Cancer Sci. 106, 1050-1056

Hayashi, K., Inoshita, N., Kawaguchi, K., Ardisasmita, A.I., Suzuki, H., Fukuhara, N., Okada, M., Nishioka, H., Takeuchi, Y., Komada, M., Takeshita, A., and Yamada, S. (2015) The USP8 mutational status may predict drug susceptibility in corticotroph adenomas of Cushing's disease. Eur. J. Endocrinol. 174, 213-226

Huarancca Reyes, T., Maekawa, S., Sato, T., and Yamaguchi, J. (2015) The Arabidopsis ubiquitin ligase ATL31 is transcriptionally controlled by WRKY33 transcription factor in response to pathogen attack. Plant Biotech., doi:10.5511/plantbiotechnology.14.1201b

Kameda, Y., Takahata, M., Mikuni, S., Shimizu, T., Hamano, H., Angata, T., Hatakeyama, S., Kinjo, M., and Iwasaki, N. (2015) Siglec-15 is a potential therapeutic target for postmenopausal osteoporosis. Bone 71, 217-226.

Kanno, Y., Mitsui, T., Kitta, T., Moriya, K,. Tsukiyama, T., Hatakeyama, S., and Nonomura, K. (2015) The inflammatory cytokine IL-1β is involved in bladder remodeling after bladder outlet obstruction in mice. Neurourol. Urodyn., doi:10.1002/nau.22721

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Anwar, D., Takahashia, H., Watanabe, M., Suzuki, M., Fukuda, S., and Hatakeyama, S. (2016) p53 represses the transcription of snRNA genes by preventing the formation of little elongation complex. Biochim. Biophys. Acta - Gene Regul. Mech., 1859, 975-982

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Misaki, T., Yamaguchi, L., Sun, J., Orii, M., *Nishiyama, A., and *Nakanishi, M. (*co-correspondence) (2016) The replication foci targeting sequence (RFTS) of DNMT1 functions as a potent histone H3 binding domain regulated by autoinhibition. Biochem. Biophys. Res. Commun. 470, 741-747

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Narushima, Y., Kozuka-Hata, H., Koyama-Nasu, R., Tsumoto, K., Inoue, J, Akiyama, T., and Oyama, M. (2016) Integrative network analysis combined with quantitative phosphoproteomics reveals TGFBR2 as a novel regulator of glioblastoma stem cell properties. Mol. Cell. Proteomics 15, 1017-1031

Nishio, K., Yoshida, Y., Tanaka, K., and Mizushima, T. (2016) Structural analysis of a function-associated loop mutant of the substrate recognition domain of Fbs1 ubiquitin ligase. Acta Cryst F72, doi:10.1107/S2053230X16011018

Nishiyama, A., Yamaguchi, L., and Nakanishi, M. (2016) Regulation of maintenance DNA methylation via histone ubiquitylation. J. Biochem. 159, 9-15

Noguchi, T., Tsuchida, M., Kogue, Y., Spadini, C., Hirata, Y., and Matsuzawa, A. (2016) Brefeldin A-inhibited guanine nucleotide-exchange factor 1 (BIG1) governs the recruitment of tumor necrosis factor receptor-associated factor 2 (TRAF2) to tumor necrosis factor receptor 1 (TNFR1) signaling complexes. Int. J. Mol. Sci. 17, E1869

Ohtake, F., Saeki, Y., Ishido, S., Kanno, J., and Tanaka, K. (2016) The K48-K63 branched ubiquitin chain regulates NF-κB signaling. Mol. Cell, doi:10.1016/j.molcel.2016.09.014

Ohtake, F. and Tsuchiya, H. (2016) The emerging complexity of ubiquitin architecture. J. Biochem., doi:10.1093/jb/mvw088

Okamura, K., Kitamura, A., Sasaki, Y., Chung, D.H., Kagami, S., Iwai, K., and Yasutomo, K. (2016) Survival of mature T cells depends on signaling through HOIP. Sci. Rep. 6, 36135

