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構造生物学｜エピジェネティクス｜タンパク質・DNA
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PUBLICATIONS

2024

  1. Wassing IE, #Nishiyama A, Shikimachi R, Jia Q, Kikuchi A, Hiruta M, Sugimura K, Hong X, Chiba Y, Peng J, Jenness C, Nakanishi M, Zhao L, #Arita K, #Funabiki H. CDCA7 is an evolutionarily conserved hemimethylated DNA sensor in eukaryotes. Science Advances 10(34):eadp5753. 2024. doi: 10.1126/sciadv.adp5753.
  2. Shiraishi N., Konuma T., Chiba Y., Hokazono S., Nakamura N., Islam MH., V Nakanishi M., Nishiyama A., #Arita K. Structure of human DPPA3 bound to the UHRF1 PHD finger reveals its functional and structural differences from mouse DPPA3. Communications Biology, 7, Article number: 7462024 2024.
  3. Arita K. Cryo-electron microscopy reveals the impact of the nucleosome dynamics on transcription activity. The Journal of Biochemistry. 2024

2023

  1. Rahayu AF, Hayashi A, Yoshimura Y, Nakagawa R, Arita K, Nakayama J. Cooperative DNA-binding activities of Chp2 are critical for its function in heterochromatin assembly. The Journal of Biochemistry 174 371-382, 2023.
  2. Miyashita R, Nishiyama A, Chiba Y, Kori S., Kato N, Konishi C, Kumamoto S, Kozuka-Hata H, Oyama M, Kawasoe Y, Tsurimoto T, Takahashi TS, Arita K, Nakanishi M. The termination of UHRF1-dependent PAF15 ubiquitin signaling is regulated by USP7 and ATAD5. eLife 2023. doi: https://doi.org/10.7554/eLife.79013

2022

  1. Unoki M, Velasco G, Kori S, Arita K, Daigaku Y, Au Yeung WK, Fujimoto A, Ohashi H, Kubota T, Miyake K, Sasaki H. Novel compound heterozygous mutations in UHRF1 are associated with atypical immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome with distinctive genome-wide DNA hypomethylation. Hum. Mol. Genet. 2022. Dec 2;ddac291. doi: 10.1093/hmg/ddac291.
  2. Hata K., Kobayashi N., Sugimura K., Qin W., Haxholli D., Chiba Y., Yoshimi S., Hayashi G., Onoda H., Ikegami T., Mulholland CB., Nishiyama A., Nakanishi M., Leonhardt H., Konuma T., Arita K. Structural basis for the unique multifaceted interaction of DPPA3 with the UHRF1 PHD finger. Nucleic Acids Res. 50, 12527-12542, 2022. doi: 10.1093/nar/gkac1082.
  3. Kikuchi A., Onoda H., Yamaguchi K., Kori S., Matsuzawa S., Chiba Y., Tanimoto S., Yoshimi S., Sato H., Yamagata A., Shirouzu M., Adachi N., Sharif J., Koseki H., Nishiyama A., Nakanishi M., Defossez PA., Arita K. Structural basis for activation of DNMT1.Nature Communications, 13, Article number: 7130, 2022. doi: 10.1038/s41467-022-34779-4.

2021

  1. Kori S*, Shibahashi Y*, Ekimoto T*, Nishiyama A, Yoshimi S, Yamaguchi K, Nagatoishi S, Ohta M, Tsumoto K, Nakanishi M, Defossez PA, Ikeguchi M, Arita K. Structure-based screening combined with computational and biochemical analyses identified the inhibitor targeting the binding of DNA Ligase 1 to UHRF1. Bioorganic & Medicinal Chemistry. Volume 52, 15 December 2021.
    DOI: https://doi.org/10.1016/j.bmc.2021.116500 *These authors equally contributed to this work.
  2. Funyu T*, Kanemaru Y*, Onoda H, Arita K. Preparation of the ubiquitination-triggered active form of SETDB1 in E. coli for biochemical and structural analyses. The Journal of Biochemistry. Accepted. *These authors equally contributed to this work.DOI: http://dx.doi.org/10.1093/jb/mvab087
  3. Ohno A, Maita N, Tabata T, Nagano H, Arita K, Ariyoshi M, Uchida T, Nakao R, Ulla A, Sugiura K, Kishimoto K, Teshima-Kondo S, Okumura Y, Nikawa T. Crystal structure of inhibitor-bound human MSPL that can activate high pathogenic avian influenza. Life Sci Alliance. Apr 5;4(6):e202000849, 2021. DOI: 10.26508/lsa.202000849.

