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Search for DNA mutations and methylated regions that regulated the length of the digestive tract that exhibit heritable and seasonal variability

Research Project

Project/Area Number 16K21352
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Biodiversity/Systematics
Genetics/Chromosome dynamics
Research InstitutionOkayama University

Principal Investigator

Katsumura Takafumi  岡山大学, 自然科学研究科, 特別研究員(PD) (10649544)

Research Collaborator Takeshima Hirohiko  
Hashiguchi Yasuyuki  
Project Period (FY) 2016-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2018: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2017: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2016: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Keywords表現型可塑性 / 遺伝的多型 / メダカ / エピジェネティクス / DNAメチル化 / 遺伝的変異 / 集団内多様性 / ゲノムワイド関連解析 / 進化 / 遺伝的多様性
Outline of Final Research Achievements

This study was carried out for the purpose of finding out DNA mutation which regulates the length of digestive tract of medaka and epigenetic change which enables the plasticity by genome wide SNP and methylome analysis, and grasping the beginning of elucidation of molecular and evolutionary mechanisms in which the phenotype diversifies by genetic polymorphism and phenotype plasticity. As the result, a gene region which genetically regulated the length of digestive tract and DNA methylation region concerning the plasticity of digestive tract were found. Molecular evolutionary analysis suggested that the functional loss of the DNA methylation region, which varies seasonally, is important for the fixation of mutations that regulate the length of the digestive tract.

Academic Significance and Societal Importance of the Research Achievements

本研究成果から,消化管の長さを規定する変異が存在すること,季節に応じてDNAメチル化
を介して可塑的に変化させる可能性が高いことが示された.環境に応じた表現型の変化がこれら2つの仕組みによってどのように制御されているのか,本成果はこの問いに答えるための糸口を与えた.本研究成果は,“遺伝的同化”の分子メカニズムおよび,進化プロセスを捉えた可能性がある.今後も本研究を進めていくことで,メダカにおける消化管の長さの多様化が遺伝的同化によるものなのか検証可能で,進化学的にも本研究の意義は高い.

Report

(4 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Research-status Report
  • 2016 Research-status Report
  • Research Products

    (28 results)

All 2019 2018 2017 2016 Other

All Journal Article (9 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 9 results,  Open Access: 8 results) Presentation (16 results) (of which Int'l Joint Research: 2 results,  Invited: 1 results) Book (1 results) Remarks (2 results)

  • [Journal Article] Medaka Population Genome Structure and Demographic History Described via Genotyping-by-Sequencing2018

    • Author(s)
      Katsumura Takafumi、Oda Shoji、Mitani Hiroshi、Oota Hiroki
    • Journal Title

      G3: GENES, GENOMES, GENETICS

      Volume: 9 Issue: 1 Pages: 217-228

    • DOI

      10.1534/g3.118.200779

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Abnormal nuclear morphology is independent of longevity in a zmpste24-deficient fish model of Hutchinson-Gilford progeria syndrome (HGPS)2018

    • Author(s)
      Tonoyama Y, Shinya M, Toyoda A, Kitano T, Oga A, Nishimaki T, Katsumura T, Oota H, Wan MT, Yip BWP, Helen MOL, Chisada S, Deguchi T, Au DWT, Naruse K, Kamei Y, Taniguchi Y
    • Journal Title

      Comp Biochem Physiol C Toxicol Pharmacol

      Volume: 209 Pages: 54-62

    • DOI

      10.1016/j.cbpc.2018.03.006

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Medaka population genome structure and demographic history unveiled via Genotyping-by-Sequencing2017

    • Author(s)
      Katsumura Takafumi、Oda Shoji、Mitani Hiroshi、Oota Hiroki
    • Journal Title

      bioRxiv

      Volume: -

    • DOI

      10.1101/233411

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Experimental evidence reveals the UCP1 genotype changes the oxygen consumption attributed to non-shivering thermogenesis in humans2017

    • Author(s)
      Nishimura Takayuki、Katsumura Takafumi、Motoi Midori、Oota Hiroki、Watanuki Shigeki
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1 Pages: 5570-5570

    • DOI

      10.1038/s41598-017-05766-3

    • NAID

      120006987436

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] An ancestral haplotype of the human PERIOD2 gene associates with reduced sensitivity to light-induced melatonin suppression2017

    • Author(s)
      Akiyama Tokiho、Katsumura Takafumi、Nakagome Shigeki、Lee Sang-il、Joh Keiichiro、Soejima Hidenobu、Fujimoto Kazuma、Kimura Ryosuke、Ishida Hajime、Hanihara Tsunehiko、Yasukouchi Akira、Satta Yoko、Higuchi Shigekazu、Oota Hiroki
    • Journal Title

