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Comparative imprintome analysis between mammalian species reveals functional diversity of genomic imprinting

Research Project

Project/Area Number 23K21282
Project/Area Number (Other) 21H02382 (2021-2023)
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeMulti-year Fund (2024)
Single-year Grants (2021-2023)
Section一般
Review Section Basic Section 42030:Animal life science-related
Research InstitutionNara Medical University

Principal Investigator

Kobayashi Hisato  奈良県立医科大学, 医学部, 准教授 (70632727)

Project Period (FY) 2024-04-01 – 2025-03-31
Project Status Completed (Fiscal Year 2024)
Budget Amount *help
¥17,160,000 (Direct Cost: ¥13,200,000、Indirect Cost: ¥3,960,000)
Fiscal Year 2024: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2023: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2022: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2021: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Keywordsゲノム刷り込み機構 / DNAメチル化 / ヒストン修飾 / レトロトランスポゾン / 胎盤 / マウス / ラット / 種間比較 / ゲノム刷り込み / エピゲノム / 胚発生 / ウサギ
Outline of Research at the Start

ラット・ウサギ・霊長動物の包括的な生殖エピゲノムおよびゲノム刷り込み機構の解明を目指す。各動物種のインプリントーム(刷り込みを受ける遺伝子座・領域の全容)比較により、種特異的なインプリント遺伝子の同定とそれらの生物学的意義を明らかにし、種多様性をもたらすゲノム的要因の特定を目標とする

Outline of Final Research Achievements

In this study, we conducted genome-wide, allele-specific analysis of genomic imprinting (the "imprintome") in rodents, using F1 hybrid embryos derived from crosses between rat and mouse strains. By analyzing both epiblast and extraembryonic tissues, we identified not only conserved imprinted genes shared between rats and mice, but also discovered eight novel paternally expressed genes specific to rats. These rat-specific genes were found to be regulated by oocyte-derived H3K27me3-dependent noncanonical imprinting, a mechanism distinct from classical DNA methylation-based imprinting. Our findings highlight both evolutionary conservation and divergence in the mammalian imprintome and suggest that species-specific differences in oocyte epigenomes may drive the emergence of lineage-specific imprinting.

Academic Significance and Societal Importance of the Research Achievements

本研究は、哺乳類の刷り込み遺伝子の保存性と多様性を、ゲノムワイドなアレル特異的解析および種間ゲノム・エピゲノム比較により明らかにしました。卵子由来H3K27me3に依存する非正準型インプリンティングが、種特異的刷り込みの獲得に関与する可能性を示し、マウスで報告されてきたこの制御機構が、ヒトでは確認されておらず、インプリンティング機構の種差の存在が示唆されました。これにより、発生異常や刷り込み疾患の種特異性の理解が進み、生殖補助医療や再生医療における安全性評価にも寄与することが期待されます。

Report

(5 results)
  • 2024 Annual Research Report   Final Research Report ( PDF )
  • 2023 Annual Research Report
  • 2022 Annual Research Report
  • 2021 Annual Research Report
  • Research Products

    (23 results)

All 2024 2023 2022 2021 Other

All Int'l Joint Research (6 results) Journal Article (12 results) (of which Int'l Joint Research: 6 results,  Peer Reviewed: 12 results,  Open Access: 8 results) Presentation (5 results)

  • [Int'l Joint Research] ブリティッシュコロンビア大学(カナダ)

    • Related Report
      2024 Annual Research Report
  • [Int'l Joint Research] ブリティッシュコロンビア大学(カナダ)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] ブリティッシュコロンビア大学(カナダ)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] パリ・シテ大学(フランス)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] ブリティッシュコロンビア大学(カナダ)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] パリ大学(フランス)

    • Related Report
      2021 Annual Research Report
  • [Journal Article] Chromosome-specific barcode system with centromeric repeat in cultivated soybean and wild progenitor2024

    • Author(s)
      Tek Ahmet L、Nagaki Kiyotaka、Yildiz Akkamis Humeyra、Tanaka Keisuke、Kobayashi Hisato
    • Journal Title

