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Mechanisms of core promoter recognition by general transcription factor TFIID

Research Project

Project/Area Number 23370077
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Molecular biology
Research InstitutionYokohama City University

Principal Investigator

KOKUBO Tetsuro  横浜市立大学, その他の研究科, 教授 (10271587)

Project Period (FY) 2011-04-01 – 2014-03-31
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥19,890,000 (Direct Cost: ¥15,300,000、Indirect Cost: ¥4,590,000)
Fiscal Year 2013: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Fiscal Year 2012: ¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000)
Fiscal Year 2011: ¥7,020,000 (Direct Cost: ¥5,400,000、Indirect Cost: ¥1,620,000)
Keywords転写調節 / 転写因子 / 基本転写因子 / 転写開始 / 出芽酵母 / TFIID / TAF / TBP / SAGA
Research Abstract

TFIID, the largest GTF composed of TBP and 14 TAFs, plays a critical role in transcription from TATA-less promoters. In metazoans, several core promoter elements (CE) other than the TATA element are thought to be recognition sites for TFIID. However, it is unclear whether functionally homologous elements also exist in TATA-less promoters in yeast.
Here we develop a novel high-throughput screening system to measure gene expression in yeast by using VTC1 as a reporter gene. This method allows us to isolate several active and novel CE by screening a randomized oligonucleotide pool for the CYC1 promoter. The TAF N-terminal domain (TAND) of the TAF1 protein plays a significant role in transcriptional activation. TAND comprises two subdomains, TAND1 and TAND2, which interact with the concave and convex surfaces of TBP, respectively. In collaboration with other groups, we determine the crystal structure of the TAND-TBP complex that provides a novel insight into transcriptional activation.

Report

(4 results)
  • 2013 Annual Research Report   Final Research Report ( PDF )
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • Research Products

    (32 results)

All 2014 2013 2012 2011 Other

All Journal Article (9 results) (of which Peer Reviewed: 6 results) Presentation (19 results) Book (3 results) Remarks (1 results)

  • [Journal Article] High-resolution structure of TBP with TAF1 reveals anchoring patterns in transcriptional regulation2013

    • Author(s)
      Anandapadamanaban M, Andresen C, Helander S, Ohyama Y, Siponen MI, Lundström P, Kokubo T, Ikura M, Moche M, Sunnerhagen M
    • Journal Title

      Nat Struct Mol Biol

      Volume: 20(8) Issue: 8 Pages: 1008-14

    • DOI

      10.1038/nsmb.2611

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Transcription in Eukaryote (review)2013

    • Author(s)
      T. Kokubo
    • Journal Title

      Encyclopedia of Systems Biology

      Volume: in press

    • Related Report
      2012 Annual Research Report
  • [Journal Article] Transcription Initiation in Eukaryote (review)2013

    • Author(s)
      T. Kokubo
    • Journal Title

      Encyclopedia of Systems Biology

      Volume: in press

    • Related Report
      2012 Annual Research Report
  • [Journal Article] Mechanisms of Transcriptional Activation and Repression (review)2013

    • Author(s)
      T. Kokubo
    • Journal Title

      Encyclopedia of Systems Biology

      Volume: in press

    • Related Report
      2012 Annual Research Report
  • [Journal Article] Identification and recombinant analysis of botrocetin-2, a snake venom cofactor for von Willebrand factor-induced platelet agglutination2012

    • Author(s)
      Yamamoto-Suzuki Y, Sakurai Y, Fujimura Y, Matsumoto M, Hamako J, Kokubo T, Kitagawa H, Kawsar SM, Fujii Y, Ozeki Y, Matsushita F, Matsui T
    • Journal Title

      Biochemistry

      Volume: 51(26) Pages: 5329-38

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Identification and recombinant analysis of botrocetin-2, a snake venom cofactor for von Willebrand factor-induced platelet agglutination2012

