Elucidation of the transcriptional regulation mechanism by ubiquitin ligase RNF126 upon DNA damage

• Project/Area Number: 20K12157
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Review Section: Basic Section 63020:Radiation influence-related
• Research Institution: Tohoku University
• Principal Investigator: Ishida Noriko 東北大学, 東北メディカル・メガバンク機構, 助教 (10361073)
• Co-Investigator(Kenkyū-buntansha): 中川 直 山陽小野田市立山口東京理科大学, 薬学部, 講師 (30707013)
• Project Period (FY): 2020-04-01 – 2025-03-31
• Project Status: Completed (Fiscal Year 2024)
• Budget Amount: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2022: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2021: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2020: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
• Keywords: ユビキチン / E3リガーゼ / タンパク分解 / ユビキチンリガーゼ / たんぱく分解 / ユビキチン化 / 転写制御 / 転写 / ヒストンシャペロン

Outline of Research at the Start

1. RNF126依存的なNAP1L1のユビキチン化およびタンパク分解： siRNA、RNF126 KOマウス初代細胞等を用いて調べる。
2. NAP1L1と結合する転写因子および転写複合体解析：細胞増殖関連の転写因子や転写複合体とNAP1L1の結合を確認する。また、NAP1L1のタンパク分解やガンマ線照射による、転写因子のクロマチン結合や下流遺伝子の発現量に与える影響を調べる。
3. 細胞周期およびDNA損傷特異的なNAP1L1タンパク分解とクロマチン構造変換を介した転写制御：siRNA、RNF126KOマウス初代細胞等を用いてmRNA発現量やChIP解析を行う。

Outline of Final Research Achievements

We have demonstrated that RNF126 (hereinafter referred to as RNF) degrades NAP1L1 via the ubiquitin-proteasome pathway, and that RNF knockdown or inactive RNF over-expressing cells arrest at the early G2 phase of the cell cycle and reduce the amount of E2F-1, a transcription factor important for proliferation, bound to chromatin. In the future, we plan to continue our research using new approaches to clarify that protein degradation by RNF is also involved in cancer cell proliferation.

Academic Significance and Societal Importance of the Research Achievements

ヒト細胞における、ユビキチンリガーゼRNF126の新たな基質を発見したことは、ユビキチン化やタンパク分解の理解に貢献できる可能性がある。また、関連するヒト細胞試料を用いた研究結果（Free Radic Biol Med. 161:71-83, 2020）およびその細胞の品質管理方法（Biopreserv Biobank. 22(4):373-382, 2024）について国際誌に報告することができ、その学術的意義は十分あると思われる。更に研究を進めてDNA損傷やがん細胞におけるRNF126の新たな機能を明らかにできれば、社会的貢献にも繋げられる可能性が高い。

