Original papers (peer-reviewed)
- Mizuho Okamoto, Masanori, Shimogishi, Akari Nakamura, Yusuke Suga, Kyosuke Sugawara, Michio Sato, Ryotaro Nishi, Akio Fujisawa, Yorihiro Yamamoto, Misato Kashiba, Differentiation of THP-1 monocytes to macrophages increased mitochondrial DNA copy number but did not increase expression of mitochondrial respiratory proteins or mitochondrial transcription factor A, Archives of Biochemistry and Biophysics, 2021, 710, 108988
- Misaki Matsui, Ryo Sakasai, Masako Abe, Yusuke Kimura, Shoki Kajita, Wakana Torii, Yoko Katsuki, Masamichi Ishiai, Kuniyoshi Iwabuchi, Minoru Takata and Ryotaro Nishi*, USP42 enhances homologous recombination repair by promoting R-loop resolution with a DNA-RNA helicase DHX9, Oncogenesis, 2020, 9, 60, *Corresponding author
- Ryotaro Nishi*, Paul W. G. Wijnhoven, Yusuke Kimura, Misaki Matsui, Rebecca Konietzny, Qian Wu, Keisuke Nakamura, Tom L. Blundell, and Benedikt M. Kessler, The deubiquitylating enzyme UCHL3 regulates Ku80 retention at sites of DNA damage, Scientific Reports, 2018, 8, 17891, *Corresponding author
- Ryotaro Nishi. Balancing act: To be, or not to be ubiquitylated. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 803-805, 43-50, 2017
- Tomohumi Nakamura, Kouichi Murakami, Haruto Tada, Yoshihiko Uehara, Jumpei Nogami, Kazumitsu Maehara, Yasuyuki Ohkawa, Hisato Saitoh, Hideo Nishitani, Tetsuya Ono, Ryotaro Nishi, Masayuki Yokoi, Wataru Sakai, and Kaoru Sugasawa, Thymine DNA glycosylase modulates the DNA damage response and gene expression by base excision repair-dependent and -independent mechanisms. Genes to Cells, 22 (4), 392-405, 2017
- Mayu Isono, Atsuko Niimi, Takahiro Oike, Yoshihiko Hagiwara, Hiro Sato, Ryota Sekine, Yukari Yoshida,Shin-Ya Isobe, Chikashi Obuse, Ryotaro Nishi, Elena Petricci, Shinichiro Nakada, Takashi Nakano and Atsushi Shibata. BRCA1 directs the repair pathway to homologous recombination by promoting 53BP1 dephosphorylation. Cell Reports, 18 (2), 520-532, 2017
- Paul Wijnhoven, Rebecca Konietzny, Andrew N. Blackford, Jonathan Travers, Benedikt M. Kessler, Ryotaro Nishi* and Stephen P. Jackson*. USP4 Auto-Deubiquitylation Promotes Homologous Recombination. Molecular Cell, 60 (3), 362-373, 2015, *Corresponding authors
- Masaki Akita, Yon-Soo Tak, Tsutomu shimura, Syota Matsumoto, Yuki Okuda-Shimizu, Yuichiro Shimizu, Ryotaro Nishi, Hisato Saitoh, Shigenori Iwai, Toshio Mori, Tsuyoshi Ikura, Wataru Sakai, Fumio Hanaoka and Kaoru Sugasawa. SUMOylation of xeroderma pigmentosum group C protein regulates DNA damage recognition during nucleotide excision repair. Scientific Reports, 5, 10984, 2015
- Syota Matsumoto, Eric S. Fisher, Takeshi Yasuda, Naoshi Dohmae, Shigenori Iwai, Toshio Mori, Ryotaro Nishi, Ken-ichi Yoshino, Wataru Sakai, Fumio Hanaoka, Nicolas H, Thomä and Kaoru Sugasawa. Functional regulation of the DNA damage-recognition factor DDB2 by ubiquitination and interaction with xeroderma pigmentosum group C protein. Nucleic Acids Research, 43 (3), 1700-1713, 2015
- Ryotaro Nishi, Paul Wijnhoven, Carlos le Sage, Jorrit Tjeertes, Yaron Galanty, Josep V. Forment, Michael J. Clague, Sylvie Urbé and Stephen P Jackson. Systematic characterization of deubiquitylating enzymes for roles in maintaining genome integrity. Nature Cell Biology, 16 (10), 1016-1026, 2014
- Ryotaro Nishi*, Wataru Sakai*, Daisuke Tone, Fumio Hanaoka and Kaoru Sugasawa. Structure-function analysis of the EF-hand protein centrin-2 for its intracellular localization and nucleotide excision repair. Nucleic Acids Research, 41 (14), 6917-6929, 2013 *; equally contributing author
- Niina Tanaka, Miki Goto, Azusa Kawasaki, Takashi Sasano, Ko Eto, Ryotaro Nishi, Kaoru Sugasawa, Shinichi Abe and Hisato Saitoh. An EF-hands protein, centrin-1, is an EGTA-sensitive SUMO-interacting protein in mouse testis. Cell Biochemistry and Function, 28 (7), 604-612, 2010
- Kaoru Sugasawa, Jun-ichi Akagi, Ryotaro Nishi, Shigenori Iwai and Fumio Hanaoka. Two-step recognition of DNA damage for mammalian nucleotide excision repair: Directional binding of the XPC complex and DNA strand scanning. Molecular Cell, 36 (4), 642-653, 2009
- Ryotaro Nishi, Sergey Alekseev, Christoffel Dinant, Deborah Hoogstraten, Adriaan B. Houtsmuller, Jan H. J. Hoeijmakers, Wim Vermeulen, Fumio Hanaoka and Kaoru Sugasawa. UV-DDB dependent regulation of nucleotide excision repair kinetics in living cells. DNA Repair, 8 (6), 767-776, 2009
- Gentaro Yasuda*, Ryotaro Nishi*, Eriko Watanabe, Toshio Mori, Shigenori Iwai, Donata Orioli, Miria Stefanini, Fumio Hanaoka, and Kaoru Sugasawa. In vivo destabilization and functional defects of the xeroderma pigmentosum C protein caused by a pathogenic missense mutation. Molecular and Cellular Biology, 27 (19), 6606-6614, 2007 *; equally contributing author
- Ryotaro Nishi, Yuki Okuda, Eriko Watanabe, Toshio Mori, Shigenori Iwai, Chikahide Masutani, Kaoru Sugasawa, and Fumio Hanaoka. Centrin 2 stimulates nucleotide excision repair by interacting with xeroderma pigmentosum group C protein. Molecular and Cellular Biology, 25 (13), 5664-5674, 2005
- Kaoru Sugasawa, Yuki Okuda, Masafumi Saijo, Ryotaro Nishi, Noriyuki Matsuda, Gilbert Chu, Toshio Mori, Shigenori Iwai, Keiji Tanaka, Kiyoji Tanaka, and Fumio Hanaoka. UV-induced ubiquitylation of XPC protein mediated by UV-DDB-ubiquitin ligase complex. Cell, 121 (3), 387-400, 2005
- Yuki Okuda, Ryotaro Nishi, Jessica M.Y. Ng, Wim Vermeulen, Gijsbertus T.J. van der Horst, Toshio Mori, Jan H.J. Hoeijmakers, Fumio Hanaoka and Kaoru Sugasawa. Relative levels of the two mammalian Rad23 homologs determine and stability of the xeroderma pigmentosum group C protein complex. DNA Repair, 3 (10), 1285-1295, 2004
