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Detection of monoallelically expressed genes under epigenetic control and quest for intraindividual genetic diversities

Research Project

Project/Area Number 16K14644
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Genome biology
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

Abe Kuniya  国立研究開発法人理化学研究所, バイオリソース研究センター, チームリーダー (40240915)

Project Period (FY) 2016-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2017: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2016: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Keywordsモノアレル発現遺伝子 / X染色体不活性化 / 刷り込み遺伝子 / 遺伝的多様性 / 多能性幹細胞 / モノアレル遺伝子発現 / 遺伝的モザイシズム / エピジェネティクス / 幹細胞 / エピブラスト幹細胞 / シングルセル解析
Outline of Final Research Achievements

Monoallelically expressed genes (MEGs), both random and imprinted MEGs, could influence genetic constitution of individuals. However, nature of these MEGs and their regulations are not fully understood. In this study, we analyzed expression dynamics of MEGs during differentiation of embryonic stem cells by single cell RNA-Seq. We could analyze and delineate expression dynamics of X-linked random MEGs during progression of X chromosome inactivation process for the first time. We unexpectedly revealed that there are significant number of MEGs expressed in genetic-origin-dependent manner.

Academic Significance and Societal Importance of the Research Achievements

本研究から得られたシングルセルRNA-Seqデータおよびこの度考案したアレル特異的発現解析パイプラインを用いることで、今回明らかにしたX染色体不活性化におけるモノアレル発現ダイナミクスに係わる知見のみならず、刷り込み型や常染色体上のランダムモノアレル発現遺伝子に関する研究にも貢献できると考えられ、本研究で得られた手法やデータは高い学術的価値を持つものと思われる。また、今回、初めて明らかになったgenetic-origin-dependent モノアレル発現遺伝子も、遺伝的多様性の創出に影響すると考えられ今後さらに追究されるべきと考えられる。

Report

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

    (43 results)

All 2019 2018 2017 2016

All Journal Article (18 results) (of which Int'l Joint Research: 8 results,  Peer Reviewed: 18 results,  Open Access: 12 results,  Acknowledgement Compliant: 1 results) Presentation (20 results) (of which Int'l Joint Research: 8 results,  Invited: 3 results) Book (2 results) Patent(Industrial Property Rights) (3 results) (of which Overseas: 2 results)

  • [Journal Article] Xist/Tsix expression dynamics during mouse peri-implantation development revealed by whole-mount 3D RNA-FISH2019

    • Author(s)
      Shiura H, Abe K.
    • Journal Title

      Sci Rep.

      Volume: 9 Issue: 1 Pages: 3637-3637

    • DOI

      10.1038/s41598-019-38807-0

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Human induced pluripotent stem cell region detection in bright-field microscopy images using convolutional neural networks2019

    • Author(s)
      Chang Y-H, Abe K, Yokota H, Sudo K, Nakamura Y, Tsai M-D
    • Journal Title

      Biomedical Engineering: applications, basis and communications

      Volume: 31 Issue: 02 Pages: 1950009-1950009

    • DOI

      10.4015/s1016237219500091

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] WNT inhibition and increased FGF signaling promotes derivation of less heterogeneous primed human embryonic stem cells, compatible with differentiation2019

    • Author(s)
      Taelman J, Popovic M, Bialecka M, Tilleman L, Warrier S, Van Der Jeught M, Menten B, Deforce D, Sutter P DE, Nieuwerburgh V, Abe K, Heindryckx B, Chuva de Sausa Lopes SM
    • Journal Title

      Stem Cells and Development

      Volume: in press Issue: 9 Pages: 579-592

    • DOI

      10.1089/scd.2018.0199

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Cell Type-Specific Survey of Epigenetic Modifications by Tandem Chromatin Immunoprecipitation Sequencing2018

    • Author(s)
      Mito Mari、Kadota Mitsutaka、Tanaka Kaori、Furuta Yasuhide、Abe Kuniya、Iwasaki Shintaro、Nakagawa Shinichi
    • Journal Title

      Scientific Reports

      Volume: 8 Issue: 1 Pages: 1143-1143

    • DOI

      10.1038/s41598-018-19494-9

    • NAID

      120006398777

    • Related Report
      2018 Annual Research Report 2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] A simplified and efficient protocol for derivation and maintenance of high-quality mouse primed pluripotent stem cells using Wnt inhibition2018

    • Author(s)
      Kondo M, Sugimoto M, Abe K.
    • Journal Title

      Curr Protoc Stem Cell Biol.

