Kubo Naoki 久保直樹

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KUBO Naoki 久保直樹

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Researcher Number	50914280
Other IDs
Affiliation (Current)	2026: 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, チームディレクター
Affiliation (based on the past Project Information) *help	2026: 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, チームディレクター 2024: 大阪大学, 微生物病研究所, 特任講師(常勤) 2024: 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 2022 – 2023: 九州大学, 生体防御医学研究所, 特任講師 2022: 九州大学, 生体防御医学研究所, 特任助教
Review Section/Research Field	Principal Investigator Transformative Research Areas, Section (III) / Basic Section 43050:Genome biology-related / Biological Sciences / Basic Section 43010:Molecular biology-related
Keywords	Principal Investigator エピゲノム / DNAメチル化 / ゲノム３次元構造 / エンハンサー・プロモーター相互作用 / 初期胚 / 転写制御 / 生殖細胞 / エピゲノム制御 / 細胞分化 / 精子形成 … More / 初期発生 / ES細胞 / クロマチン構造 / KMT2C/D / H3K4me1 / ヒストン修飾 / 遺伝子発現制御 / エンハンサー / 3Dゲノム Less

Research Projects
(4 results)
Research Products
(57 results)

多生物エピゲノム情報統合による初期胚エンハンサー制御予測モデルの開発Principal Investigator
- Principal Investigator
  
  久保直樹
- Project Period (FY)
  2026 – 2027
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (A)
- Review Section
  
  Transformative Research Areas, Section (III)
- Research Institution
  Institute of Physical and Chemical Research
精子形成過程のDNAメチル化と３Dゲノム変化が織りなす遺伝子制御ネットワークの解明Principal Investigator
- Principal Investigator
  
  久保直樹
- Project Period (FY)
  2024 – 2026
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Review Section
  
  Basic Section 43050:Genome biology-related
- Research Institution
  Institute of Physical and Chemical Research
Exploring CTCF-Mediated 3D Genome Dynamics and Gene Regulation in Early Embryonic DevelopmentPrincipal Investigator
- Principal Investigator
  
  KUBO Naoki
- Project Period (FY)
  2022 – 2024
- Research Category
  
  Grant-in-Aid for Early-Career Scientists
- Review Section
  
  Basic Section 43010:Molecular biology-related
- Research Institution
  Osaka University
  Kyushu University
初期胚の全能性獲得と消失で起こるエンハンサー・プロモーター相互作用のダイナミクスPrincipal Investigator
- Principal Investigator
  
  久保直樹
- Project Period (FY)
  2022 – 2023
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Biological Sciences
- Research Institution
  Kyushu University

All 2024 2023 2022

All Journal Article Presentation Book

[Book] 月間『細胞』、 Vol 56 (3) 2024、ゲノム３次元構造が司る遺伝子制御2024
- Author(s)
  久保直樹
- Total Pages
  2
- Publisher
  ニューサイエンス
- Data Source
  KAKENHI-PROJECT-22K15037
[Book] 月間『細胞』、 Vol 56 (3) 2024、ゲノム３次元構造が司る遺伝子制御2024
- Author(s)
  久保直樹
- Total Pages
  2
- Publisher
  ニューサイエンス
- Data Source
  KAKENHI-PUBLICLY-22H04675
[Book] 月間『細胞』, Vol 56 (3)、2024、ゲノム３次元構造が司る遺伝子制御2024
- Author(s)
  久保直樹
- Total Pages
  2
- Publisher
  ニューサイエンス社
- Data Source
  KAKENHI-PROJECT-22K15037
[Book] Medical Science Digest、Vol 49 (2)、2023、ゲノム３次元構造が司る遺伝子制御2024
- Author(s)
  久保直樹
- Total Pages
  2
- Publisher
  ニューサイエンス社
- Data Source
  KAKENHI-PROJECT-22K15037
[Book] Medical Science Digest、Vol 49 (2)、2023、ゲノム３次元構造が司る遺伝子制御2023
- Author(s)
  久保直樹
- Total Pages
  2
- Publisher
  ニューサイエンス
- Data Source
  KAKENHI-PUBLICLY-22H04675
[Journal Article] Combined and differential roles of ADD domains of DNMT3A and DNMT3L on DNA methylation landscapes in mouse germ cells2024
- Author(s)
  Naoki Kubo、Ryuji Uehara、Shuhei Uemura、Hiroaki Ohishi、Kenjiro Shirane、Hiroyuki Sasaki
- Journal Title
  