      PLoS One

      Volume: 12 Issue: 6 Pages: e0178373-e0178373

    • DOI

      10.1371/journal.pone.0178373

    • NAID

      120006891149

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] An approach to elucidate NBS1 function in DNA repair using frequent nonsynonymous polymorphism in wild medaka (Oryzias Latipes) populations2017

    • Author(s)
      K. Igarashi, J. Kobayashi, T. Katsumura, Y. Urushibara, K. Hida, T. Watanabe-Asaka, H. Oota, S. Oda and H. Mitani
    • Journal Title

      PLOS ONE

      Volume: 12(1) Issue: 1 Pages: e0170006-e0170006

    • DOI

      10.1371/journal.pone.0170006

    • NAID

      120005980875

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] A comparative study on the regulatory region of the PERIOD1 gene among diurnal/nocturnal primates.2016

    • Author(s)
      Katsumura T, Fukuyo Y, Kawamura S, Oota H.
    • Journal Title

      Journal of Physiological Anthropology

      Volume: 35(1) Pages: 21-21

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] In vivo 3D analysis of systemic effects after local heavy-ion beam irradiation in an animal model2016

    • Author(s)
      Nagata K, Hashimoto C, Watanabe-Asaka T, Itoh K, Yasuda T, Ohta K, Oonishi H, Igarashi K, Suzuki M, Funayama T, Kobayashi Y, Nishimaki T, Katsumura T, Oota H, Ogawa M, Oga A, Ikemoto K, Itoh H, Kutsuna N, Oda S, and Mitani H
    • Journal Title

      Scientific Reports

      Volume: 6 Issue: 1 Pages: 28691-28691

    • DOI

      10.1038/srep28691

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] ミトコンドリアDNA解析から推定する香川県メダカの集団史/Population history of medaka (Oryzias latipes) in Kagawa Prefecture inferred from mitochondrial DNA analysis2016

    • Author(s)
      山下佳那,勝村啓史,尾田正二,今井正,吉浦康寿,太田博樹
    • Journal Title

      地域自然史と保全

      Volume: 38(1) Pages: 41-50

    • Related Report
      2016 Research-status Report
    • Peer Reviewed
  • [Presentation] メダカ消化管でみられるPlasticity-first evolutionの分子メカニズムとその集団遺伝学的プロセス2019

    • Author(s)
      勝村啓史,佐藤克,山下佳那,尾田正二,覚張隆史,田中翔大, 藤谷和子,西槇俊之,今井正,吉浦康寿,武島弘彦,橋口康之, 三谷啓志,小川元之,竹内秀明,太田博樹
    • Organizer
      第124回日本解剖学会総会全国学術集会
    • Related Report
      2018 Annual Research Report
  • [Presentation] ヒト拡散に関する“冒険遺伝子仮説”のメダカを用いた検証2018

    • Author(s)
      勝村啓史,尾田正二,上岡史享,三谷啓志,太田博樹,竹内秀明
    • Organizer
      第72回日本人類学会大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] メダカ (Oryzias latipes) におけるRosette agentの病理学的解析2018

    • Author(s)
      西槇俊之,勝村啓史,根本典子,尾田正二,小賀厚徳,岡安勲,太田博樹,小川元之
    • Organizer
      平成30年度日本魚病学会秋季大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Loss of epigenetic modification sites drives plasticity-first evolution.2018

    • Author(s)
      Katsumura T., Sato S., Yamashita K., Oda S., Gakuhari T., Tanaka S., Imai T., Yoshiura Y., Takeshima H., Hashiguchi Y., Mitani M., Ogawa M., Takeuchi H., Oota H.
    • Organizer
      24th Japanese Medaka and Zebrafish Meeting
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Molecular mechanisms and evolutionary processes underlying genetic assimilation in the digestive tract of medaka.2018

    • Author(s)
      Katsumura T., Sato S., Yamashita K., Oda S., Gakuhari T., Tanaka S., Imai T., Yoshiura Y., Takeshima H., Hashiguchi Y., Mitani M., Ogawa M., Takeuchi H., Oota H.
    • Organizer
      Society for Molecular Biology & Evolution 2018
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] メダカ消化管長で観察される表現型可塑性とその進化2018

    • Author(s)
      勝村啓史
    • Organizer
      日本進化学会第20回大会シンポジウム「表現型の可塑性~ホモ・サピエンスの環境適応のヒントを探る」
    • Related Report
      2018 Annual Research Report
  • [Presentation] wy変異体メダカを用いた側弯症発症メカニズムの微細形態学的解析2018

    • Author(s)
      西槇俊之,内田健太郎,勝村啓史,山田稔,尾田正二,小賀厚徳,太田博樹,高相晶士,小川元之
    • Organizer
      第123回日本解剖学会総会全国学術集会
    • Related Report
      2017 Research-status Report
  • [Presentation] 奨励研究の申請許可と採択を受けて -メダカ全身組織バーチャルスライドの作製とそのデータベース化-2018