      Volume: 46 Issue: 1

    • DOI

      10.1002/cpsc.60

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Female mice lacking Ftx lncRNA exhibit impaired X-chromosome inactivation and a microphthalmia-like phenotype.2018

    • Author(s)
      Hosoi Y, Soma M, Shiura H, Sado T, Hasuwa H, Abe K, Kohda T, Ishino F, Kobayashi S
    • Journal Title

      Nat Commun

      Volume: 9(1) Issue: 1 Pages: 4618-4618

    • DOI

      10.1038/s41467-018-06327-6

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] RNA-FISH and Immunofluorescence of Mouse Preimplantation and Postimplantation Embryos2018

    • Author(s)
      Shiura H, Sakata, Abe K, Sado T.
    • Journal Title

      Methods Mol Biol.

      Volume: 1861 Pages: 161-176

    • DOI

      10.1007/978-1-4939-8766-5_13

    • ISBN
      9781493987658, 9781493987665
    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A simplified and efficient protocol for derivation and maintenance of high-quality mouse primed pluripotent stem cells using Wnt inhibition.2018

    • Author(s)
      Kondo M, Sugimoto M, Abe K
    • Journal Title

      Current Protocol Protocols in Stem Cell Biology

      Volume: in print

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Locus coeruleus input to hippocampal CA3 drives single-trial learning of a novel context2017

    • Author(s)
      Wagatsuma Akiko、Okuyama Teruhiro、Sun Chen、Smith Lillian M.、Abe Kuniya、Tonegawa Susumu
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 115 Issue: 2 Pages: 2-2

    • DOI

      10.1073/pnas.1714082115

    • Related Report
      2018 Annual Research Report 2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Genome-wide DNA methylation sequencing revealed that miR-663a is a novel epimutation candidate in CIMP- high endometrial cancer.2017

    • Author(s)
      Megumi Yanokura, Kouji Banno, Masataka Adachi, Daisuke Aoki, Kuniya Abe
    • Journal Title

      International Journal of Oncology

      Volume: - Issue: 6 Pages: 1934-1946

    • DOI

      10.3892/ijo.2017.3966

    • Related Report
      2017 Research-status Report 2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] SCPortalen: human and mouse single-cell centric database2017

    • Author(s)
      Abugessaisa Imad、Noguchi Shuhei、Bottcher Michael、Hasegawa Akira、Kouno Tsukasa、Kato Sachi、Tada Yuhki、Ura Hiroki、Abe Kuniya、Shin Jay W、Plessy Charles、Carninci Piero、Kasukawa Takeya
    • Journal Title

      Nucleic Acids Research

      Volume: 46 Issue: D1 Pages: D781-D787

    • DOI

      10.1093/nar/gkx949

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Automated Detection and Tracking of Cell Clusters in Time-Lapse Fluorescence Microscopy Images2017

    • Author(s)
      Yuan-Hsiang Chang, Hideo Yokota, Kuniya Abe, Chia-Tong, TangMing-Dar Tasi
    • Journal Title

      Journal of Medical and Biological Engineering

      Volume: 37,1 Issue: 1 Pages: 18-25

    • DOI

      10.1007/s40846-016-0216-y

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Conserved role of Ovo in germline development in mouse and Drosophila.2017

    • Author(s)
      Hayashi, M., Shinozuka, Y., Shigenobu, S., Sato, M., Sugimoto, M., Ito, S., Abe, K., Kobayashi, S.
    • Journal Title

      Scientific Report

      Volume: 6 Issue: 1 Pages: 40056-40056

    • DOI

      10.1038/srep40056

    • NAID

      120007135169

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] CRISPR/Cas9-mediated genome editing in wild-derived mice: generation of tamed wild-derived strains by mutation of the a (nonagouti) gene2017

    • Author(s)
      Michiko Hirose, Ayumi Hasegawa, Keiji Mochida, Shogo Matoba, Yuki Hatanaka, Kimiko Inoue, Tatsuhiko Goto, Hideki Kaneda, Ikuko Yamada, Tamio Furuse, Kuniya Abe, Yoshihisa Uenoyama, Hiroko Tsukamura, Shigeharu Wakana, Arata Honda, and Atsuo Ogura
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1 Pages: 42476-42476

    • DOI

      10.1038/srep42476

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A simplified and efficient protocol for derivation and maintenance of high-quality mouse primed pluripotent stem cells using Wnt inhibition.2017

    • Author(s)
      Kondo M, Sugimoto M, Abe K
    • Journal Title

      Current Protocol Protocols in Stem Cell Biology

      Volume: -

    • Related Report
      2016 Research-status Report
    • Peer Reviewed
  • [Journal Article] Cellular dynamics of mouse trophoblast stem cells: Identification of a persistent stem cell type.2016

    • Author(s)
      Motomura K, Oikawa M, Hirose M, Honda A, Togayachi S, Miyoshi H, Ohinata Y, Sugimoto M, Abe K, Inoue K, Ogura A.
    • Journal Title