      Life Science Alliance

      Volume: 7 Issue: 12 Pages: e202402802-e202402802

    • DOI

      10.26508/lsa.202402802

    • Related Report
      2024 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Rat post-implantation epiblast-derived pluripotent stem cells produce functional germ cells2023

    • Author(s)
      Iwatsuki Kenyu、Oikawa Mami、Kobayashi Hisato、Penfold Christopher A.、Sanbo Makoto、Yamamoto Takuya、Hochi Shinichi、Kurimoto Kazuki、Hirabayashi Masumi、Kobayashi Toshihiro
    • Journal Title

      Cell Reports Methods

      Volume: 3 Issue: 8 Pages: 100542-100542

    • DOI

      10.1016/j.crmeth.2023.100542

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] ADAD2 functions in spermiogenesis and piRNA biogenesis in mice2023

    • Author(s)
      Lu Yonggang、Nagamori Ippei、Kobayashi Hisato、Kojima‐Kita Kanako、Shirane Kenjiro、Chang Hsin‐Yi、Nishimura Toru、Koyano Takayuki、Yu Zhifeng、Castaneda Julio M.、Matsuyama Makoto、Kuramochi‐Miyagawa Satomi、Matzuk Martin M.、Ikawa Masahito
    • Journal Title

      Andrology

      Volume: 11 Issue: 4 Pages: 698-709

    • DOI

      10.1111/andr.13400

    • Related Report
      2023 Annual Research Report 2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Conservation and divergence of canonical and non-canonical imprinting in murids2023

    • Author(s)
      Richard Albert Julien、Kobayashi Toshihiro、Inoue Azusa、Monteagudo-S?nchez Ana、Kumamoto Soichiro、Takashima Tomoya、Miura Asuka、Oikawa Mami、Miura Fumihito、Takada Shuji、Hirabayashi Masumi、Korthauer Keegan、Kurimoto Kazuki、Greenberg Maxim V. C.、Lorincz Matthew、Kobayashi Hisato
    • Journal Title

      Genome Biology

      Volume: 24 Issue: 1 Pages: 48-48

    • DOI

      10.1186/s13059-023-02869-1

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Upregulated Ribosomal Pathway Impairs Follicle Development in a Polycystic Ovary Syndrome Mouse Model: Differential Gene Expression Analysis of Oocytes2023

    • Author(s)
      Nakanishi N, Osuka S, Kono T, Kobayashi H, Ikeda S, Bayasula B, Sonehara R, Murakami M, Yoshita S, Miyake N, Muraoka A, Kasahara Y, Murase T, Nakamura T, Goto M, Iwase A, Kajiyama H.
    • Journal Title

      Reprod Sci

      Volume: 30 Issue: 4 Pages: 1306-1315

    • DOI

      10.1007/s43032-022-01095-7

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Repeated translocation of a supergene underlying rapid sex chromosome turnover in <i>Takifugu</i> pufferfish2022

    • Author(s)
      Kabir Ahammad、Ieda Risa、Hosoya Sho、Fujikawa Daigaku、Atsumi Kazufumi、Tajima Shota、Nozawa Aoi、Koyama Takashi、Hirase Shotaro、Nakamura Osamu、Kadota Mitsutaka、Nishimura Osamu、Kuraku Shigehiro、Nakamura Yasukazu、Kobayashi Hisato、Toyoda Atsushi、Tasumi Satoshi、Kikuchi Kiyoshi
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 119 Issue: 23 Pages: 1901-1909

    • DOI

      10.1073/pnas.2121469119

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Functional primordial germ cell?like cells from pluripotent stem cells in rats2022

    • Author(s)
      Oikawa Mami、Kobayashi Hisato、Sanbo Makoto、Mizuno Naoaki、Iwatsuki Kenyu、Takashima Tomoya、Yamauchi Keiko、Yoshida Fumika、Yamamoto Takuya、Shinohara Takashi、Nakauchi Hiromitsu、Kurimoto Kazuki、Hirabayashi Masumi、Kobayashi Toshihiro
    • Journal Title