    • Author(s)
      Yamamoto-Suzuki Y, Sakurai Y, Fujimura Y, Matsumoto M, Hamako J, Kokubo T, Kitagawa H, Kawsar SMA, Fujii Y, Ozeki Y, Matsushita F, Matsui T
    • Journal Title

      Biochemistry

      Volume: 51 Issue: 26 Pages: 5329-5338

    • DOI

      10.1021/bi300442c

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Rapid cell division contributes to efficient induction of A/T mutations during Ig gene hypermutation2011

    • Author(s)
      Kano C, Ouchida R, Kokubo T, Wane JY
    • Journal Title

      Molecular Immunology

      Volume: 48(15-16) Issue: 15-16 Pages: 1993-1999

    • DOI

      10.1016/j.molimm.2011.06.218

    • Related Report
      2013 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Cell polarity in Saccharomyces cerevisiae depends on proper localization of the Bud9 landmark protein by the EKC/KEOPS complex2011

    • Author(s)
      Kato Y, Kawasaki H, Ohyama Y, Morishita T, Iwasaki H, Kokubo T, Hirano H
    • Journal Title

      Genetics

      Volume: 188(4) Issue: 4 Pages: 871-882

    • DOI

      10.1534/genetics.111.128231

    • Related Report
      2013 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Hmol directs pre-initiation complex assembly to an appropriate site on its target gene promoters by masking a nucleosome-free region2011

    • Author(s)
      Kasahara K, Ohyama Y, Kokubo T
    • Journal Title

      Nucleic Acids Research

      Volume: 39(10) Issue: 10 Pages: 4136-4150

    • DOI

      10.1093/nar/gkq1334

    • Related Report
      2013 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Presentation] 二種類の異なる機能を持つG1サイクリンCln2pの転写段階での運命決定2014

    • Author(s)
      高井直樹, 大山良文, 古久保哲朗
    • Organizer
      転写研究会・転写サイクル・転写代謝システム共催「冬の若手ワークショップ2014」
    • Place of Presentation
      軽井沢
    • Year and Date
      2014-01-31
    • Related Report
      2013 Final Research Report
  • [Presentation] リボソーム構成因子の発現調節に関わる酵母Hmo1タンパク質のDNA結合機構2013

    • Author(s)
      東野綺子, 雲財悟, 中山理紗, 土屋奈穂, 吉川博文, 古久保哲朗, 笠原浩司
    • Organizer
      日本分子生物学会第36回年会
    • Place of Presentation
      神戸
    • Year and Date
      2013-12-04
    • Related Report
      2013 Final Research Report
  • [Presentation] 出芽酵母におけるTFIIDを介したGAL遺伝子群の脱抑制機構2013

    • Author(s)
      矢部誠, 大山良文, 高井直樹, 古久保哲朗
    • Organizer
      日本分子生物学会第36回年会
    • Place of Presentation
      神戸
    • Year and Date
      2013-12-03
    • Related Report
      2013 Final Research Report
  • [Presentation] 母性mRNAの3'非翻訳領域を標的としたアンチセンスモルフォリノオリゴによるpoly(A)鎖短小化機構の解析2012

    • Author(s)
      茂呂華奈子, 古久保哲朗, 和田忠士
    • Organizer
      日本分子生物学会第35回年会
    • Place of Presentation
      福岡
    • Year and Date
      2012-12-14
    • Related Report
      2013 Final Research Report
  • [Presentation] 出芽酵母のTFIIDとSAGAは細胞の極成長に関わるRAMシグナル経路と遺伝学的に相互作用する2012

    • Author(s)
      大山良文, 和田忠士, 古久保哲朗
    • Organizer
      新学術領域研究「転写代謝システム」・転写研究会共催「若手ワークショップ@湯河原」
    • Place of Presentation
      湯河原
    • Year and Date
      2012-02-09
    • Related Report
      2013 Final Research Report
  • [Presentation] 出芽酵母における新規ハイスループット型プロモーター活性測定法の開発とその応用2012

