{"id":190,"date":"2020-04-23T15:39:15","date_gmt":"2020-04-23T06:39:15","guid":{"rendered":"https:\/\/nishi-lab.bs.teu.ac.jp\/?page_id=190"},"modified":"2022-01-05T10:46:42","modified_gmt":"2022-01-05T01:46:42","slug":"publications","status":"publish","type":"page","link":"https:\/\/nishi-lab.bs.teu.ac.jp\/?page_id=190&lang=en","title":{"rendered":"Publications"},"content":{"rendered":"\n<p><strong>Original papers (peer-reviewed)<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>Mizuho Okamoto, Masanori, Shimogishi, Akari Nakamura, Yusuke Suga, Kyosuke Sugawara, Michio Sato,\u00a0<strong>Ryotaro Nishi,<\/strong> 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,\u00a0<strong>Archives of Biochemistry and Biophysics<\/strong>, 2021, 710, 108988<\/li><\/ul>\n\n\n\n<ul class=\"wp-block-list\" type=\"1\"><li>Misaki Matsui, Ryo Sakasai, Masako Abe, Yusuke Kimura, Shoki Kajita, Wakana Torii, Yoko Katsuki, Masamichi Ishiai, Kuniyoshi Iwabuchi, Minoru Takata and <strong>Ryotaro Nishi*<\/strong>,&nbsp;USP42 enhances homologous recombination repair by promoting R-loop resolution with a DNA-RNA helicase DHX9, <strong>Oncogenesis<\/strong>, 2020, 9, 60, *Corresponding author<\/li><\/ul>\n\n\n\n<ul class=\"wp-block-list\"><li><strong><u>Ryotaro Nishi<\/u><\/strong><sup>*<\/sup>, Paul W. G. Wijnhoven, Yusuke Kimura, Misaki Matsui,&nbsp;Rebecca Konietzny, Qian Wu, Keisuke Nakamura, Tom L. Blundell, and&nbsp;Benedikt M. Kessler,&nbsp;The deubiquitylating enzyme UCHL3 regulates Ku80 retention at sites of DNA damage<strong>, Scientific Reports<\/strong>,<strong>&nbsp;<\/strong>2018, 8,&nbsp;17891,<strong>&nbsp;<\/strong>*Corresponding author<\/li><\/ul>\n\n\n\n<ul class=\"wp-block-list\"><li><strong><u>Ryotaro Nishi<\/u><\/strong>. Balancing act: To be, or not to be ubiquitylated.&nbsp;<strong>Mutation Research<\/strong><strong>\/Fundamental and Molecular Mechanisms of Mutagenesis<\/strong>, 803-805, 43-50, 2017<\/li><\/ul>\n\n\n\n<ul class=\"wp-block-list\"><li>Tomohumi Nakamura, Kouichi Murakami, Haruto Tada, Yoshihiko Uehara, Jumpei Nogami, Kazumitsu Maehara, Yasuyuki Ohkawa, Hisato Saitoh, Hideo Nishitani, Tetsuya Ono,&nbsp;<strong><u>Ryotaro Nishi<\/u><\/strong>, 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.&nbsp;<strong>Genes to Cells<\/strong>, 22 (4), 392-405, 2017<\/li><\/ul>\n\n\n\n<ul class=\"wp-block-list\"><li>Mayu Isono,&nbsp;Atsuko Niimi,&nbsp;Takahiro Oike,&nbsp;Yoshihiko Hagiwara,&nbsp;Hiro Sato,&nbsp;Ryota Sekine,&nbsp;Yukari Yoshida,Shin-Ya Isobe,&nbsp;Chikashi Obuse,&nbsp;<strong><u>Ryotaro Nishi<\/u><\/strong>,&nbsp;Elena Petricci,&nbsp;Shinichiro Nakada,&nbsp;Takashi Nakano and Atsushi Shibata. BRCA1 directs the repair pathway to homologous recombination by promoting 53BP1 dephosphorylation.&nbsp;<strong>Cell Reports<\/strong>, 18 (2), 520-532, 2017<\/li><\/ul>\n\n\n\n<ul class=\"wp-block-list\"><li>Paul Wijnhoven,&nbsp;Rebecca&nbsp;Konietzny, Andrew N. Blackford, Jonathan Travers, Benedikt M. Kessler,&nbsp;<strong><u>Ryotaro Nishi*<\/u><\/strong>&nbsp;and Stephen P. Jackson*.&nbsp;USP4 Auto-Deubiquitylation Promotes Homologous Recombination.&nbsp;<strong>Molecular Cell<\/strong>, 60 (3), 362-373, 2015, *Corresponding authors<\/li><\/ul>\n\n\n\n<ul class=\"wp-block-list\"><li>Masaki Akita, Yon-Soo Tak, Tsutomu shimura, Syota Matsumoto, Yuki Okuda-Shimizu, Yuichiro Shimizu,&nbsp;<strong><u>Ryotaro Nishi<\/u><\/strong>, 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.&nbsp;<strong>Scientific Reports,&nbsp;<\/strong>5, 10984, 2015<\/li><\/ul>\n\n\n\n<ul class=\"wp-block-list\"><li>Syota Matsumoto, Eric S. Fisher, Takeshi Yasuda, Naoshi Dohmae, Shigenori Iwai, Toshio Mori,&nbsp;<strong><u>Ryotaro Nishi<\/u><\/strong>, Ken-ichi Yoshino, Wataru Sakai, Fumio Hanaoka, Nicolas H, Thom\u00e4 and Kaoru Sugasawa. Functional regulation of the DNA damage-recognition factor DDB2 by ubiquitination and interaction with xeroderma pigmentosum group C protein.&nbsp;<strong>Nucleic Acids Research<\/strong>, 43 (3), 1700-1713, 2015<\/li><\/ul>\n\n\n\n<ul class=\"wp-block-list\"><li><strong><u>Ryotaro Nishi<\/u><\/strong>, Paul Wijnhoven, Carlos le Sage, Jorrit Tjeertes, Yaron Galanty, Josep V. Forment, Michael J. Clague, Sylvie Urb\u00e9 and Stephen P Jackson. Systematic characterization of deubiquitylating enzymes for roles in maintaining genome integrity.