Analysis of genome maintenance system by the combination of proteomics and genetic approach

• Project/Area Number: 25281021
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Partial Multi-year Fund
• Section: 一般
• Research Field: Risk sciences of radiation and chemicals
• Research Institution: Tokyo Metropolitan University
• Principal Investigator: hirota kouji 首都大学東京, 理工学研究科, 教授 (00342840)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥18,200,000 (Direct Cost: ¥14,000,000、Indirect Cost: ¥4,200,000); Fiscal Year 2015: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000); Fiscal Year 2014: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000); Fiscal Year 2013: ¥6,760,000 (Direct Cost: ¥5,200,000、Indirect Cost: ¥1,560,000)
• Keywords: DNA修復 / DNA損傷応答 / クロマチン / ユビキチン / 染色体 / ゲノム / 複製 / 質量分析 / SILAC

Outline of Final Research Achievements

DNA damages caused by environmental genotoxic agents and ionizing radiations induce genome instability. Genome instability is a cause of cancer and cellular senescence, and thus understanding of the genome maintenance system is important issue. Here we defined genome maintenance system including chromatin regulation and DNA repair as ‘Genome maintenance machinery’ and studied this by the use of genetic approach and proteomics approach. To this end, we applied SILAC technique to DT40 DNA repair mutant panel. Our comprehensive approach revealed the relationship among signal pathway, repair factor and chromatin modifications. In this report, we explain about the identification of ubiquitination target proteins of RNF4 ubiquitin ligase.

Research Products

• [Journal Article] Local potentiation of stress-responsive genes by upstream noncoding transcription. (2016)
  • Author(s): Takemata N, Oda A, Yamada T, Galipon J, Miyoshi T, Suzuki Y, Sugano S, Hoffman CS, Hirota K, Ohta K.
  • Journal Title: Nucleic Acids Res Volume: -
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Cytotoxic and genotoxic profiles of benzo[a]pyrene and N-nitrosodimethylamine demonstrated using DNA repair deficient DT40 cells with metabolic activation. (2016)
  • Author(s): Ooka M, Takazawa H, Takeda S, Hirota K.
  • Journal Title: Chemosphere Volume: 144 Pages: 1901-7
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Abacavir, an anti–HIV-1 drug, targets TDP1-deficient adult T cell leukemia. (2015)
  • Author(s): Tada K, Kobayashi M, Takiuchi Y, Iwai F, Sakamoto T, Nagata K, Shinohara M, Io K, Shirakawa K, Hishizawa M, Shindo K, Kadowaki N, Hirota K, Yamamoto J, Iwai S, Sasanuma H, Takeda S, Takaori-Kondo A.
  • Journal Title: Science Advances Volume: 1 Issue: 3 Pages: 1-9
  • DOI: 10.1126/sciadv.1400203
  • NAID: 120005601014
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Relative contribution of four nucleases, CtIP, Dna2, Exo1 and Mre11, to the initial step of DNA double‐strand break repair by homologous recombination in both the chicken DT40 and human TK6 cell lines (2015)
  • Author(s): Hoa NN, Akagawa R, Yamasaki T, Hirota K, Sasa K, Natsume T, Kobayashi J, Sakuma T, Yamamoto T, Komatsu K, Kanemaki MT, Pommier Y, Takeda S, Sasanuma H
  • Journal Title: Genes to Cells Volume: 20 Issue: 12 Pages: 1059-1076
  • DOI: 10.1111/gtc.12310
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Distinct DNA damage spectra induced by ionizing radiation in normoxic and hypoxic cells. (2015)
  • Author(s): Shimizu N, Ooka M, Takagi T, Takeda S, Hirota K.
  • Journal Title: Radiation Res Volume: 184(4) Issue: 4 Pages: 442-8
  • DOI: 10.1667/rr14117.1
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Development of a targeted flip-in system in avian DT40 cells. (2015)
  • Author(s): Kobayashi, K., Fujii, T., Asada, R., Ooka, M., Hirota, K.
