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Structural and functional analyses of chromatin assembly factors

Planned Research

Project AreaStructural basis of cell-signalling complexes mediating signal perception, transduction and responses
Project/Area Number 22121005
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionHigh Energy Accelerator Research Organization (2012-2014)
National Institute of Advanced Industrial Science and Technology (2010-2011)

Principal Investigator

SENDA Toshiya  大学共同利用機関法人高エネルギー加速器研究機構, 物質構造科学研究所, 教授 (30272868)

Co-Investigator(Renkei-kenkyūsha) HORIKOSHI Masami  東京大学, 分子細胞生物学研究所, 准教授 (70242089)
SEKI Masayuki  東北薬科大学, 薬学部, 教授 (70202140)
Project Period (FY) 2010-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥194,350,000 (Direct Cost: ¥149,500,000、Indirect Cost: ¥44,850,000)
Fiscal Year 2014: ¥29,120,000 (Direct Cost: ¥22,400,000、Indirect Cost: ¥6,720,000)
Fiscal Year 2013: ¥30,550,000 (Direct Cost: ¥23,500,000、Indirect Cost: ¥7,050,000)
Fiscal Year 2012: ¥31,980,000 (Direct Cost: ¥24,600,000、Indirect Cost: ¥7,380,000)
Fiscal Year 2011: ¥31,720,000 (Direct Cost: ¥24,400,000、Indirect Cost: ¥7,320,000)
Fiscal Year 2010: ¥70,980,000 (Direct Cost: ¥54,600,000、Indirect Cost: ¥16,380,000)
KeywordsX線結晶構造解析 / クロマチン / ヌクレオソーム / 転写 / 複製 / CAF-I / HIRA / CAF-I複合体 / 精製 / タンパク質複合体 / 結晶化 / ヒストン / ヒストンシャペロン / 昆虫細胞 / 発現・精製系 / 複合体
Outline of Final Research Achievements

Nucleosomes are the fundamental repeating units of chromatin. Nucleosomes must be disassembled and reassembled during nuclear reactions, such as replication, transcription, repair, and recombination. During the reassembly of nucleosomes, histones need to be deposited on genomic DNA in the correct procedure. If not, epigenetic information, which is encoded on the N-tail of histones, is eliminated in the course of nuclear reaction coupled nucleosome reassembly. Here, we focused on the histone deposition factors, CAF-I and HIRA. We established a protocol for the large-scale purification of CAF-1 (a replication-dependent histone deposition factor), which enabled us to obtain images from EM analyses. Regarding HIRA, which is a replication-independent histone deposition factor, we have obtained crystals of the HIRA-C domain. We will now try crystal optimization. In addition, we have determined the crystal structure of CagA, which has been implicated in Helicobacter pylori pathogenicity.

Report

(6 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Research Products

    (40 results)

All 2015 2014 2013 2012 2011 2010 Other

All Journal Article (12 results) (of which Peer Reviewed: 11 results,  Open Access: 2 results,  Acknowledgement Compliant: 1 results) Presentation (27 results) (of which Invited: 6 results) Remarks (1 results)

  • [Journal Article] Structure of a BAG6 (Bcl-2-associated Athanogene 6)-Ubl4a (Ubiquitin-like Protein 4a) Complex Reveals a Novel Binding Interface That Functions in Tail-anchored Protein Biogenesis.2015

    • Author(s)
      Kuwabara N, Minami R, Yokota N, Matsumoto H, Senda T, Kawahara H, Kato R.
    • Journal Title

      J. Biol. Chem.

      Volume: 290 Issue: 15 Pages: 9387-9398

    • DOI

      10.1074/jbc.m114.631804

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Molecular mechanism of strict substrate specificity of an Extradiol Dioxygenase, DesB, derived from Sphingobium sp. SYK-6.2014

    • Author(s)
      Sugimoto, K., Senda, M., Kasai, D., Fukuda, M., Masai, E. and Senda, T.
    • Journal Title

      PLoS One

      Volume: 9 Issue: 3 Pages: 257-265

    • DOI

      10.1371/journal.pone.0092249

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Molecular mechanism of strict substrate specificity of an Extradiol Dioxygenase, DesB, derived from Sphingobium sp. SYK-6.2014