      Biology of Reproduction

      Volume: 94 Issue: 6 Pages: 122-122

    • DOI

      10.1095/biolreprod.115.137125

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Detection and Localization of Mouse Induced Pluripotent Stem Cell Formation using Time-Lapse Fluorescence Microscopy Images.2016

    • Author(s)
      Yuan-Hsiang Chang, Hideo Yokota, Kuniya Abe, Jung Hsien Liu, Ming-Dar Tsai
    • Journal Title

      Accepted as a contributed paper for the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society

      Volume: - Pages: 3914-3917

    • DOI

      10.1109/embc.2016.7591583

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Fluorescence Microscopy Image Processing and Visualization for Analyzing Cell Kinematics, Proliferation and Attachment in Mouse Embryonic Stem Cell Culture.2016

    • Author(s)
      Yuan-Hsiang Chang, Hideo Yokota, Kuniya Abe, Chih-Cheng Li, Ming-Dar Tsai
    • Journal Title

      Accepted as a contributed paper for 2016 IEEE 16th International Conference on Bioinformatics and Bioengineering (BIBE)

      Volume: - Pages: 222-229

    • DOI

      10.1109/bibe.2016.44

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Presentation] Molecular characterizations of developing male germ cells and GS cell lines by single cell transcriptome analysis2019

    • Author(s)
      Kuniya Abe
    • Organizer
      The 4th URICAS Symposium
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Ectopic expression of Ctcfl/Boris in multipotent mouse embryoid body affects the embryonic differentiation program in vitro2019

    • Author(s)
      Maisarah Ab Samad, Shinnosuke Suzuki, Kuniya Abe, Daruliza Kernain Mohd Azman, Shaharum Shamsuddin
    • Organizer
      International Congress on ageing
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] シングルセルRNA-Seq解析によるナイーブ型からプライム型への多能性幹細胞の変換過程における転写動態の解明2018

    • Author(s)
      田夛祐喜、浦大樹、Michael Boettcher、鈴木伸之介、Piero Carninci、阿部訓也
    • Organizer
      日本遺伝学会第90回大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] シングルセルRNA-Seqを用いたオスES細胞プライム化過程における遺伝子発現動態解析2018

    • Author(s)
      田夛祐喜、阿部訓也
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] シングルセル技術を用いた多能性細胞・生殖細胞の分化遷移過程とそのエピゲノム制御の解析2018

    • Author(s)
      阿部訓也
    • Organizer
      文部科学省科学研究費補助金・新学術領域研究「生殖細胞のエピゲノムダイナミクスとその制御」成果取りまとめ公開シンポジウム
    • Related Report
      2018 Annual Research Report
  • [Presentation] Technology development for gene function analysis by CRISPR/Cas9 system2017

    • Author(s)
      Shinnosuke Suzuki and Kuniya Abe
    • Organizer
      4th World Congress of Reproductive Biology
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Comprehensive single-cell analyses on developmental transitions in mouse pluripotent stem cells.2017

    • Author(s)
      Bottcher M, Ura H, Tada Y, Suzuki S, Carninci P, Abe K
    • Organizer
      Single Cell Genomics 2017
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Study on Epigenetic Barrier Formation in Mammalian Stem Cells2017

    • Author(s)
      阿部訓也
    • Organizer
      RIKEN・MARC・KMPC Mouse Workshop
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] 2つの異なる多能性幹細胞状態を分けるエピジェネティックバリアー形成における新規DNAメチル化の役割2017

    • Author(s)
      浦大樹、阿部訓也
    • Organizer
      第11回日本エピジェネティクス研究会年会
    • Related Report
      2017 Research-status Report
  • [Presentation] 2つの多能性状態であるナイーブ状態とプライム状態を分けるエピジェネティックバリアーにおけるDNAメチル化の役割2017

    • Author(s)
      浦大樹、鈴木伸之介、田夛祐喜、阿部訓也
    • Organizer
      日本遺伝学会第89回大会
    • Related Report
      2017 Research-status Report
  • [Presentation] 生殖系列細胞の発生サイクルにおける減数分裂プログラムの獲得メカニズム2017

    • Author(s)
      細川美穂子、刀谷在美、林瑛理、望月綾子、沼田興治、阿部訓也、末盛博文、中辻憲夫、中馬新一郎
    • Organizer
      日本遺伝学会第89回大会
    • Related Report
      2017 Research-status Report
  • [Presentation] ナイーブ型とプライム型多能性幹細胞をわけるエピジェネティックバリアー形成におけるDNAメチル化の役割2017