  • Journal Title: PLoS One Volume: 10(3) Issue: 3 Pages: e0122006-e0122006
  • DOI: 10.1371/journal.pone.0122006
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] The POLD3 subunit of DNA polymerase δ can promote translesion synthesis independently of DNA polymerase ζ. (2015)
  • Author(s): Hirota K, Yoshikiyo K, Guilbaud G, Tsurimoto T, Murai J, Tsuda M, Phillips L, Narita T, Nishihara K, Kobayashi K, Yamada K, Nakamura J, Pommier Y, Lehmann, A, Sale J, Takeda S
  • Journal Title: Nucleic Acids Res. Volume: 43 Issue: 3 Pages: 1671-1683
  • DOI: 10.1093/nar/gkv023
  • NAID: 120005825923
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Rad18 and Rnf8 facilitate homologous recombination by two distinct mechanisms, promoting Rad51 focus formation and suppressing the toxic effect of nonhomologous end joining. (2015)
  • Author(s): Kobayashi S, Kasaishi Y, Nakada S, Takagi T, Era S, Motegi A, Chiu R.K, Takeda S, Hirota K.
  • Journal Title: Oncogene Volume: 34 Pages: 4403-4411
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Antagonistic controls of chromatin and mrna start site selection by Tup family corepressors and the CCAAT-binding factor. (2015)
  • Author(s): Asada R, Takemata N, Hoffman CS, Ohta K, Hirota K.
  • Journal Title: Mol Cell Biol. Volume: 35 Issue: 5 Pages: 847-855
  • DOI: 10.1128/mcb.00924-14
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] SUMO-targeted ubiquitin ligase RNF4 plays a critical role in preventing chromosome loss. (2014)
  • Author(s): Hirota K, Tsuda M, Murai J, Takagi T, Keka IS, Narita T, Fujita M, Sasanuma H, Kobayashi J, Takeda S
  • Journal Title: Genes Cells Volume: 19 Issue: 10 Pages: 743-754
  • DOI: 10.1111/gtc.12173
  • Peer Reviewed / Open Access
• [Journal Article] RNA cytidine acetyltransferase of small-subunit ribosomal RNA: identification of acetylation sites and the responsible acetyltransferase in fission yeast, Schizosaccharomyces pombe. (2014)
  • Author(s): Taoka M, Ishikawa D, Nobe Y, Ishikawa H, Yamauchi Y, Terukina G, Nakayama H, Hirota K, Takahashi N, Isobe T
  • Journal Title: PLoS One Volume: 9 Issue: 11 Pages: e112156-e112156
  • DOI: 10.1371/journal.pone.0112156
  • Peer Reviewed / Open Access
• [Journal Article] Evolution of Pre-Existing versus Acquired Resistance to Platinum Drugs and PARP Inhibitors in BRCA-Associated Cancers. (2014)
  • Author(s): Kimiyo N.Yamamoto, Hirota Kouji, Shunichi Takeda, and Hiroshi Haeno.
  • Journal Title: PLos One Volume: 9 Issue: 8 Pages: e105724-e105724
  • DOI: 10.1371/journal.pone.0105724
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] RNase MRP cleaves pre-tRNASer-Met in the tRNA maturation pathway. (2014)
  • Author(s): Saito, Y., Takeda, J., Adachi, K., Nobe, Y., Kobayashi, J., Hirota, K., Oliveira, D.V., Taoka, M., Isobe, T.