  Nature Communications（暫定受理、2024年3月時点）
  
  Volume: -
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PUBLICLY-22H04675
[Journal Article] H3K4me1 facilitates promoter-enhancer interactions and gene activation during embryonic stem cell differentiation2024
- Author(s)
  Kubo Naoki、Chen Poshen B.、Hu Rong、Ye Zhen、Sasaki Hiroyuki、Ren Bing
- Journal Title
  
  Molecular Cell
  
  Volume: - Issue: 9 Pages: 1742-1752.e5
- DOI
  10.1016/j.molcel.2024.02.030
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PUBLICLY-22H04675, KAKENHI-PROJECT-22K15037
[Journal Article] Combined and differential roles of ADD domains of DNMT3A and DNMT3L on DNA methylation landscapes in mouse germ cells2024
- Author(s)
  Kubo Naoki、Uehara Ryuji、Uemura Shuhei、Ohishi Hiroaki、Shirane Kenjiro、Sasaki Hiroyuki
- Journal Title
  
  Nature Communications
  
  Volume: 15 Issue: 1 Pages: 3266-3266
- DOI
  10.1038/s41467-024-47699-2
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-22K15037, KAKENHI-PROJECT-22K15084, KAKENHI-PROJECT-24K01938, KAKENHI-PROJECT-24K09414
[Journal Article] Combined and differential roles of ADD domains of DNMT3A and DNMT3L on DNA methylation landscapes in mouse germ cells2024
- Author(s)
  Naoki Kubo、Ryuji Uehara、Shuhei Uemura、Hiroaki Ohishi、Kenjiro Shirane、Hiroyuki Sasaki
- Journal Title
  
  Nature Communications (暫定受理、2024年3月時点)
  
  Volume: -
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-22K15037
[Journal Article] ゲノム３次元構造が司る遺伝子制御2023
- Author(s)
  久保直樹
- Journal Title
  
  Medical Science Digest
  
  Volume: 49 Pages: 40-41
- Data Source
  KAKENHI-PUBLICLY-22H04675
[Journal Article] The DNMT3A ADD domain is required for efficient de novo DNA methylation and maternal imprinting in mouse oocytes2023
- Author(s)
  Uehara Ryuji、Au Yeung Wan Kin、Toriyama Keisuke、Ohishi Hiroaki、Kubo Naoki、Toh Hidehiro、Suetake Isao、Shirane Kenjiro、Sasaki Hiroyuki
- Journal Title
  
  PLOS Genetics
  
  Volume: 19 Issue: 8 Pages: e1010855-e1010855
- DOI
  10.1371/journal.pgen.1010855
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-22K15037, KAKENHI-PROJECT-22K15084, KAKENHI-PROJECT-22K06174, KAKENHI-PROJECT-18K06095, KAKENHI-PROJECT-22K15125, KAKENHI-PUBLICLY-22H04675
[Journal Article] ゲノム３次元構造が司る遺伝子制御2023
- Author(s)
  久保直樹
- Journal Title
  