Omura, H., Oikawa, D., Nakane, T., Kato, M., Ishii, R., Ishitani, R., Tokunaga, F., and Nureki, O. (2016) Structural and functional analysis of DDX41: a bispecific immune receptor for DNA and cyclic dinucleotide. Sci. Rep., doi: 10.1038/srep34756

Sasaki, Y. and Iwai, K. (2016) Roles of the NF-kB pathway in B-lymphocyte biology. Curr. Top. Microbiol. Immunol. 393, 177-209

Saito, T., Ichimura, Y., Taguchi, K., Suzuki, T., Mizushima, T., Takagi, K., Hirose, Y., Nagahashi, M., Iso, T., Fukutomi, T., Ohishi, M., Endo, K., Uemura, T., Nishito Y., Okuda, S., Obata, M., Kouno, T., Imamura, R., Tada, Y., Obata, R., Yasuda, D., Takahashi, K., Fujimura, T., Pi, J., Lee, M.S., Ueno, T., Ohe, T., Mashino, T., Wakai, T., Kojima, H., Okabe, T., Nagano, T., Motohashi, H., Waguri, S., Soga, T., Yamamoto, M., Tanaka, K., and Komatsu, M. (2016) p62/Sqstm1 promotes malignancy of HCV-positive hepatocellular carcinoma through Nrf2-dependent metabolic reprogramming. Nat. Commun., doi: 10.1038/ncomms12030

Saitoh, Y., Hamano, A., Mochida, K., Kakeya, A., Uno, M., Tsuruyama, E., Ichikawa, H., Tokunaga, F., Utsunomiya, A., Watanabe, T., and Yamaoka, S. (2016) A20 targets caspase-8 and FADD to protect HTLV-I infected cells. Leukemia, doi: 10.1038/leu.2015.267

Shimizu, S., Fujita, H., Sasaki, Y., Tsuruyama, T., Fukuda, K., and Iwai, K. (2016) Differential involvement of the NZF domains of SHARPIN and HOIL-1L in LUBAC-mediated cell death protection. Mol. Cell. Biol. 36, 1569-1583

Shinohara, H., Inoue, K., Yumoto, N., Nagashima, T., and Okada-Hatakeyama, M. (2016) Stimulus-dependent inhibitor of apoptosis protein expression prolongs the duration of B cell signalling. Sci. Rep., doi:10.1038/srep27706

Shinohara, H. and Kurosaki, T. (2016) Negative role of TAK1 in marginal zone B-cell development incidental to NF-κB noncanonical pathway activation. Immunol. Cell Biol., doi:10.1038/icb.2016.44

Shinohara, H., Nagashima, T., Cascalho, M.I., and Kurosaki, T. (2016) TAK1 maintains the survival of immunoglobulin λ-chain-positive B cells. Genes Cells, doi:10.1111/gtc.12442

Shinohara, H., Yasuda, T., and Kurosaki, T. (2016) TAK1 adaptor proteins, TAB2 and TAB3, link the signalosome to B-cell receptor-induced IKK activation. FEBS Lett., doi:10.1002/1873-3468.12342

Shizu, R., Abe, T., Benoki, S., Takahashi, M., Kodama, S., Miayata, M., Matsuzawa, A., and Yoshinari, K. (2016) PXR stimulates growth factor-mediated hepatocyte proliferation by cross-talk with the FOXO transcription factor. Biochem. J. 473, 257-266

Suzuki, R. and Kawahara, H. (2016) UBQLN4 recognizes mislocalized transmembrane domain proteins and targets these to proteasomal degradation. EMBO Rep., doi:10.15252/embr.201541402

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Yamaki, Y., Kagawa, H., Hatta, T., Natsume, T., and Kawahara, H. (2016) The C-terminal cytoplasmic tail of hedgehog receptor Patched1 is a platform for E3 ubiquitin ligase complexes. Mol. Cell. Biochem. 414, 1-12

Yamano, K., Matsuda, N., and Tanaka, K. (2016) The ubiquitin signal and autophagy: an orchestrated dance leading to mitochondrial degradation. EMBO Rep. 17, 300-316

Yanagawa, T., Denda, K., Inatani, T., Fukushima, T., Tanaka, T., Kumaki, N., Inagaki, Y., and Komada, M. (2016) Deficiency of X-linked protein kinase Nrk during pregnancy triggers breast tumor in mice. Am. J. Pathol. 186, 2751-2760