    • Author(s)
      Sugimoto K, Senda M, Kasai E, Fukuda M, and Senda T
    • Journal Title

      PLoS One

      Volume: 9

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 大気圧電子顕微鏡(ASEM)による抗体を選ばない水中免疫電顕法:細胞・タンパク質ミクロ結晶の液中観察2014

    • Author(s)
      海老原達彦・西山英利・佐藤真理・千田俊哉・須賀三雄・佐藤主税
    • Journal Title

      生化学

      Volume: 86 Pages: 103-110

    • Related Report
      2013 Annual Research Report
  • [Journal Article] Structural basis of the γ-lactone-ring formation in ascorbic acid biosynthesis by the senescence marker protein-30/gluconolactonase.2013

    • Author(s)
      Aizawa, S., Senda, M., Harada, A., Maruyama, N., Ishida, T., Aigaki, T., Ishigami, A., Senda, T.
    • Journal Title

      PLoS One

      Volume: 8 Issue: 1 Pages: e53706-e53706

    • DOI

      10.1371/journal.pone.0053706

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Tertiary structure-function analysis reveals the pathogenic signaling potentiation mechanism of Helicobacter pylori oncogenic effector CagA2012

    • Author(s)
      Hayashi T., Senda M., Morohashi H., Higashi H., Horio M., Kashiba Y., Nagase L., Sasaya D., Shimizu T., Venugopalan N., Kumeta H., Noda N.N., Inagaki F., Senda T., Hatakeyama M.
    • Journal Title

      Cell Host Microbe

      Volume: 12 Issue: 1 Pages: 20-33

    • DOI

      10.1016/j.chom.2012.05.010

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of a zinc-dependent D-serine dehydratase from chicken kidney2011

    • Author(s)
      Tanaka, H.
    • Journal Title

      J.Biol.Chem.

      Volume: 286 Issue: 31 Pages: 27548-27558

    • DOI

      10.1074/jbc.m110.201160

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The roles of histone chaperone CIA/Asf1 in nascent DNA elongation during nucleosome replication.2011

    • Author(s)
      K.Ishikawa, T.Ohsumi, S.Tada, R.Natsume, L.R.Kundu, N.Nozaki, T.Senda, T.Enomoto, M.Horikoshi & M.Seki
    • Journal Title

      Genes Cells

      Volume: 16 Issue: 10 Pages: 1050-1062

    • DOI

      10.1111/j.1365-2443.2011.01549.x

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Regulatory system of the protocatechuate 4,5-cleavage pathway genes essential for lignin downstream catabolism.2010

    • Author(s)
      Kamimura, N.
    • Journal Title

      J.Bacteriol.

      Volume: 192 Pages: 3394-3405

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystallization and preliminary crystallographic analysis of D-serine dehydratase from chicken kidney.2010

    • Author(s)
      Senda, M.
    • Journal Title

      Acta Crystallogr.F

      Volume: 67 Pages: 147-149

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering.2010

    • Author(s)
      Prokop, Z.
    • Journal Title

      Angew.Chem.Int.Ed.Engl.

      Volume: 49 Pages: 6111-6115

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystallization ana preliminary crystallographic analysis of D-asparatate oxidase from procine kidney

    • Author(s)
      Senda, M.
    • Journal Title

      Acta Crystallogr.F

      Volume: (印刷中)

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Presentation] 創薬等支援技術基盤プラットフォームにおける構造研究2015

    • Author(s)
      千田俊哉
    • Organizer
      日本薬学会
    • Place of Presentation
      神戸・神戸学院大学/兵庫医療大学
    • Year and Date
      2015-03-26
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] エピジェネティックおよび疾病関連タンパク質の構造生物学研究2014

    • Author(s)
      千田俊哉
    • Organizer
      日本結晶学会
    • Place of Presentation
      東京・東京大学農学部弥生キャンパス
    • Year and Date
      2014-11-01
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] ピロリ菌由来のがんタンパク質CagAの構造-機能相関研究2014

    • Author(s)
      千田俊哉
    • Organizer
      日本生化学会
    • Place of Presentation
      京都・国立京都国際会館
    • Year and Date
      2014-10-16
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] ヒストンシャペロンHIRA C domainの精製系の確立2014