    • Author(s)
      渡邉清, 矢部誠, 古久保哲朗
    • Organizer
      新学術領域研究「転写代謝システム」・転写研究会共催「若手ワークショップ@湯河原」
    • Place of Presentation
      湯河原
    • Year and Date
      2012-02-09
    • Related Report
      2013 Final Research Report
  • [Presentation] 出芽酵母のTFIIDとSAGAは細胞の極成長に関わるRAMシグナル経路と遺伝学的に相互作用する2012

    • Author(s)
      大山良文、和田忠士、古久保哲朗
    • Organizer
      新学術領域研究「転写代謝システム」・転写研究会共催「若手ワークショップ@湯河原」
    • Place of Presentation
      湯河原(和光純薬・湯河原研修所)
    • Year and Date
      2012-02-09
    • Related Report
      2011 Annual Research Report
  • [Presentation] 出芽酵母における新規ハイスループット型プロモーター活性測定法の開発とその応用2012

    • Author(s)
      渡邉清、矢部誠、古久保哲朗
    • Organizer
      新学術領域研究「転写代謝システム」・転写研究会共催「若手ワークショップ@湯河原」
    • Place of Presentation
      湯河原(和光純薬・湯河原研修所)
    • Year and Date
      2012-02-09
    • Related Report
      2011 Annual Research Report
  • [Presentation] 基本転写因子TFIIDの機能発現における天然変性領域の役割2012

    • Author(s)
      古久保哲朗
    • Organizer
      新学術領域研究「天然変性タンパク質の分子認識機構と機能発現」第2回公開シンポジウム
    • Place of Presentation
      大阪
    • Year and Date
      2012-01-24
    • Related Report
      2013 Final Research Report
  • [Presentation] 基本転写因子TFIIDの機能発現における天然変性領域の役割2012

    • Author(s)
      古久保哲朗
    • Organizer
      新学術領域研究「天然変性タンパク質の分子認識機構と機能発現」第2回公開シンポジウム
    • Place of Presentation
      大阪(千里ライフサイエンスセンター)
    • Year and Date
      2012-01-24
    • Related Report
      2011 Annual Research Report
  • [Presentation] TFIID and SAGA regulate the fate of CLN2 mRNA cooperatively with the RAM signaling network2011

    • Author(s)
      大山良文, 和田忠士, 古久保哲朗
    • Organizer
      日本分子生物学会第34回年会
    • Place of Presentation
      横浜
    • Year and Date
      2011-12-15
    • Related Report
      2013 Final Research Report
  • [Presentation] Novel regulatory mechanism for transcriptional initiation of ribosomal protein genes in S. cerevisiae2011

    • Author(s)
      笠原浩司, 大山良文, 古久保哲朗
    • Organizer
      日本分子生物学会第34回年会
    • Place of Presentation
      横浜
    • Year and Date
      2011-12-15
    • Related Report
      2013 Final Research Report
  • [Presentation] A novel high-throughput screening system to measure gene expression in Saccharomyces cerevisiae2011

    • Author(s)
      渡邉清, 古久保哲朗
    • Organizer
      日本分子生物学会第34回年会
    • Place of Presentation
      横浜
    • Year and Date
      2011-12-15
    • Related Report
      2013 Final Research Report
  • [Presentation] TFIID and SAGA regulate the fate of CLN2 mRNA cooperatively with the RAM signaling network2011

    • Author(s)
      大山良文、和田忠士、古久保哲朗
    • Organizer
      日本分子生物学会第34回年会
    • Place of Presentation
      横浜(パシフィコ横浜)
    • Year and Date
      2011-12-15
    • Related Report
      2011 Annual Research Report
  • [Presentation] Novel regulatory mechanism for transcriptional initiation of ribosomal protein genes in S.cerevisiae2011

    • Author(s)
      笠原浩司、大山良文、古久保哲朗
    • Organizer
      日本分子生物学会第34回年会
    • Place of Presentation
      横浜(パシフィコ横浜)
    • Year and Date
      2011-12-15
    • Related Report
      2011 Annual Research Report
  • [Presentation] A novel high-throughput screening system to measure gene expression in Saccharomyces cerevisiae2011