  Medical Science Digest
  
  Volume: 49 Pages: 40-41
- Data Source
  KAKENHI-PROJECT-22K15037
[Presentation] エピゲノム・3Dゲノム解析による細胞分化過程の転写制御機構の解明2024
- Author(s)
  久保直樹
- Organizer
  若手支援技術講習会
- Data Source
  KAKENHI-PROJECT-24K09414
[Presentation] The functional role of histone H3K4me1 in chromatin contacts and gene activation during embryonic stem cell differentiation2024
- Author(s)
  久保直樹
- Organizer
  第47回日本分子生物学会年会
- Data Source
  KAKENHI-PROJECT-24K09414
[Presentation] 3Dゲノム解析で解き明かす細胞分化過程の転写制御機構2024
- Author(s)
  久保直樹
- Organizer
  NGS EXPO 2024
- Data Source
  KAKENHI-PROJECT-24K09414
[Presentation] ヒストンH3K4me1が関与するエンハンサー・プロモーター相互作用を介した転写制御機構2024
- Author(s)
  久保直樹
- Organizer
  第4回 Hi-C研究会
- Invited
- Data Source
  KAKENHI-PROJECT-24K09414
[Presentation] KMT2C/D- and KMT2B-dependent H3Kme1 Facilitates Promoter-Enhancer Interactions and Gene Activation During Cell Differentiation2024
- Author(s)
  久保直樹
- Organizer
  理研国際シンポジウム　「The 3D genome」
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K15037
[Presentation] 一細胞3Dゲノム・変異解析による悪性化機序の解明2024
- Author(s)
  久保直樹
- Organizer
  上原財団研究計画発表会
- Data Source
  KAKENHI-PROJECT-22K15037
[Presentation] エピゲノム・3Dゲノム解析で迫る細胞分化過程の転写制御機構2024
- Author(s)
  久保直樹
- Organizer
  第34回モロシヌス研究会
- Data Source
  KAKENHI-PROJECT-22K15037
[Presentation] エピゲノム・3Dゲノム解析で迫る細胞分化過程の転写制御機構2024
- Author(s)
  久保直樹
- Organizer
  第34回モロシヌス研究会
- Data Source
  KAKENHI-PROJECT-24K09414
[Presentation] Fine-tuned gene expression dynamics regulated by non-coding regions2024
- Author(s)
  久保直樹
- Organizer
  Cold Spring Harbor Asia, Frontiers in Single Cell Genomics Cold Spring Harbor Asia, Frontiers in Single Cell Genomics, AWAJI, JAPAN
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K15037
[Presentation] Epigenetic mechanisms of lineage-specific enhancer-promoter contacts and gene expression during cell differentiation2024
- Author(s)
  久保直樹
- Organizer
  RIKEN IMS Chromatin & Transcription symposium 2024
- Data Source
  KAKENHI-PROJECT-24K09414
[Presentation] The functional role of histone H3K4me1 in chromatin contacts and gene activation during embryonic stem cell differentiation2024
- Author(s)
  久保直樹
- Organizer
  第47回日本分子生物学会年会
- Data Source
  KAKENHI-PROJECT-22K15037
[Presentation] 3Dゲノム解析で解き明かす細胞分化過程の転写制御機構2024
- Author(s)
  久保直樹
- Organizer
  NGS EXPO 2024
- Data Source
  KAKENHI-PROJECT-22K15037
[Presentation] ヒストンH3K4me1が関与するエンハンサー・プロモーター相互作用を介した転写制御機構2024
- Author(s)
  久保直樹
- Organizer
  第4回 Hi-C研究会
- Invited
- Data Source
  KAKENHI-PROJECT-22K15037
[Presentation] Fine-tuned Gene Expression Dynamics Regulated by Non-coding Regions2024
- Author(s)
  久保直樹
- Organizer
  Young Scientists Networking Symposium 2024
- Data Source
  KAKENHI-PUBLICLY-22H04675
[Presentation] Epigenetic mechanisms of lineage-specific enhancer-promoter contacts and gene expression during cell differentiation2024
- Author(s)
  久保直樹
- Organizer
  RIKEN IMS Chromatin & Transcription symposium2024
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K15037
[Presentation] Fine-tuned gene expression dynamics regulated by non-coding regions2024
- Author(s)
  久保直樹
- Organizer
  Cold Spring Harbor Asia, Frontiers in Single Cell Genomics Cold Spring Harbor Asia, Frontiers in Single Cell Genomics
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-24K09414
[Presentation] KMT2C/D- and KMT2B-dependent H3Kme1 Facilitates Promoter-Enhancer Interactions and Gene Activation During Cell Differentiation2024