    • Author(s)
      佐藤優花里
    • Organizer
      日本生化学会
    • Place of Presentation
      京都・国立京都国際会館
    • Year and Date
      2014-10-16
    • Related Report
      2014 Annual Research Report
  • [Presentation] Structure and Function of an Oncoprotein CagA from Helicobacter Pylori2014

    • Author(s)
      千田俊哉
    • Organizer
      8th Asia-Ocdania Forum for synchrotron radiation research
    • Place of Presentation
      新竹(台湾)・National Synchrotron Radiation Research Center
    • Year and Date
      2014-09-16
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Large-scale purification of general transcription factor TFIIF2014

    • Author(s)
      Naruhiko Adachi, Kyohei Aizawa, Yuka Yamaguchi, and Toshiya Senda
    • Organizer
      Epigenetics & chromatin
    • Place of Presentation
      米国・コールドスプリングハーバー研究所
    • Year and Date
      2014-09-09 – 2014-09-13
    • Related Report
      2014 Annual Research Report
  • [Presentation] Expression and purification of histone chaperone HIRA2013

    • Author(s)
      佐藤優花里
    • Organizer
      Nagoya Symposium Frontiers in Structural Physiology
    • Place of Presentation
      名古屋
    • Year and Date
      2013-01-22
    • Related Report
      2012 Annual Research Report
  • [Presentation] Mechanistic insights revealed by the crystal structures of the Nucleotide-bound PIP5P4K IIβ2013

    • Author(s)
      羅羽華・千田俊哉
    • Organizer
      American Crystallographic Association (ACA) 2013
    • Place of Presentation
      ハワイ(アメリカ合衆国)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Tertiary structure and functional analysis of the Helicobacter pylori CagA oncoprotein.2012

    • Author(s)
      千田俊哉
    • Organizer
      The 3rd international symposium on drug discovery and design by NMR
    • Place of Presentation
      名古屋
    • Year and Date
      2012-10-11
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Purification and crystallization of TAF subunits of general transcription initiation factor TFIID.2012

    • Author(s)
      安達成彦
    • Organizer
      Cold Spring Harbor Laboratory Meeting: Epigenetics Chromatin
    • Place of Presentation
      Cold Spring Harbor, NY, USA
    • Year and Date
      2012-09-11
    • Related Report
      2012 Annual Research Report
  • [Presentation] Analysis of the mechanisms of transcriptional activation by TFIID2011

    • Author(s)
      安達成彦
    • Organizer
      第34回日本分子生物学会
    • Place of Presentation
      パシフィコ横浜(神奈川県)
    • Year and Date
      2011-12-15
    • Related Report
      2011 Annual Research Report
  • [Presentation] TATAボックス結合因子TFIID複合体による転写開始及び制御機構の解析2011

    • Author(s)
      安達成彦
    • Organizer
      BMB2010
    • Place of Presentation
      神戸市
    • Year and Date
      2011-12-08
    • Related Report
      2010 Annual Research Report
  • [Presentation] ヒストンシャペロン複合体の結晶構造とヌクレオソーム構造変換2011

    • Author(s)
      千田俊哉
    • Organizer
      日本結晶学会
    • Place of Presentation
      海道大学学術交流会館(北海道)
    • Year and Date
      2011-11-25
    • Related Report
      2011 Annual Research Report
  • [Presentation] 結晶化スクリーニングのスピードアップに有効な観察方法「すぐ見る法」2011

    • Author(s)
      千田美紀
    • Organizer
      日本結晶学会
    • Place of Presentation
      北海道大学学術交流会館(北海道)
    • Year and Date
      2011-11-24
    • Related Report
      2011 Annual Research Report
  • [Presentation] フェレドキシン還元酵素BphA4のNADH/NADPH特異性変換の構造的基盤2011

    • Author(s)
      原田彩佳
    • Organizer
      第84回日本生化学会大会
    • Place of Presentation
      国立京都国際会館(京都府)
    • Year and Date
      2011-09-23
    • Related Report
      2011 Annual Research Report
  • [Presentation] 転写基本因子TAF7の結晶化に向けた精製2011

