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Computational reconstruction of the higher-order structure of chromosomes and linkage analysis between chromosome structure and phenotype

Planned Research

Project AreaChromosome Orchestration System
Project/Area Number 15H05979
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 InstitutionTokyo Institute of Technology

Principal Investigator

Itoh Takehiko  東京工業大学, 生命理工学院, 教授 (90501106)

Co-Investigator(Kenkyū-buntansha) 昆 彩奈  京都大学, 医学研究科, 助教 (20772403)
吉田 健一  京都大学, 医学研究科, 助教 (50738226)
Project Period (FY) 2015-06-29 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥95,290,000 (Direct Cost: ¥73,300,000、Indirect Cost: ¥21,990,000)
Fiscal Year 2019: ¥18,460,000 (Direct Cost: ¥14,200,000、Indirect Cost: ¥4,260,000)
Fiscal Year 2018: ¥18,590,000 (Direct Cost: ¥14,300,000、Indirect Cost: ¥4,290,000)
Fiscal Year 2017: ¥18,590,000 (Direct Cost: ¥14,300,000、Indirect Cost: ¥4,290,000)
Fiscal Year 2016: ¥18,590,000 (Direct Cost: ¥14,300,000、Indirect Cost: ¥4,290,000)
Fiscal Year 2015: ¥21,060,000 (Direct Cost: ¥16,200,000、Indirect Cost: ¥4,860,000)
KeywordsHi-C法 / 染色体高次構造 / エピゲノム / ゲノム情報 / 染色体構造 / 染色体動態 / 染色体立体構造解析
Outline of Final Research Achievements

The construction of a 4C, Hi-C and other higher order structure analysis pipeline including the original analysis method was realized. Also, the development of a novel high-precision genome assembly method and the construction of various NGS analysis pipelines such as ChIP-seq analysis was performed. By using these, we have realized various chromosomal structure analyzes from yeast to human and mouse, and succeeded in achieving joint research results with many members. In the analysis of myelodysplastic syndrome, analysis of mouse experimental data led to the discovery of a mechanism of abnormal gene expression regulation. On the other hand, the developed pipeline and various analyzed data are stored together with various public data on the newly constructed chromosome OS platform. By uploading the users own NGS data through WWW service, the user can perform various analysis in the platform, and the result can be browsed and compared with the public data on this platform.

Academic Significance and Societal Importance of the Research Achievements

本研究により開発された解析手法およびパイプラインの活用により、種々の高次構造解析データを比較的容易に解析することが可能となり、当該分野の研究発展に寄与することが期待される。これらの手法、パイプラインは、ダウンロードして使用することも可能であるとともに、染色体OSプラットフォームにNGSデータをWWW経由でアップロードすることにより解析できる機能も実装しているため、計算環境が整っていない研究者においても容易に使用することができる。また、染色体OSプラットフォームでは、公開データとともに自身の解析結果を視覚的に確認することが可能であり、新規知見を見出すための手助けとして機能することが期待される。

Report

(6 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • Research Products

    (13 results)

All 2020 2019 2018 2017 2016

All Journal Article (4 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 4 results,  Open Access: 4 results) Presentation (9 results)

  • [Journal Article] Evaluation of SNP calling methods for closely related bacterial isolates and a novel high-accuracy pipeline: BactSNP2019

    • Author(s)
      Yoshimura Dai、Kajitani Rei、Gotoh Yasuhiro、Katahira Katsuyuki、Okuno Miki、Ogura Yoshitoshi、Hayashi Tetsuya、Itoh Takehiko
    • Journal Title

      Microbial Genomics

      Volume: 5 Issue: 5

    • DOI

      10.1099/mgen.0.000261

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Platanus-allee is a de novo haplotype assembler enabling a comprehensive access to divergent heterozygous regions.2019

    • Author(s)
      Kajitani R, Yoshimura D, Okuno M, Minakuchi Y, Kagoshima H, Fujiyama A, Kubokawa K, Kohara Y, Toyoda A, Itoh T
    • Journal Title

      Nat Commun

      Volume: - Issue: 1 Pages: 1702-1702

    • DOI

      10.1038/s41467-019-09575-2

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] 3D genomic architecture reveals that neocentromeres associate with heterochromatin regions2018

    • Author(s)
      Nishimura Kohei、Komiya Masataka、Hori Tetsuya、Itoh Takehiko、Fukagawa Tatsuo
    • Journal Title

      The Journal of Cell Biology

      Volume: 218 Issue: 1 Pages: 134-149

    • DOI

      10.1083/jcb.201805003

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Complete genome sequence and expression profile of the commercial lytic enzyme producer Lysobacter enzymogenes M497-12017

    • Author(s)
      H Takami, A Toyoda, I Uchiyama, T Itoh, Y Takaki, W.Arai, S Nishi, M Kawai, K Shin-ya, H Ikeda
    • Journal Title

      DNA Research

      Volume: 24 Pages: 169-177

    • DOI

      10.1093/dnares/dsw055

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] Platanus-allee is a de novo haplotype assembler designed for organisms with highly divergent haplotypes: an update2020

    • Author(s)
      Rei Kajitani, Miki Okuno, Hiroyuki Tanaka, Atsushi Toyoda, Takehiko Itoh
    • Organizer
      Plant and Animal Genome XXVIII Conference
    • Related Report
      2019 Annual Research Report
  • [Presentation] 様々なゲノム解析から見えてきたゲノムの不均一な多様性とその意義2019

    • Author(s)
      伊藤武彦
    • Organizer
      第71回日本細胞生物学会大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] ドラフトゲノムの不完全性が遺伝子構造アノテーションに及ぼす影響の解析2019

    • Author(s)
      Yuta Nakamura, Rei Kajitani, Fumiya Kobayashi, Hideaki Yuasa and Takehiko Itoh
    • Organizer
      第8回生命医薬情報学連合大会IIBMP2019
    • Related Report
      2019 Annual Research Report
  • [Presentation] ドラフトゲノムに対応した遺伝子構造アノテーション自動構築パイプラインの開発2019

    • Author(s)
      Fumiya Kobayashi, Rei Kajitani, Miki Okuno, Hideaki Yuasa, Yuta Nakamura and Takehiko Itoh
    • Organizer
      第8回生命医薬情報学連合大会IIBMP2019
    • Related Report
      2019 Annual Research Report
  • [Presentation] Hi-Cを用いたネオセントロメア形成に伴う染色体高次構造の変化の解析2019

    • Author(s)
      佐藤柾幸,西村浩平,堀哲也,深川竜郎,伊藤武彦
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Y染色体をもたないアマミトゲネズミの遺伝子配列を用いた進化学的解析2018

    • Author(s)
      岡野真佑,奥野未来,梶谷嶺,黒岩麻里,伊藤武彦
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 4C-Seqを用いたネオセントロメア形成に伴う染色体高次構造変化の解析2017

    • Author(s)
      古宮正隆,西村浩平,堀哲也,深川竜郎,伊藤武彦
    • Organizer
      第40回日本分子生物学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Hi-Cを用いた二倍体出芽酵母の染色体構造解析2017

    • Author(s)
      角崎太郎,石毛大輔,岩崎博史,伊藤武彦
    • Organizer
      第40回日本分子生物学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 全ゲノムシークエンスデータに基づいた高精度配列構造変異検出プロトコルの構築2016

    • Author(s)
      西村浩平,堀哲也,古宮正隆,伊藤武彦,深川竜郎
    • Organizer
      第39回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2016-11-30
    • Related Report
      2016 Annual Research Report

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Published: 2015-07-02   Modified: 2022-11-04  

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