Research Products

• [Journal Article] Pancreatic β cell-secreted factor FGF23 attenuates Alzheimer's disease-related amyloid β-induced neuronal death. (2025)
  • Author(s): Yazawa K, Nakashima M, Nakagawa T, Yanase Y, Yoda Y, Ozawa K, Hosoi T.
  • Journal Title: PNAS Nexus Volume: 28 Issue: 1 Pages: 1-11
  • DOI: 10.1093/pnasnexus/pgae542
  • Peer Reviewed / Open Access
• [Journal Article] CUL4-Based Ubiquitin Ligases in Chromatin Regulation: An Evolutionary Perspective. (2025)
  • Author(s): Nakagawa M, Nakagawa T.
  • Journal Title: Cells Volume: 14 Issue: 2 Pages: 1-27
  • DOI: 10.3390/cells14020063
  • Peer Reviewed / Open Access
• [Journal Article] Profiling of runs of homozygosity from whole-genome sequence data in Japanese biobank. (2025)
  • Author(s): Minn AKK, Matsuzaki M, Narita A, Funayama T, Kotsar Y, Makino S, Takayama J; Tohoku Medical Megabank Project Study Group; Kuriyama S, Tamiya G.
  • Journal Title: J Hum Genet. Volume: - Issue: 6 Pages: 287-296
  • DOI: 10.1038/s10038-025-01331-3
  • Peer Reviewed
• [Journal Article] Heme regulates protein interactions and phosphorylation of BACH2 intrinsically disordered region in humoral response. (2024)
  • Author(s): Watanabe-Matsui M, Kadoya S, Segawa K, Shima H, Nakagawa T, Nagasawa Y, Hayashi S, Matsumoto M, Ikeda M, Muto A, Ochiai K, Nguyen LC, Doh-Ura K, Shirouzu M, Nakayama K, Murayama K, Igarashi K.
  • Journal Title: iScience Volume: 28 Issue: 1 Pages: 111529-111529
  • DOI: 10.1016/j.isci.2024.111529
  • Peer Reviewed / Open Access
• [Journal Article] A Case of Pathological Complete Response after Nivolumab Therapy in Unresectable Advanced Gastric Cancer (2024)
  • Author(s): Ogura R, Migita K, Nishioka A, Komeda Y, Nakagawa T, Inoue T, Nakata Y, Yoshikawa T, Kamitani N, Nezu D, Kanai H, Kubo T, Matsushita M, Matsuo H, Moriya K, Ko S.
  • Journal Title: Gan To Kagaku Ryoho Volume: 51 Pages: 1263-1265
  • Peer Reviewed
• [Journal Article] Midnolin, a Genetic Risk Factor for Parkinson's Disease, Promotes Neurite Outgrowth Accompanied by Early Growth Response 1 Activation in PC12 Cells. (2024)
  • Author(s): Chiba A, Kato C, Nakagawa T, Osaki T, Nakamura K, Norota I, Nagashima M, Hosoi T, Ishii K, Obara Y.
  • Journal Title: Mol Cell Biol. Volume: 44 Issue: 11 Pages: 516-527
  • DOI: 10.1080/10985549.2024.2399358
  • Peer Reviewed / Open Access
• [Journal Article] TANK Binding Kinase 1 Promotes BACH1 Degradation through Both Phosphorylation-Dependent and -Independent Mechanisms without Relying on Heme and FBXO22 (2024)
  • Author(s): Liu Liang、Matsumoto Mitsuyo、Watanabe-Matsui Miki、Nakagawa Tadashi、Nagasawa Yuko、Pang Jingyao、Callens Bert K. K.、Muto Akihiko、Ochiai Kyoko、Takekawa Hirotaka、Alam Mahabub、Nishizawa Hironari、Shirouzu Mikako、Shima Hiroki、Nakayama Keiko、Igarashi Kazuhiko
  • Journal Title: International Journal of Molecular Sciences Volume: 25 Issue: 8 Pages: 4141-4141
  • DOI: 10.3390/ijms25084141
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Whole blood transcriptome analysis for age- and gender-specific gene expression profiling in Japanese individuals (2023)
  • Author(s): Aoki YI, Taguchi K, Anzawa H, Kawashima J, Ishida N, Otuki A, Hasegawa A, Baird L, Suzuki T, Motoike IN, Ohneda K, Kumada K, Katsuoka F, Kinoshita K, Yamamoto M.
  • Journal Title: J Biochem Volume: Online ahead of print. Issue: 6 Pages: 611-627
  • DOI: 10.1093/jb/mvae008