    • Author(s)
      長澤貴俊
    • Organizer
      第84回日本生化学会大会
    • Place of Presentation
      国立京都国際会館(京都府)
    • Year and Date
      2011-09-22
    • Related Report
      2011 Annual Research Report
  • [Presentation] Crystal structure of a zinc-dependent D-serine dehydratase from Chicken kidney2011

    • Author(s)
      Miki Senda
    • Organizer
      IUCr2011
    • Place of Presentation
      Palacio Municipal de Congresos de Madrid (Spain)
    • Year and Date
      2011-08-23
    • Related Report
      2011 Annual Research Report
  • [Presentation] Crystal structures of histone chaperone CIA/ASF1-containing complexes2011

    • Author(s)
      Toshiya Senda
    • Organizer
      IUCr2011
    • Place of Presentation
      Palacio Municipal de Congresos de Madrid (Spain)
    • Year and Date
      2011-08-23
    • Related Report
      2011 Annual Research Report
  • [Presentation] TATAボックス結合因子TFIIDによる転写活性化の分子機構の解析2011

    • Author(s)
      安達成彦
    • Organizer
      第11回日本蛋白質科学会年会
    • Place of Presentation
      ホテル阪急エキスポパーク(大阪府)
    • Year and Date
      2011-06-07
    • Related Report
      2011 Annual Research Report
  • [Presentation] ヒストンシャペロン複合体の結晶構造解析2010

    • Author(s)
      千田俊哉
    • Organizer
      BMB2010
    • Place of Presentation
      神戸市
    • Year and Date
      2010-12-10
    • Related Report
      2010 Annual Research Report
  • [Presentation] Optimization of the packing in the haloalkane dehalogenase crystal by seeding.2010

    • Author(s)
      佐藤優花里
    • Organizer
      26th European Crystallographic Meeting
    • Place of Presentation
      ダルムシュタット(独)
    • Year and Date
      2010-08-30
    • Related Report
      2010 Annual Research Report
  • [Presentation] Structure of the histone chaperone CIA/ASF1-double bromodomain complex liking histone modifications and stie-specific histone evicition.2010

    • Author(s)
      安達成彦
    • Organizer
      9th EMBL conference Transcription and Chromatin
    • Place of Presentation
      ハイデルベルグ(独)
    • Year and Date
      2010-08-29
    • Related Report
      2010 Annual Research Report
  • [Presentation] Redox-dependent conformational changes of NADH-dependent ferredoxin reductase under various conditions2010

    • Author(s)
      千田俊哉
    • Organizer
      2010 Annual meeting of American Crystallographic Association
    • Place of Presentation
      シカゴ(米国)
    • Year and Date
      2010-07-27
    • Related Report
      2010 Annual Research Report
  • [Presentation] Structure-Based Model of the Biological Signaling from Histone Modifications to Structural Change of the Nucleosome.2010

    • Author(s)
      千田俊哉
    • Organizer
      International symposium on the physicochemical field for genetic activities
    • Place of Presentation
      兵庫県淡路市
    • Year and Date
      2010-01-24
    • Related Report
      2010 Annual Research Report
  • [Presentation] PFの現状とピロリ菌発がんタンパク質CagAの結晶構造解析

    • Author(s)
      千田俊哉
    • Organizer
      蛋白質科学会
    • Place of Presentation
      鳥取
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Human Type II PIPKβ-ヌクレオチド複合体のX線結晶構造解析

    • Author(s)
      羅羽華・竹内恒・千田美紀・嶋田一夫・Lewis C Cantley・佐々木敦朗・千田俊哉
    • Organizer
      蛋白質科学会
    • Place of Presentation
      鳥取
    • Related Report
      2013 Annual Research Report
  • [Presentation] Sphingobium sp. SYK-6由来バニリン酸脱メチル酵素LigMの立体構造解析に向けた精製

    • Author(s)
      原田彩佳・佐藤優花里・上村直史・政井英司・千田俊哉
    • Organizer
      日本生化学会
    • Place of Presentation
      横浜
    • Related Report
      2013 Annual Research Report
  • [Remarks] KEK, IMSS, SBRC

    • URL

      http://pfweis.kek.jp/index.html

    • Related Report
      2014 Annual Research Report

URL: 

Published: 2010-08-23   Modified: 2019-07-29  

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