      Science

      Volume: 376 Issue: 6589 Pages: 176-179

    • DOI

      10.1126/science.abl4412

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Characterization of Frond and Flower Development and Identification of FT and FD Genes From Duckweed Lemna aequinoctialis Nd2021

    • Author(s)
      Yoshida Akiko、Taoka Ken-ichiro、Hosaka Aoi、Tanaka Keisuke、Kobayashi Hisato、Muranaka Tomoaki、Toyooka Kiminori、Oyama Tokitaka、Tsuji Hiroyuki
    • Journal Title

      Frontiers in Plant Science

      Volume: 12 Pages: 697206-697206

    • DOI

      10.3389/fpls.2021.697206

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Deciphering two rounds of cell lineage segregations during bovine preimplantation development2021

    • Author(s)
      Akizawa Hiroki, Saito Shun, Kohri Nanami, Furukawa Eri, Hayashi Yoshihiro, Bai Hanako, Nagano Masashi, Yanagawa Yojiro, Tsukahara Hayato, Takahashi Masashi, Kagawa Shinjiro, Kawahara‐Miki Ryouka, Kobayashi Hisato、Kono Tomohiro、Kawahara Manabu
    • Journal Title

      The FASEB Journal

      Volume: 35 Issue: 10

    • DOI

      10.1096/fj.202002762rr

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Canonical and Non-canonical Genomic Imprinting in Rodents2021

    • Author(s)
      Kobayashi Hisato
    • Journal Title

      Frontiers in Cell and Developmental Biology

      Volume: 9 Pages: 713878-713878

    • DOI

      10.3389/fcell.2021.713878

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Dorso-ventral heterogeneity in tracheal basal stem cells.2021

    • Author(s)
      Tadokoro T, Tanaka K, Osakabe S, Kato M, Kobayashi H, Hogan BLM, Taniguchi H.
    • Journal Title

      Biology Open

      Volume: 10 Issue: 9

    • DOI

      10.1242/bio.058676

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Loop-mediated isothermal amplification (LAMP) and machine learning application for early pregnancy detection using bovine vaginal mucosal membrane2021

    • Author(s)
      Kunii Hiroki, Kubo Tomoaki, Asaoka Natsuki, Balboula Ahmed Z, Hamaguchi Yu, Shimasaki Tomoya, Bai Hanako, Kawahara Manabu, Kobayashi Hisato, Ogawa Hidehiko, Takahashi Masashi
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 569 Pages: 179-186

    • DOI

      10.1016/j.bbrc.2021.07.015

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Presentation] 種特異的インプリンティング遺伝子の確立における内在性レトロトランスポゾンの役割2024

    • Author(s)
      小林久人
    • Organizer
      第47回日本分子生物学会大会
    • Related Report
      2024 Annual Research Report
  • [Presentation] ZDBF2遺伝子刷り込みの起源を探るLTR介在型転写物の種間比較2023

    • Author(s)
      小林久人
    • Organizer
      第46回日本分子生物学会大会
    • Related Report
      2023 Annual Research Report
  • [Presentation] ZDBF2遺伝子刷り込みの起源を探るLTR介在型転写物の種間比較2023

    • Author(s)
      小林久人
    • Organizer
      第116回日本繁殖生物学会大会
    • Related Report
      2023 Annual Research Report
  • [Presentation] マウス・ラット間におけるカノニカル・非カノニカル型刷り込み機構の保存性と多様性2022

    • Author(s)
      小林久人
    • Organizer
      第45回 日本分子生物学会
    • Related Report
      2022 Annual Research Report
  • [Presentation] ラットのゲノムワイドなインプリントーム解析2022

    • Author(s)
      小林久人
    • Organizer
      第115回 日本繁殖生物学会大会
    • Related Report
      2022 Annual Research Report

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Published: 2021-04-28   Modified: 2026-01-16  

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