2020

  1. Furukawa A., Walinda E., Arita K., Sugase K. Structural dynamics of double-stranded DNA with epigenome modification. Nucleic Acids Res., 49 1152-1162, 2021. doi: 10.1093/nar/gkaa1210
  2. Kori S*, Jimenji T*, Ekimoto T*, Sato M, Kusano F, Oda T, Unoki M, Ikeguchi M, Arita K. (*These authors equally contributed to this work.) Serine 298 phosphorylation in linker 2 of UHRF1 regulates ligand-binding property of its tandem Tudor domain. J. Mol. Biol., 432 4061-4075, 2020. doi: 10.1016/j.jmb.2020.05.006.
  3. *Nishiyama A, Mulholland C, Bultmann S, Kori S, Endo A, Saeki Y, Qin W, Trummer C, Chiba Y, Yokoyama H, Kumamoto S, Kawakami T, Hojo H, Nagae G, Aburatani H, Tanaka K, *Arita K, *Leonhardt H, and *Nakanishi M. Two distinct modes of DNMT1 recruitment ensure stable maintenance DNA methylation. Nature Communications. 11 Article number:1222. 2020
    DOI: 10.1038/s41467-020-15006-4
  4. Mishima Y, Brueckner L, Takahashi S, Kawakami T, Otani J, Shinohara A, Takeshita K, Garvilles RG, Watanabe M, Sakai N, Takeshima H, Nachtegael C, Nishiyama A, Nakanishi M, Arita K, Nakashima K, Hojo H, Suetake I. Enhanced processivity of Dnmt1 by monoubiquitinated histone H3.Genes to Cells. 25 22-32, 2020.
    DOI: 10.1111/gtc.12732

2019

  1. Jimenji T., Matsumura R., Kori S. and *Arita K. Structure of PCNA in complex with DNMT1 PIP box reveals the basis for the molecular mechanism of the interaction. Biochemical and Biophysical Research Communications 516, 578-583, 2019
  2. Kori S., Ferry L., Matano S., Jimenji T., Kodera N., Tsusaka T., Matsumura R., Oda T., Sato M.,Dohmae N., Ando T., Shinkai Y., *Defossez PA and *Arita K. Structure of the UHRF1 Tandem Tudor Domain Bound to a Methylated Non-histone Protein, LIG1, Reveals Rules for Binding and Regulation. Structure 27, 485-496, 2019

2017

  1. *Ishiyama S, *Nishiyama A, Saeki Y, Moritsugu K, Morimoto D, Yamaguchi L, Arai N, Matsumura R, Kawakami T, Mishima Y, Hojo H, Shimamura S, Ishikawa F, Tajima S, Tanaka K, Ariyoshi M, Shirakawa M, Ikeguchi M, Kidera A, **Suetake I, **Arita K, **Nakanishi M. Structure of the Dnmt1 reader module complexed with a unique two-mono-ubiquitin mark on histone H3 reveals the basis for DNA methylation maintenance. Molecular Cell 68 350-360, 2017. Elected to Featured article
    doi: http://dx.doi.org/10.1016/j.molcel.2017.09.037
  2. L. Mishima Y*, Brueckner L*, Takahashi S, Kawakami T, Arita K, Oka S, Otani J, Hojo H, Shirakawa M, Suetake I. RFTS-dependent negative regulation of Dnmt1 by nucleosome. The FEBS Journal 284, 3455-3469 2017 doi: 10.1111/febs.14205
  3. Ferry L*, Fournier A*, Tsusaka T*, Adelmant G, Shimazu T, Matano S, Kirsh O, Amouroux R, Dohmae N, Suzuki T, Filion GJ, Deng W, de Dieuleveult M, Fritsch L, Kudithipudi S, Jeltsch A, Leonhardt H, Hajkova P, Marto JA, Arita K, Shinkai Y**, Defossez PA**. Methylation of DNA Ligase 1 by G9a/GLP recruits UHRF1 to replicating DNA and regulates DNA methylation. Molecular Cell 67, 550-565, 2017 doi: 10.1016/j.molcel.2017.07.012
  4. Yamaguchi L, Nishiyama A, Misaki T, Johmura Y, Ueda J, Arita K, Nagao K, Obuse C, Nakanishi M. Usp7-dependent histone H3 deubiquitylation regulates maintenance of DNA methylation. Sci Rep. 2017 Dec;7(1):55. doi: 10.1038/s41598-017-00136-5.