  • Journal Title: PLoS One Volume: 9(11)
  • Peer Reviewed / Open Access
• [Journal Article] C-terminal region of activation-induced cytidine deaminase (AID) is required for efficient class switch recombination and gene conversion. (2014)
  • Author(s): Sabouri S, Kobayashi M, Begum NA, Xu J, Hirota K, Honjo T
  • Journal Title: Proc Natl Acad Sci U S A. Volume: 111 Issue: 6 Pages: 2253-2258
  • DOI: 10.1073/pnas.1324057111
  • NAID: 120005395696
  • Peer Reviewed
• [Journal Article] Compensatory functions and interdependency of the DNA-binding domain of BRCA2 with the BRCA1-PALB2-BRCA2 complex. (2014)
  • Author(s): Al Abo M, Dejsuphong D, Hirota K, Yonetani Y, Yamazoe M, Kurumizaka H, Takeda S
  • Journal Title: Cancer Res. Volume: 74 Issue: 3 Pages: 797-807
  • DOI: 10.1158/0008-5472.can-13-1443
  • Peer Reviewed
• [Journal Article] A novel genotoxicity assay of carbon nanotubes using functional macrophage receptor with collagenous structure (MARCO)-expressing chicken B lymphocytes. (2014)
  • Author(s): Mohiuddin, Keka IS, Evans TJ, Hirota K, Shimizu H, Kono K, Takeda S, Hirano S
  • Journal Title: Arch Toxicol. Volume: 88 Issue: 1 Pages: 145-160
  • DOI: 10.1007/s00204-013-1084-7
  • Peer Reviewed
• [Journal Article] Structure-specific endonucleases Xpf and Mus81 play overlapping but essential roles in DNA repair by homologous recombination. (2013)
  • Author(s): Kikuchi K, Narita T, Pham 〓, Iij〓 J, Hirota K, Islam SK, Mohiuddin M, Okawa K, Bori T, Fukagama T, Essers J, Kanser R, Whithy NC, Sugasawa K, Taniguchi T, Kitagawa K. Takeda S.
  • Journal Title: Cancer Res. Volume: (in press) Issue: 14 Pages: 6917-6929
  • DOI: 10.1158/0008-5472.can-12-3154
  • Peer Reviewed
• [Journal Article] The proteasome factor Bag101 binds to Rad22 and suppresses homologous recombination. (2013)
  • Author(s): Saito Y, Takeda J, Okada M, Kobayashi J, Kato A, Hirota K, Taoka M, Matsumoto T, Komatsu K, Isobe T.
  • Journal Title: Sci Rep. Volume: 3 Issue: 1 Pages: 2022-2022
  • DOI: 10.1038/srep02022
  • Peer Reviewed
• [Journal Article] Interference in DNA replieation can cause mitotic chromosomal breakage unassociated with double-strand breaks (2013)
  • Author(s): Fujita Mari, Sasanuma H, Kimiyo N. Yamamoto Harada H, Kurosawa A, Adachi N, Omura M, Hiraoka M, Takeda S, Hirota K.
  • Journal Title: PLos One Volume: 8 Issue: 4 Pages: 60043-60043
  • DOI: 10.1371/journal.pone.0060043
  • Peer Reviewed
• [Presentation] SUMO化蛋白質を認識するRING型ユビキチンリガーゼRNF4による、スピンドルアセンブリチェックポイント(SAC)活性維持と染色体ロスの防止 (2016)
  • Author(s): 廣田耕志,高木季代,津田雅貴,村井純子,Keka Islam, 成田岳雄,藤田真梨,笹沼博之,小林純也,武田俊一
  • Organizer: SUMO研究会
  • Place of Presentation: 関西学院大学大阪梅田キャンパス（大阪府・大阪市）
  • Year and Date: 2016-01-22