    • Author(s)
      渡邉清、古久保哲朗
    • Organizer
      日本分子生物学会第34回年会
    • Place of Presentation
      横浜(パシフィコ横浜)
    • Year and Date
      2011-12-15
    • Related Report
      2011 Annual Research Report
  • [Presentation] 出芽酵母におけるTFIIDを介したGAL遺伝子群の脱抑制機構

    • Author(s)
      矢部 誠,大山 良文,高井 直樹,古久保 哲朗
    • Organizer
      日本分子生物学会第36回年会
    • Place of Presentation
      神戸(ポートピアホテル)
    • Related Report
      2013 Annual Research Report
  • [Presentation] リボソーム構成因子の発現調節に関わる酵母Hmo1タンパク質のDNA 結合機構

    • Author(s)
      東野 綺子,雲財 悟,中山 理紗,土屋 奈穂,吉川 博文,古久保 哲朗,笠原 浩司
    • Organizer
      日本分子生物学会第36回年会
    • Place of Presentation
      神戸(ポートピアホテル)
    • Related Report
      2013 Annual Research Report
  • [Presentation] 母性mRNAの3’非翻訳領域を標的としたアンチセンスモルフォリノオリゴによるpoly(A)鎖短小化機構の解析

    • Author(s)
      茂呂華奈子
    • Organizer
      日本分子生物学会第35回年会
    • Place of Presentation
      福岡
    • Related Report
      2012 Annual Research Report
  • [Book] Essay; Mechanisms of Transcriptional Activation and Repression (p1210-1217). Definitions; Activation Domain Shielding (p4-6), ATAC (p49-50), Chromatin Helicase DNA binding (CHD) (p402-404), INO80 (p1033-1035), ISWI (p1058-1060), Mammalian HDAC (p1173-1174), PIC Disassembly (p1715), Set3C (p1932-1933), TAND (p2121-2122), Tra1p (p2218-2219) : Encyclopedia ofSystems Biology, W. Dubitzky, O. Wolkenhauer, K. H. Cho, H. Yokota (Eds.)2013

    • Author(s)
      T. Kokubo
    • Publisher
      Springer Science + Business Media LLC
    • Related Report
      2013 Final Research Report
  • [Book] Essay; Transcription in Eukaryote (p2239-2245). Definitions; Cofactors (p436-437), Core Promoter Elements (p502-504), General Transcription Factors (p813-814), Mediator (p1217-1218), PIC Assembly Pathways (p1714-1715), RNA Polymerase I, II and III (p1862-1863), SAGA (p1890-1891), Type 3 Promoters (p2306-2307) : Encyclopedia of Systems Biology, W. Dubitzky, O. Wolkenhauer, K. H. Cho, H. Yokota (Eds.)2013

    • Author(s)
      T. Kokubo
    • Publisher
      Springer Science + Business Media LLC
    • Related Report
      2013 Final Research Report
  • [Book] Essay; Transcription Initiation in Eukaryote (p2245-2251). Definitions; Immobilized Template Assay (p989-990), Phosphodiester Bond Formation (p1702-1703), Stalk of RNAPII (p1982-1984), TAF Paralogs (p2120-2121), TFIIA-Like Factor (ALF) (p2163), TRF1 (p2299-2300), TRF2 (p2300-2301), TRF3 (p2301-2302) : Encyclopedia ofSystems Biology, W. Dubitzky, O. Wolkenhauer, K. H. Cho, H. Yokota (Eds.)2013

    • Author(s)
      T. Kokubo
    • Publisher
      Springer Science + Business Media LLC
    • Related Report
      2013 Final Research Report
  • [Remarks]

    • URL

      http://www.tsurumi.yokohama-cu.ac.jp/mcbl/index2.html

    • Related Report
      2013 Final Research Report

URL: 

Published: 2011-04-06   Modified: 2019-07-29  

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