&nbsp;<strong>Nature Cell Biology<\/strong>, 16 (10), 1016-1026, 2014<\/li><\/ul>\n\n\n\n<ul class=\"wp-block-list\" type=\"1\"><li><strong><u>Ryotaro Nishi*<\/u><\/strong>, 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.&nbsp;<strong>Nucleic Acids Research<\/strong>, 41 (14), 6917-6929, 2013&nbsp;*; equally contributing author<\/li><\/ul>\n\n\n\n<ul class=\"wp-block-list\" type=\"1\"><li>Niina Tanaka, Miki Goto, Azusa Kawasaki, Takashi Sasano, Ko Eto,&nbsp;<strong><u>Ryotaro Nishi,<\/u><\/strong>&nbsp;Kaoru Sugasawa, Shinichi Abe and Hisato Saitoh. An EF-hands protein, centrin-1, is an EGTA-sensitive SUMO-interacting protein in mouse testis.&nbsp;<strong>Cell Biochemistry and Function,<\/strong>&nbsp;28 (7), 604-612, 2010<\/li><\/ul>\n\n\n\n<ul class=\"wp-block-list\" type=\"1\"><li>Kaoru Sugasawa, Jun-ichi Akagi,&nbsp;<strong><u>Ryotaro Nishi<\/u><\/strong>, 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.&nbsp;<strong>Molecular Cell<\/strong>, 36 (4), 642-653, 2009<\/li><\/ul>\n\n\n\n<ul class=\"wp-block-list\" type=\"1\"><li><strong><u>Ryotaro Nishi<\/u><\/strong>, 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.&nbsp;<strong>DNA Repair<\/strong>, 8 (6), 767-776, 2009<\/li><\/ul>\n\n\n\n<ul class=\"wp-block-list\" type=\"1\"><li>Gentaro Yasuda*,&nbsp;<strong><u>Ryotaro Nishi*<\/u><\/strong>, Eriko Watanabe, Toshio Mori, Shigenori Iwai, Donata Orioli, Miria Stefanini, Fumio Hanaoka, and Kaoru Sugasawa.&nbsp;<em>In vivo<\/em>&nbsp;destabilization and functional defects of the xeroderma pigmentosum C protein caused by a pathogenic missense mutation.&nbsp;<strong>Molecular and Cellular Biology,<\/strong>&nbsp;27 (19), 6606-6614, 2007&nbsp;*; equally contributing author<\/li><\/ul>\n\n\n\n<ul class=\"wp-block-list\" type=\"1\"><li><strong><u>Ryotaro Nishi<\/u><\/strong>, 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.&nbsp;<strong>Molecular and Cellular Biology<\/strong>, 25 (13), 5664-5674, 2005<\/li><\/ul>\n\n\n\n<ul class=\"wp-block-list\" type=\"1\"><li>Kaoru Sugasawa, Yuki Okuda, Masafumi Saijo,&nbsp;<strong><u>Ryotaro Nishi<\/u><\/strong>,&nbsp;Noriyuki Matsuda, Gilbert Chu, Toshio Mori, Shigenori Iwai, Keiji Tanaka, Kiyoji Tanaka, and Fumio Hanaoka.&nbsp;UV-induced ubiquitylation of XPC protein mediated by UV-DDB-ubiquitin ligase complex.&nbsp;<strong>Cell<\/strong>,<strong>&nbsp;<\/strong>121 (3), 387-400, 2005<\/li><\/ul>\n\n\n\n<ul class=\"wp-block-list\"><li>Yuki Okuda,&nbsp;<strong>Ryotaro Nishi<\/strong>, Jessica M.Y. Ng, Wim Vermeulen, Gijsbertus T.J. van der Horst, Toshio Mori, Jan H.J. Hoeijmakers, Fumio Hanaoka and Kaoru Sugasawa.&nbsp;Relative levels of the two mammalian Rad23 homologs determine and stability of the xeroderma pigmentosum group C protein complex.&nbsp;<strong>DNA Repair<\/strong>,&nbsp;3 (10), 1285-1295, 2004<\/li><\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Original papers (peer-reviewed) Mizuho Okamoto, Masanori, Shimogishi, Akari Nakamura, Yusuke Suga, Kyosuke Sug &#8230;<\/p>\n","protected":false},"author":3,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-190","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/nishi-lab.bs.teu.ac.jp\/index.php?rest_route=\/wp\/v2\/pages\/190","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/nishi-lab.bs.teu.ac.jp\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/nishi-lab.bs.teu.ac.jp\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/nishi-lab.bs.teu.ac.jp\/index.php?rest_route=\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/nishi-lab.bs.teu.ac.jp\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=190"}],"version-history":[{"count":3,"href":"https:\/\/nishi-lab.bs.teu.ac.jp\/index.php?rest_route=\/wp\/v2\/pages\/190\/revisions"}],"predecessor-version":[{"id":375,"href":"https:\/\/nishi-lab.bs.teu.ac.jp\/index.php?rest_route=\/wp\/v2\/pages\/190\/revisions\/375"}],"wp:attachment":[{"href":"https:\/\/nishi-lab.bs.teu.ac.jp\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=190"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}