BEFORE

  1. Kobayashi T, Obana Y, Kuboi N, Kitayama Y, Hayashi S, Oka M, Wada N, Arita K, Shimizu T, Sato M, Kanaly RA, Kutsuna S. Analysis of the Fine-Tuning of Cyanobacterial Circadian Phase by Monochromatic Light and Long-Day Conditions. Plant Cell Physiol, 57, 105-114, 2016.
  2. Morimoto D, Walinda E, Fukada H, Sou YS, Kageyama S, Hoshino M, Fujii T, Tsuchiya H, Saeki Y, Arita K, Ariyoshi M, Tochio H, Iwai K, Namba K, Komatsu M, Tanaka K, Shirakawa M. The unexpected role of polyubiquitin chains in the formation of fibrillar aggregates. Nature Communications 2015 Jan 20;6:6116. 2015. doi: 10.1038/ncomms7116.
  3. Tsutsumi N, Kimura T, Arita K, Ariyoshi M, Ohnishi H, Yamamoto T, Zuo X, Maenaka K, Park EY, Kondo N, Shirakawa M, Tochio H, Kato Z. The structural basis for receptor recognition of human interleukin-18. Nature Communications 5, 5340- 2014. doi: 10.1038/ncomms6340.
  4. Kimura T, Tsutsumi N, Arita K, Ariyoshi M, Ohnishi H, Kondo N, Shirakawa M, Kato Z, Tochio H. Purification, crystallization and preliminary X-ray crystallographic analysis of human IL-18 and its extracellular complexes. Acta Crystallogr F Struct Biol Commun. 70, 1351-6, 2014. doi: 10.1107/S2053230X14016926.
  5. Berkyurek AC, Suetake I, Arita K, Takeshita K, Nakagawa A, Shirakawa M, Tajima S. The DNA Methyltransferase Dnmt1 Directly Interacts with the SET and RING Finger Associated (SRA) Domain of the Multifunctional Protein Uhrf1 to Facilitate Accession of the Catalytic Center to Hemi-methylated DNA. JBC 289, 379-86, 2014.
  6. Nishiyama A, Yamaguchi L, Sharif J, Johmura Y, Kawamura T, Nakanishi K, Shimamura S, Arita K, Kodama T, Ishikawa F, Koseki H, and Nakanishi M . Uhrf1-dependent ubiquitylation of histone H3 at lysine 23 couples maintenance DNA methylation and DNA replication. Nature 502, 249-253, 2013.
  7. Hori Y, Norinobu T, Sato M, Arita K, Shirakawa M, Kikuchi K. Development of Fluorogenic Probes for Quick No-Wash Live-Cell Imaging of Intracellular Proteins. JACS. 135, 12360-12365, 2013.
  8. Takaoka Y, Kioi Y, Morito A, Otani J, Arita K, Ashihara E, Ariyoshi M, Tochio H, Shirakawa M, Hamachi I. Quantitative comparison of protein dynamics in live cells and in vitro by in-cell (19)F-NMR. Chem Commun (Camb). 49, 2801-2803, 2013.
  9. Otani J, Arita K, Kato T, Kinoshita M, Kimura H, Suetake I, Tajima S, Ariyoshi M, Shirakawa M. Structural basis of the versatile DNA recognition ability of the methyl CpG binding domain of methyl-CpG binding domain protein 4. J. Biol. Chem. 288, 6351-6362, 2013.
  10. Unoki M, Masuda A, Dohmae N, Arita K, Yoshimatsu M, Iwai Y, Fukui Y, Ueda K, Hamamoto R, Shirakawa M, Sasaki H, Nakamura Y. Lysyl 5-Hydroxylation, a Novel Histone Modification, by Jumonji Domain Containing 6 (JMJD6). J. Biol. Chem. 288, 6053-6062, 2013.