  • Peer Reviewed / Open Access
• [Journal Article] Detection and Correction of Sample Misidentifications in a Biobank Using the MassARRAY System and Genomic Information (2023)
  • Author(s): Kudo Hisaaki、Ishida Noriko、Nobukuni Takahiro、Aoki Yuichi、Saito Sakae、Nishijima Ichiko、Terakawa Takahiro、Yamamoto Masayuki、Minegishi Naoko、Yamashita Riu、Kumada Kazuki
  • Journal Title: Biopreservation and Biobanking Volume: - Issue: 4 Pages: 373-382
  • DOI: 10.1089/bio.2022.0211
  • Peer Reviewed / Open Access
• [Journal Article] Neurobehavioral characteristics of mice with SETD5 mutations as models of IDD23 and KBG syndromes. (2023)
  • Author(s): Nakagawa T, Hattori S, Hosoi T, Nakayama K.
  • Journal Title: Front Genet. Volume: 13 Pages: 1022339-1022339
  • DOI: 10.3389/fgene.2022.1022339
  • Peer Reviewed / Open Access
• [Journal Article] SPT16 ubiquitylation by DCAF14-CRL4 regulates FACT binding to histones (2022)
  • Author(s): Nakagawa T, Morohoshi A, Nagasawa Y, Nakagawa M, Hosogane M, Noda Y, Hosoi T, Nakayama K.
  • Journal Title: Cell Reports Volume: 38 Issue: 12 Pages: 110541-110541
  • DOI: 10.1016/j.celrep.2022.110541
  • Peer Reviewed / Open Access
• [Journal Article] Insulin enhances gene expression of Midnolin, a novel genetic risk factor for Parkinson's disease, via ERK, PI3-kinase and multiple transcription factors in SH-SY5Y cells. (2022)
  • Author(s): Naoki Sagehashi, Yutaro Obara, Ohki Maruyama, Tadashi Nakagawa, Toru Hosoi, Kuniaki Ishii
  • Journal Title: J. Pharmacol. Exp. Ther. Volume: - Issue: 2 Pages: 68-78
  • DOI: 10.1124/jpet.121.001076
  • Peer Reviewed
• [Journal Article] COOH-terminal fragment of APP interacts with p62, forms an aggregate, and induces autophagic degradation in Alzheimer's cell model. (2022)
  • Author(s): Tanaka K, Kuramoto K, Nakagawa T, Nomura Y, Ozawa K, Hosoi T.
  • Journal Title: Am J Physiol Cell Physiol. Volume: 323 Issue: 6 Pages: C1633-C1641
  • DOI: 10.1152/ajpcell.00003.2022
  • Peer Reviewed
• [Journal Article] Construction of a trio-based structural variation panel utilizing activated T lymphocytes and long-read sequencing technology. (2022)
  • Author(s): Otsuki A, Okamura Y, Ishida N, Tadaka S, Takayama J, Kumada K, Kawashima J, Taguchi K, Minegishi N, Kuriyama S, Tamiya G, Kinoshita K, Katsuoka F, Yamamoto M.
  • Journal Title: Commun Biol. Volume: 5 Issue: 1 Pages: 991-991
  • DOI: 10.1038/s42003-022-03953-1
  • Peer Reviewed / Open Access
• [Journal Article] Reduced PHOX2B stability causes axonal growth impairment in motor neurons with TARDBP mutations (2021)
  • Author(s): Mitsuzawa S, Suzuki N, Akiyama T, Ishikawa M, Sone T, Kawada J, Funayama R, Shirota M, Mitsuhashi H, Morimoto S, Ikeda K, Shijo T, Ohno A, Nakamura N, Ono H, Ono R, Osana S, Nakagawa T, Nishiyama A, Izumi R, Kaneda S, Ikeuchi Y, Nakayama K, Fujii T, Warita H, Okano H, Aoki M.
  • Journal Title: Stem Cell Reports Volume: 16 Issue: 6 Pages: 1527-1541
  • DOI: 10.1016/j.stemcr.2021.04.021
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Landscape of electrophilic and inflammatory stress-mediated gene regulation in human lymphoblastoid cell lines (2020)
  • Author(s): Ishida Noriko、Aoki Yuichi、Katsuoka Fumiki、Nishijima Ichiko、Nobukuni Takahiro、Anzawa Hayato、Bin Li、Tsuda Miyuki、Kumada Kazuki、Kudo Hisaaki、Terakawa Takahiro、Otsuki Akihito、Kinoshita Kengo、Yamashita Riu、Minegishi Naoko、Yamamoto Masayuki