• [Presentation] PAR結合蛋白質ALC1/CHDL1とXRCC1による単鎖切断修復 (2016)
  • Author(s): 廣田耕志,安井明,荻朋男,原田浩,中村純,Yves Pommier, 武田俊一
  • Organizer: 染色体ワークショップ
  • Place of Presentation: 松島一の坊（宮城県・宮城郡）
  • Year and Date: 2016-01-12
• [Presentation] RNF4によるH2A.Zを介した染色体制御機構の解明 (2016)
  • Author(s): 髙木季代,廣田耕志
  • Organizer: 染色体ワークショップ
  • Place of Presentation: 松島一の坊（宮城県・宮城郡）
  • Year and Date: 2016-01-12
• [Presentation] 分裂酵母fbp1におけるゲノム高次構造変化による遺伝子発現精密制御機構の解明 (2016)
  • Author(s): 浅田隆大,廣田耕志
  • Organizer: 染色体ワークショップ
  • Place of Presentation: 松島一の坊（宮城県・宮城郡）
  • Year and Date: 2016-01-12
• [Presentation] 分裂酵母fbp１遺伝子の転写活性化におけるGcn5HATとクロマチンリモデリング因子Snf21およびSnf22の機能の解析 (2015)
  • Author(s): 足立朗,廣田耕志
  • Organizer: 日本分子生物学会年会
  • Place of Presentation: 神戸国際展示場（兵庫県・神戸市)
  • Year and Date: 2015-12-04
• [Presentation] 酸素の有無による電離放射線照射時のDNA損傷の種類の解析 (2015)
  • Author(s): 大岡正人,清水直登,高木季代,武田俊一,廣田耕志
  • Organizer: 日本分子生物学会年会
  • Place of Presentation: 神戸国際展示場（兵庫県・神戸市)
  • Year and Date: 2015-12-03
• [Presentation] 分裂酵母fbp1におけるゲノム高次構造変化による遺伝子発現精密制御機構の解明 (2015)
  • Author(s): 浅田隆大,廣田耕志
  • Organizer: 日本分子生物学会年会
  • Place of Presentation: 神戸国際展示場（兵庫県・神戸市)
  • Year and Date: 2015-12-03
• [Presentation] 分裂酵母fbp1の転写抑制時のクロマチン再構築機構の解明 (2015)
  • Author(s): 梅田未来,廣田耕志
  • Organizer: 日本分子生物学会年会
  • Place of Presentation: 神戸国際展示場（兵庫県・神戸市）
  • Year and Date: 2015-12-01
• [Presentation] Capability of proofreading-exonucrease-deficient replicative DNA polymerased to performtranslesion DNA synthesis (2015)
  • Author(s): Kouji Hirota, Masataka Tsuda, Mohiudin, Toshiki Tsurimoto, Zvi Livneh, Shigenori Iwai, Julian Sale, and Shunichi Takeda
  • Organizer: 日本分子生物学会年会
  • Place of Presentation: 神戸国際展示場（兵庫県・神戸市）
  • Year and Date: 2015-12-01
  • Invited
• [Presentation] 分裂酵母fbp1の転写抑制時のクロマチン再構築機構の解明 (2015)
  • Author(s): 梅田未来,廣田耕志
  • Organizer: バイオコンファレンス2015
  • Place of Presentation: 首都大学東京（東京都・八王子市）
  • Year and Date: 2015-11-06
• [Presentation] DNA修復経路欠損細胞を用いたタバコに含まれる化学物質の遺伝毒性評価 (2015)
  • Author(s): 大岡正人,高沢浩則,武田俊一,廣田耕志
  • Organizer: バイオコンファレンス2015
  • Place of Presentation: 首都大学東京（東京都・八王子市）
  • Year and Date: 2015-11-06
• [Presentation] SUMO-Targeted Ubiquitin Ligase RNF4 required for genome maintenance regulates stability of the histone variant H2A.Z. (2015)
  • Author(s): 廣田耕志
  • Organizer: international symposium on chromatin structure, dynamics and function.
  • Place of Presentation: 淡路夢舞台（兵庫県・淡路市）
  • Year and Date: 2015-08-23
  • Int'l Joint Research
• [Presentation] The regulation of Schizosaccharomyces pombe fbp1 gene transcription through local DNA looping structure by transcription regulators. (2015)
  • Author(s): 浅田隆大,廣田耕志
  • Organizer: international symposium on chromatin structure, dynamics and function.