  11. Arita K, Isogai S, Oda T, Unoki M, Sugita K, Sekiyama N, Kuwata K, Hamamoto R, Tochio H, Sato M, Ariyoshi M, Shirakawa M. Recognition of modification status on a histone H3 tail by linked histone reader modules of the epigenetic regulator UHRF1. PNAS. 109, 12950-12955, 2012.
  12. Isogai S, Morimoto D, Arita K, Unzai S, Tenno T, Hasegawa J, Sou YS, Komatsu M, Tanaka K, Shirakawa M, Tochio H. Crystal structure of the UBA domain of p62 and its interaction with ubiquitin. J Biol Chem. 286, 31864-31874, 2011.
  13. Sekiyama N., Arita K., Ikeda Y., Hashiguchi K., Ariyoshi M., Tochio H., Saitoh H. and Shirakawa M. Structural basis for regulation of poly-SUMO chain by SUMO-like domain of Nip45. Proteins 78, 1491-1502, 2010.
  14. Otani J., Nankumo T., Arita K., Inamoto S., Ariyoshi M.,and Shirakawa M. Structural basis for recognition of H3K4 methylation status by the DNMT3A ADD domain. Embo Rep. 11, 1235-1241, 2009.
  15. Arita K., Ariyoshi M., Tochio H., Nakamura Y., and Shirakawa M. Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism. Nature 455, 818-821, 2008.
  16. Arita K., Hashimoto H., Igari K., Akaboshi M., Kutsuna S., Sato M. and Shimizu T. Structural and Biochemical Characterization of a Cyanobacterium Circadian Clock-modifier Protein. J. Biol. Chem. 282, 1128-1135, 2007.
  17. Luo Y., Arita K., Bhatia M., Knuckley B., Lee Y. H., Stallcup M. R., Sato M. and Thompson PR. Inhibitors and inactivators of protein arginine deiminase 4: functional and structural characterization. Biochemistry 45, 11727-11736, 2006.
  18. Arita K., Shimizu T., Hashimoto H., Hidaka Y., Yamada M., Sato M. Structural basis for histone N-terminal recognition by human peptidylarginine deiminase 4. PNAS. 103, 5291-5296, 2006.
  19. Naoe, Y,. Arita K., Hashimoto, H., Kanazawa, H., Sato, M. and Shimizu, T. Structural characterization of calcineurin B homologous protein 1. J. Biol. Chem. 280, 32372-32378, 2005.
  20. Naoe, Y,. Arita K., Hashimoto, H., Kanazawa, H., Sato, M. and Shimizu, T. Crystallization and preliminary X-ray crystallographic analysis of rat calcineurin B homologous protein 1. Acta Cryst. F61, 612-613, 2005.
  21. Arita K., Hashimoto, H., Shimizu, T., Nakashima, K., Yamada, M. and Sato, M. Structure basis for Ca2+-induced activation of human PAD4. Nature Structural and Molecular Biology 11, 777-783, 2004.
  22. Arita K., Hashimoto, H., Shimizu, T., Yamada, M. and Sato, M. Crystallization and preliminary X-ray crystallographic analysis of human peptidylarginine deiminase V. Acta Cryst. D59, 2332-2333, 2003.