    • Author(s)
      浦大樹、阿部訓也
    • Organizer
      第40回日本分子生物学会年会
    • Related Report
      2017 Research-status Report
  • [Presentation] シングルセルRNA-Seqを用いたナイーブ型 -プライム型多能性幹細胞変換過程におけるモノアレル遺伝子発現解析2017

    • Author(s)
      田夛祐喜、阿部訓也
    • Organizer
      第40回日本分子生物学会年会
    • Related Report
      2017 Research-status Report
  • [Presentation] Xist/Tsix expression dynamics during mouse peri-implantation development revealed by whole-mout 3D RNA-FISH2016

    • Author(s)
      Hirosuke Shiura and Kunia Abe
    • Organizer
      X-Chromosome inactivation: a tribute to Mary Lyon
    • Place of Presentation
      London and Oxford ( UK)
    • Year and Date
      2016-10-03
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] Robust induction of primed pluripotency in mammals: Wnt inhibition is critical for derivation and maintenance of mouse epiblast stem cells.2016

    • Author(s)
      Abe K, Kondo M, Sugimoto M
    • Organizer
      INASCON (International Scientific Conference) 2016
    • Place of Presentation
      Kelantan ( Malaysia)
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Studies on mouse peri-implantation development using developmental mutant and stem cells.2016

    • Author(s)
      阿部 訓也
    • Organizer
      熊本大学リエゾンラボ研究会/HIGOプログラム最先端研究セミナー
    • Place of Presentation
      熊本大学(熊本県)
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] Robust induction of primed pluripotency in mammals: Wnt inhibition is critical for derivation and maintenance of mouse epiblast stem cells.2016

    • Author(s)
      Kuniya Abe
    • Organizer
      Tsukuba Global Science Week 2016
    • Place of Presentation
      つくば国際会議場(茨城県)
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Visualization tools for epigenomics.2016

    • Author(s)
      阿部 訓也
    • Organizer
      The 5th BRC-MARC Mouse Resource Workshop
    • Place of Presentation
      理化学研究所バイオリソースセンター(茨城県)
    • Related Report
      2016 Research-status Report
  • [Presentation] Comprehensive study on naive-to-primed stem cell conversion process by integration of single-cell transcriptomics and epigenetic analysis.2016

    • Author(s)
      Hiroki Ura, Michael Bottcher, Shinnosuke Suzuki, Piero Carninci, Kuniya Abe
    • Organizer
      QBiC Symposium 2016 「Decording Organisms by Quantitative Cell Profiling」
    • Place of Presentation
      理化学研究所生命システム研究センター(大阪府)
    • Related Report
      2016 Research-status Report
  • [Presentation] Germline Stem (GS)細胞における複数遺伝子の高効率機能解析技術の開発2016

    • Author(s)
      鈴木伸之介、阿部訓也
    • Organizer
      第109回日本繁殖生物学会大会
    • Place of Presentation
      麻布大学(神奈川県)
    • Related Report
      2016 Research-status Report
  • [Book] 遺伝単 遺伝学用語集 対訳付き 日本遺伝学会監修・編「生物の科学 遺伝」別冊2017

    • Author(s)
      日本遺伝学会監修・編
    • Total Pages
      371
    • Publisher
      エヌ・ティー・エス社
    • Related Report
      2017 Research-status Report
  • [Book] 遺伝単 遺伝学用語集 対訳付き 日本遺伝学会監修・編「生物の科学 遺伝」別冊2017

    • Author(s)
      阿部 訓也
    • Publisher
      NTS社
    • Related Report
      2016 Research-status Report
  • [Patent(Industrial Property Rights)] Method and apparatus for detecting cell reprogramming2018

    • Inventor(s)
      張元翔, 横田秀夫, 阿部訓也, 蔡明達
    • Industrial Property Rights Holder
      国立研究開発法人理化学研究所, 中原大學
    • Industrial Property Rights Type
      特許
    • Filing Date
      2018
    • Related Report
      2018 Annual Research Report
    • Overseas
  • [Patent(Industrial Property Rights)] iPS細胞の白色光観察+機械学習判定2017

    • Inventor(s)
      張元翔, 横田秀夫, 阿部訓也, 蔡明達
    • Industrial Property Rights Holder
      張元翔, 横田秀夫, 阿部訓也, 蔡明達
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2017-026477
    • Filing Date
      2017
    • Related Report
      2017 Research-status Report
  • [Patent(Industrial Property Rights)] METHOD AND APPARATUS FOR DETECTING CELL REPROGRAMMING2017

    • Inventor(s)
      張 元翔, 横田 秀夫, 阿部 訓也, 蔡 明達
    • Industrial Property Rights Holder
      国立研究開発法人理化学研究所, 中原大學
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2017-026477
    • Filing Date
      2017-02-15
    • Related Report
      2016 Research-status Report
    • Overseas

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

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