  • Place of Presentation: 淡路夢舞台（兵庫県・淡路市）
  • Year and Date: 2015-08-23
  • Int'l Joint Research
• [Presentation] The regulation of Schizosaccharomyces pombe fbp1 gene transcription through local DNA looping structure by transcription regulators. (2015)
  • Author(s): 浅田隆太,廣田耕志
  • Organizer: Pombe 2015
  • Place of Presentation: 生田神社会館（兵庫県・神戸市）
  • Year and Date: 2015-06-21
  • Int'l Joint Research
• [Presentation] 複製ポリメラーゼδPOLD3/p66サブユニットはポリメラーゼζ経路と独立に損傷乗り越えに寄与する (2014)
  • Author(s): 廣田耕志、村井純子、Guillaume Guilbaud、津田雅貴、成田岳雄、西原佳那、笹沼博之、釣本俊樹、Julian Sale、武田俊一
  • Organizer: 染色体ワークショップ
  • Place of Presentation: 広島
  • Year and Date: 2014-12-15
• [Presentation] 分裂酵母fbp1におけるクロマチン構造・ゲノム高次構造変化による遺伝子発現制御機構の解明 (2014)
  • Author(s): 浅田隆大、竹俣直道、Charles Hoffman、太田邦史、廣田耕志
  • Organizer: 染色体ワークショップ
  • Place of Presentation: 広島
  • Year and Date: 2014-12-15
• [Presentation] RNF4は染色体ロスを防止する (2014)
  • Author(s): 高木季代、津田雅貴、村井純子、武田俊一、廣田耕志
  • Organizer: 染色体ワークショップ
  • Place of Presentation: 広島
  • Year and Date: 2014-12-15
• [Presentation] 損傷乗り越えniokeruPrimPolと損傷乗り越えポリメラーぜPolζ/ηの関係 (2014)
  • Author(s): 小林香、武田俊一、廣田耕志
  • Organizer: 染色体ワークショップ
  • Place of Presentation: 広島
  • Year and Date: 2014-12-15
• [Presentation] SUMOターゲットユビキチンリガーゼ(STUbL)、RNF111は複製ストレストレランスに重要な役割を果たす (2014)
  • Author(s): 川澄遼太郎、廣田耕志
  • Organizer: 分子生物学会
  • Place of Presentation: 横浜
  • Year and Date: 2014-11-27
• [Presentation] 損傷乗り越えPrimPolと損傷乗り越えポリメラーぜPolζ/ηの関係 (2014)
  • Author(s): 小林香、廣田耕志、武田俊一
  • Organizer: 分子生物学会
  • Place of Presentation: 横浜
  • Year and Date: 2014-11-27
• [Presentation] SUMO化タンパク質を認識するRING型ユビキチンリガーゼRNF4による、スピンドルアセンブリチェックポイント(SAC)の活性維持と染色体ロスの防止 (2014)
  • Author(s): 廣田耕志、高木季代、津田雅貴、村井純子、Keka Islam、成田岳雄、藤田真梨、笹沼博之、小林純也、武田俊一
  • Organizer: 分子生物学会
  • Place of Presentation: 横浜
  • Year and Date: 2014-11-26
• [Presentation] Tup family corepressor とCCAATーbinding factorによるクロマチン構造変化の拮抗的な制御がmRNA転写開始点を決定する (2014)
  • Author(s): 浅田隆大、竹俣直道、太田邦史、廣田耕志
  • Organizer: 分子生物学会
  • Place of Presentation: 横浜
  • Year and Date: 2014-11-26
• [Presentation] 分裂酵母fbp1におけるクロマチン構造変化を利用した遺伝子発現制御機構の解明 (2014)
  • Author(s): 浅田隆大、廣田耕志
  • Organizer: 酵母遺伝学フォーラム
  • Place of Presentation: 東京大学
  • Year and Date: 2014-09-01
• [Presentation] ニワトリBリンパ球DT40細胞を用いた遺伝毒物学手法による有害化学物質の検出法の開発と、その応用による抗がんシーズ化合物のスクリーニング (2013)
  • Author(s): 廣田耕志
  • Organizer: MMS研究会
  • Place of Presentation: 山梨
  • Invited
• [Presentation] 遺伝子シナジーを作動原理とする抗がん治療薬品の探索 (2013)
  • Author(s): 廣田耕志
  • Organizer: Biotech 2013
  • Place of Presentation: お台場
• [Presentation] 染色体断裂はいつもDNA２重鎖切断が原因とは限らない (2013)
  • Author(s): 廣田耕志
  • Organizer: 日本癌学会
  • Place of Presentation: 横浜
  • Invited
• [Presentation] クロマチンリモデリング因子ALC1はPARP経路による酸化DNA損傷トレランスに必須の役割を果たす (2013)
  • Author(s): 廣田耕志
  • Organizer: 第３6回日本分子生物学会
  • Place of Presentation: 神戸
• [Book] 医学の歩み DNA損傷修復の概念提起からメカニズム解明へ (2015)
  • Author(s): 廣田耕志 武田俊一
  • Total Pages: 3
  • Publisher: 医歯薬出版
• [Book] 実験医学増刊 酵母SRG1, mlonRNAによる遺伝子発現制御 (2015)
  • Author(s): 浅田隆大 廣田耕志
  • Total Pages: 2
  • Publisher: 羊土社