  • Journal Title: Free Radical Biology and Medicine Volume: 161 Pages: 71-83
  • DOI: 10.1016/j.freeradbiomed.2020.09.023
  • Peer Reviewed / Open Access
• [Journal Article] The Autism-Related Protein SETD5 Controls Neural Cell Proliferation through Epigenetic Regulation of rDNA Expression. (2020)
  • Author(s): Nakagawa T, Hattori S, Nobuta R, Kimura R, Nakagawa M, Matsumoto M, Nagasawa Y, Funayama R, Miyakawa T, Inada T, Osumi N, Nakayama KI, Nakayama K.
  • Journal Title: iScience Volume: 23 Issue: 4 Pages: 101030-101030
  • DOI: 10.1016/j.isci.2020.101030
  • Peer Reviewed / Open Access
• [Journal Article] Knockout Mouse Models Provide Insight into the Biological Functions of CRL1 Components. (2020)
  • Author(s): Nakagawa T, Nakayama K, Nakayama KI.
  • Journal Title: Adv Exp Med Biol. Volume: 1217 Pages: 147-171
  • DOI: 10.1007/978-981-15-1025-0_10
  • ISBN: 9789811510243, 9789811510250
  • Peer Reviewed
• [Journal Article] Identification of Dominant Transcripts in Oxidative Stress Response by a Full-Length Transcriptome Analysis (2020)
  • Author(s): Otsuki Akihito、Okamura Yasunobu、Aoki Yuichi、Ishida Noriko、Kumada Kazuki、Minegishi Naoko、Katsuoka Fumiki、Kinoshita Kengo、Yamamoto Masayuki
  • Journal Title: Molecular and Cellular Biology Volume: 41 Issue: 2 Pages: 1-18
  • DOI: 10.1128/mcb.00472-20
  • Peer Reviewed / Open Access
• [Journal Article] A multi-ethnic meta-analysis identifies novel genes, including ACSL5, associated with amyotrophic lateral sclerosis. (2020)
  • Author(s): Nakamura R, Misawa K, Tohnai G, Nakatochi M, Furuhashi S, Atsuta N, Hayashi N, Yokoi D, Watanabe H, Watanabe H, Katsuno M, Izumi Y, Kanai K, Hattori N, Morita M, Taniguchi A, Kano O, Oda M, Shibuya K, Kuwabara S, Suzuki N, Aoki M, Ohta Y, Yamashita T, Abe K, Hashimoto R, Aiba I, Okada Y, Nagasaki M, Sobue G. et al.,
  • Journal Title: Commun Biol. Volume: 23 Issue: 1 Pages: 526-526
  • DOI: 10.1038/s42003-020-01251-2
  • NAID: 120007178464
  • Peer Reviewed / Open Access
• [Journal Article] USP15 suppresses tumor immunity via deubiquitylation and inactivation of TET2 (2020)
  • Author(s): Chen LL, Smith MD, Lv L, Nakagawa T, Li Z, Sun SC, Brown NG, Xiong Y, Xu YP.
  • Journal Title: Science Advances Volume: 6 Issue: 38 Pages: 1-13
  • DOI: 10.1126/sciadv.abc9730
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] An Amyotrophic Lateral Sclerosis-Associated Mutant of C21ORF2 Is Stabilized by NEK1-Mediated Hyperphosphorylation and the Inability to Bind FBXO3 (2020)
  • Author(s): Watanabe Y, Nakagawa T, Akiyama T, Nakagawa M, Suzuki N, Warita H, Aoki M, Nakayama K.
  • Journal Title: iScience Volume: 23 Issue: 9 Pages: 1-15
  • DOI: 10.1016/j.isci.2020.101491
  • Peer Reviewed / Open Access
• [Journal Article] Longitudinal plasma amino acid profiling with maternal genomic background throughout human pregnancy (2020)
  • Author(s): M Shirota, D Saigusa, R Yamashita, Y Kato, M Matsumoto, J Yamagishi, N Ishida, K Kumada, Y Oe, H Kudo, J Yokozawa, Y Kuroki, I Motoike, F Katsuoka, M Nagasaki, S Koshiba, K Nakayama, O Tanabe, J Yasuda, S Kure, K Kinoshita, H Metoki, S Kuriyama, N Yaegashi, M Yamamoto, J Sugawara
  • Journal Title: Medical Mass Spectrometry Volume: 4 Pages: 36-49
  • NAID: 130007897968
  • Peer Reviewed
• [Presentation] 自閉症関連タンパク質SETD5によるrDNAのエピジェネティック制御を介した神経細胞の増殖促進 (2020)
  • Author(s): 中川 直、中山 啓子
  • Organizer: 第10回武田科学振興財団 薬科学シンポジウム(国際学会)
  • Int'l Joint Research