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Cis-regulatory polymorphism responsible for allele-expression-bias that contributes to mouse phenotype

Research Project

Project/Area Number 15H02412
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Genetics/Chromosome dynamics
Research InstitutionNational Institute of Genetics

Principal Investigator

Toshihiko Shiroishi  国立遺伝学研究所, 系統生物研究センター, 教授 (90171058)

Co-Investigator(Renkei-kenkyūsha) TAKADA Toyoyuki  国立遺伝学研究所, 系統生物研究センター, 助教 (20356257)
AMANO Takanori  国立遺伝学研究所, 系統生物研究センター, 助教 (20419849)
KISO Ayako (OKA Ayako)  国立遺伝学研究所, 系統生物研究センター, 博士研究員 (80425834)
Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥40,170,000 (Direct Cost: ¥30,900,000、Indirect Cost: ¥9,270,000)
Fiscal Year 2017: ¥11,700,000 (Direct Cost: ¥9,000,000、Indirect Cost: ¥2,700,000)
Fiscal Year 2016: ¥14,040,000 (Direct Cost: ¥10,800,000、Indirect Cost: ¥3,240,000)
Fiscal Year 2015: ¥14,430,000 (Direct Cost: ¥11,100,000、Indirect Cost: ¥3,330,000)
Keywords遺伝学 / ゲノム / 進化 / 発生制御 / 発生・分化 / 進化・分化 / マウス / 遺伝子発現制御
Outline of Final Research Achievements

In order to identify genomic polymorphisms on cis-control sequences, which are responsible for strain differences in mouse phenotype, we conducted a genetic study with mouse strains derived from two genetically differentiated subspecies. We quantified gnome-wide expression levels of alleles in liver, testis, and growth cartilage tissues prepared from interspecific F1 cross of the two different subspecies-derived strains and intersubspecific consomic strains. Next, we explored chromatin modification sites by ChIP-seq method and open chromatin sites by ATAC-seq method, and found numerous cis-control sequence candidates, which were correlated with difference in the allele expression level. Furthermore, we identified genomic polymorphisms (SNPs) that cause the allele expression differences in specified genes by reporter expression assays using cultured cells and transgenic mice.

Report

(4 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • Research Products

    (6 results)

All 2017 2016 2015

All Journal Article (2 results) (of which Peer Reviewed: 2 results,  Open Access: 2 results,  Acknowledgement Compliant: 1 results) Presentation (4 results)

  • [Journal Article] SHH signaling directed by two oral epithelium-specific enhancers controls tooth and oral development2017

    • Author(s)
      Sagai Tomoko、Amano Takanori、Maeno Akiteru、Kiyonari Hiroshi、Seo Hyejin、Cho Sung-Won、Shiroishi Toshihiko
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1

    • DOI

      10.1038/s41598-017-12532-y

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Evolution of Shh endoderm enhancers during morphological transition from ventral lungs to dorsal gas bladder2017

    • Author(s)
      Tomoko Sagai, Takanori Amano, Akiteru Maeno, Tetsuaki Kimura, Masatoshi Nakamoto, Yusuke Takehana, Kiyoshi Naruse, Norihiro Okada, Hiroshi Kiyonari & Toshihiko Shiroishi
    • Journal Title

      Nature Communications 8

      Volume: 14300 Issue: 1

    • DOI

      10.1038/ncomms14300

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] X染色体連鎖遺伝子のエンハンサー多型がマウス亜種間の生殖隔離に及ぼす影響2017

    • Author(s)
      岡(木曾)彩子
    • Organizer
      日本遺伝学会第89回大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] エネルギー代謝表現型の亜種間差に関わる遺伝子発現動態の探索2016

    • Author(s)
      高田豊行、近藤伸二、矢坂 拓、阿部貴志、清澤秀孔、鈴木 穣、豊田 敦、藤山秋佐夫、城石俊彦
    • Organizer
      日本遺伝学会 第88回大会
    • Place of Presentation
      静岡県三島市
    • Year and Date
      2016-09-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] マウス亜種系統間の胃形態差に寄与するShh遺伝子のシス多型2016

    • Author(s)
      天野孝紀、城石俊彦
    • Organizer
      日本遺伝学会 第88回大会
    • Place of Presentation
      静岡県三島市
    • Year and Date
      2016-09-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] マウス亜種間表現型多様性を生むアレル発現量差のゲノムワイド解析2015

    • Author(s)
      高田豊行
    • Organizer
      第62回日本実験動物学会総会
    • Place of Presentation
      京都
    • Year and Date
      2015-05-28
    • Related Report
      2015 Annual Research Report

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Published: 2015-04-16   Modified: 2019-03-29  

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