Yutthanasirikul, R., Nagano, T., Jimbo, H., Hihara, Y., Kanamori, T., Ueda, T., Maruyama, T, Konno, H., Yoshida, K., Hisabori, T., and Nishiyama, Y. (2016) Oxidation of a cysteine residue in elongation factor EF-Tu reversibly inhibits translation in the cyanobacterium Synechocystis sp. PCC 6803. J. Biol. Chem., doi: 10.1074/jbc.M115.706424

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2017

Abe, T., Takahashi, M., Kano, M., Amaike, Y., Ishii, C., Maeda, K., Kudoh, Y., Morishita, T., Hosaka, T., Sasaki, T., Kodama, S., Matsuzawa, A., Kojima, H., and Yoshinari, K. (2017) Activation of nuclear receptor CAR by an environmental pollutant perfluorooctanoic acid. Arch. Toxicol., doi:10.1007/s00204-016-1888-3

Fujimoto, K., Kinoshita, M., Tanaka, H., Okuzaki, D., Shimada, Y., Kayama, H., Okumura, R., Furuta, Y., Narazaki, M., Tamura, A., Hatakeyama, S., Ikawa, M., Tsuchiya, K., Watanabe, M., Kumanogoh, A., Tsukita, S., and Takeda, K. (2017) Regulation of intestinal homeostasis by the ulcerative colitis-associated gene RNF186. Mucosal Immunol., 10, 446-459

Fukushima, T., Yoshihara, H., Furuta, H., Hakuno, F., Iemura, S-I., Natsume, T., Nakatsu, Y., Kamata, H., Asano, T., Komada, M., and Takahashi, S. (2017) USP15 attenuates IGF-I signaling by antagonizing Nedd4-induced IRS-2 ubiquitination. Biochem. Biophys. Res. Commun. 484, 522-528

Goto, E. and Tokunaga, F. (2017) Decreased linear ubiquitination of NEMO and FADD on apoptosis with caspase-mediated cleavage of HOIP. Biochem. Biophys. Res. Commun., doi:10.1016/j.bbrc.2017.02.040

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Sato, T., Maekawa, S., Konishi, M., Yoshioka, N., Sasaki, Y., Maeda, H., Ishida, T., Kato, Y., Yamaguchi, J., and Yanagisawa, S. (2017) Direct transcriptional activation of BT genes by NLP transcription factors is a key component of the nitrate response in Arabidopsis. Biochem. Biophys. Res. Commun., doi:10.1016/j.bbrc.2016.12.135

Shibata, Y., Tokunaga, F., Goto, E., Komatsu, G., Gohda, J., Saeki, Y., Tanaka, K., Takahashi, H., Sawasaki, T., Inoue, S., Oshiumi, H., Seya, T., Nakano, H., Tanaka, Y., Iwai, K., and Inoue, J.I. (2017) HTLV-1 Tax induces formation of the active macromolecular IKK complex by generating Lys63- and Met1-linked hybrid polyubiquitin chains. PLoS Pathog.13, e1006162

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Yamamotoya, T., Nakatsu, Y., Matsunaga, Y., Fukushima, T., Yamazaki, H., Kaneko, S., Fujishiro, M., Kikuchi, T., Kushiyama, A., Tokunaga, F., Asano, T., and Sakoda, H. (2017) Reduced SHARPIN and LUBAC formation may contribute to CCl4- or acetaminophen-induced liver cirrhosis in mice. Int. J. Mol. Sci., doi:10.3390/ijms18020326

Yasuda, S., Aoyama, S., Hasegawa, Y., Sato, T., and Yamaguchi, J. (2017) Arabidopsis CBL-interacting protein kinases regulate carbon/nitrogen-nutrient response by phosphorylating ubiquitin ligase ATL31. Mol. Plant, doi:10.1016/j.molp.2017.01.005

武田啓佑、柳茂（2017）小胞体-ミトコンドリア接触場の形成制御とアルツハイマー病. 医学のあゆみ「ミトコンドリア研究UPDATE」 260, 24-30