    • Author(s)
      西槇俊之,勝村啓史,太田博樹,小川元之
    • Organizer
      第29回生物学技術研究会
    • Related Report
      2017 Research-status Report
  • [Presentation] 野生メダカにみられる消化管長の季節変動に相関するDNAメチル化変動領域の網羅的な探索2017

    • Author(s)
      勝村啓史,佐藤克,山下佳那,覚張隆史,尾田正二,今井正,吉浦康寿,武島弘彦,竹内秀明,小川元之,太田博樹
    • Organizer
      第122回日本解剖学会総会全国学術集会
    • Place of Presentation
      長崎
    • Year and Date
      2017-03-28
    • Related Report
      2016 Research-status Report
  • [Presentation] 脊椎変異体メダカに対するX線マイクロCTと連続切片法によるアプローチ -詳細な形態解析を目指して-2017

    • Author(s)
      西槇俊之,内田健太郎,木森義隆,勝村啓史,大貫裕子,尾田正二,小賀厚徳,高相晶士,太田博樹,小川元之
    • Organizer
      第122回日本解剖学会総会全国学術集会
    • Place of Presentation
      長崎
    • Year and Date
      2017-03-28
    • Related Report
      2016 Research-status Report
  • [Presentation] 性皮膨張メカニズムの解明に向けて~ニホンザルのメンス前血中ホルモン濃度変動と相関する血球の発現変動遺伝子の検出~2017

    • Author(s)
      勝村啓史,太田博樹
    • Organizer
      第46回ホミニゼーション研究会
    • Place of Presentation
      犬山
    • Year and Date
      2017-03-24
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] メダカ全身組織切片からのバーチャルスライド化 -理科教育教材を目指して-2017

    • Author(s)
      西槇俊之,勝村啓史,小賀厚徳,尾田正二,太田博樹,小川元之
    • Organizer
      第28回生物学技術研究会
    • Place of Presentation
      岡崎
    • Year and Date
      2017-02-16
    • Related Report
      2016 Research-status Report
  • [Presentation] UCP1遺伝子型による寒冷環境下のヒト非震え産熱能変化2017

    • Author(s)
      勝村啓史,西村貴孝,本井碧,綿貫茂喜,太田博樹
    • Organizer
      日本遺伝学会第89回大会
    • Related Report
      2017 Research-status Report
  • [Presentation] 脊椎弯曲 wy メダカを用いた整形外科的疾患解明へのアプローチ2017

    • Author(s)
      西槇俊之,内田健太郎,山田稔,勝村啓史,大貫裕子,尾田正二,小賀厚徳,太田博樹,高相晶士,小川元之
    • Organizer
      第51回日本側彎症学会学術集会
    • Related Report
      2017 Research-status Report
  • [Presentation] 野生メダカをモデルとした消化管長多型をもたらす進化メカニズムの解明2017

    • Author(s)
      勝村啓史,太田博樹
    • Organizer
      第33回日本霊長類学会大会 自由集会
    • Related Report
      2017 Research-status Report
  • [Presentation] 愛知県渥美半島・伊川津貝塚遺跡出土縄文人骨のゲノム解析(予報)2016

    • Author(s)
      覚張隆史,シコラ マーチン・コルネリウセ トーフィン,シュミット ライアン・松前ひろみ,小金渕佳江,勝村啓史,埴原恒彦,小川元之,佐藤丈寛,木村亮介,石田肇,設楽博己,山田康弘,柴田弘紀,田嶋敦,ウイラースレブ エスケ,太田博樹
    • Organizer
      第70回日本人類学会大会
    • Place of Presentation
      新潟
    • Year and Date
      2016-10-08
    • Related Report
      2016 Research-status Report
  • [Book] 性的二型の分子進化学的理解ーメダカの尻鰭と性ステロイドホルモンー、pp156-173. ホルモンから見た生命現象と進化シリーズIII, 成長・成熟・性決定 伊藤道彦、高橋明義(共編)2016

    • Author(s)
      勝村啓史、太田博樹
    • Total Pages
      183
    • Publisher
      裳華房
    • Related Report
      2016 Research-status Report
  • [Remarks] 岡山大学プレスリリース:ゲノム解析から明らかになった日本列島メダカの2つの旅路

    • URL

      https://www.okayama-u.ac.jp/tp/release/release_id582.html

    • Related Report
      2018 Annual Research Report
  • [Remarks] 日本のメダカの故郷はどこだ ゲノム解析で2カ所を解明

    • URL

      https://www.asahi.com/articles/ASLD84HS3LD8PPZB009.html

    • Related Report
      2018 Annual Research Report

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Published: 2016-04-21   Modified: 2020-03-30  

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