- Author(s)
  久保直樹
- Organizer
  理研国際シンポジウム　「The 3D genome」
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-24K09414
[Presentation] エピゲノム・3Dゲノム解析による細胞分化過程の転写制御機構の解明2024
- Author(s)
  久保直樹
- Organizer
  若手支援技術講習会
- Data Source
  KAKENHI-PROJECT-22K15037
[Presentation] Fine-tuned Gene Expression Dynamics Regulated by Non-coding Regions2024
- Author(s)
  久保直樹
- Organizer
  Young Scientists Networking Symposium 2024
- Data Source
  KAKENHI-PROJECT-22K15037
[Presentation] Dynamics of chromatin organization at distal enhancers during cell differentiation2023
- Author(s)
  久保直樹
- Organizer
  Human Genetics Asia 2023
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K15037
[Presentation] 卵子・精子のDNAメチル化修飾におけるDNMT3AとDNMT3LのADDドメインの協調的役割2023
- Author(s)
  久保直樹
- Organizer
  全能性プログラム第5回公開シンポジウム
- Data Source
  KAKENHI-PROJECT-22K15037
[Presentation] KMT2C/KMT2D (MLL3/MLL4) のヒストンメチル化活性依存的または非依存的なエンハンサーによる、細胞分化過程におけるクロマチン構造変化と遺伝子制御の仕組み2023
- Author(s)
  久保直樹
- Organizer
  第46回　分子生物学会
- Data Source
  KAKENHI-PUBLICLY-22H04675
[Presentation] KMT2ファミリータンパク質によるES細胞の分化過程におけるエンハンサー活性とクロマチン構造変化2023
- Author(s)
  久保直樹
- Organizer
  全能性プログラム第5回公開シンポジウム
- Data Source
  KAKENHI-PROJECT-22K15037
[Presentation] 生殖細胞のDNAメチル化へのDNMT3AとDNMT3LのADDドメインの協調的役割2023
- Author(s)
  久保直樹
- Organizer
  全能性プログラム若手勉強会 2023
- Data Source
  KAKENHI-PROJECT-22K15037
[Presentation] 細胞分化における遠位エンハンサーとクロマチン構造変化の役割2023
- Author(s)
  久保直樹
- Organizer
  第21回ゲノム医科学とバイオインフォマティクスの接点と集学研究
- Invited
- Data Source
  KAKENHI-PROJECT-22K15037
[Presentation] Dynamics of chromatin organization at distal enhancers during cell differentiation2023
- Author(s)
  久保直樹
- Organizer
  Human Genetics Asia 2023
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-22H04675
[Presentation] KMT2C/KMT2D (MLL3/MLL4) histone methyltranferase activity dependent chromatin organization at enhancers during embryonic stem cell differentiation2023
- Author(s)
  久保直樹
- Organizer
  第16回日本エピジェネティクス研究会年会
- Data Source
  KAKENHI-PUBLICLY-22H04675
[Presentation] 細胞分化における遠位エンハンサーとクロマチン構造変化の役割2023
- Author(s)
  久保直樹
- Organizer
  第21回ゲノム医科学とバイオインフォマティクスの接点と集学研究
- Invited
- Data Source
  KAKENHI-PUBLICLY-22H04675
[Presentation] KMT2C/KMT2D (MLL3/MLL4) のヒストンメチル化活性によるES 細胞分化過程におけるクロマチン構造制御と転写制御2023
- Author(s)
  久保直樹
- Organizer
  全能性プログラム若手勉強会 2023
- Data Source
  KAKENHI-PROJECT-22K15037
[Presentation] "KMT2C/KMT2D (MLL3/MLL4) のヒストンメチル化活性によるES 細胞分化過程におけるクロマチン構造制御と転写制御"2023
- Author(s)
  久保直樹
- Organizer
  全能性プログラム若手勉強会 2023
- Data Source
  KAKENHI-PUBLICLY-22H04675
[Presentation] KMT2ファミリータンパク質によるES細胞の分化過程におけるエンハンサー活性とクロマチン構造変化2023
- Author(s)
  久保直樹
- Organizer
  全能性プログラム第5回公開シンポジウム
- Data Source
  KAKENHI-PUBLICLY-22H04675
[Presentation] "生殖細胞のDNAメチル化へのDNMT3AとDNMT3LのADDドメインの協調的役割"2023
- Author(s)
  久保直樹
- Organizer
  全能性プログラム若手勉強会 2023
- Data Source
  KAKENHI-PUBLICLY-22H04675
[Presentation] KMT2C/KMT2D (MLL3/MLL4) のヒストンメチル化活性依存的または非依存的なエンハンサーによる、細胞分化過程におけるクロマチン構造変化と遺伝子制御の仕組み2023
- Author(s)
  久保直樹
- Organizer
  第46回　分子生物学会
- Data Source
  KAKENHI-PROJECT-22K15037
[Presentation] KMT2C/KMT2D (MLL3/MLL4) histone methyltranferase activity dependent chromatin organization at enhancers during embryonic stem cell differentiation2023
- Author(s)
  久保直樹
- Organizer
  第16回日本エピジェネティクス研究会年会
- Data Source
  KAKENHI-PROJECT-22K15037
[Presentation] 卵子・精子のDNAメチル化修飾におけるDNMT3AとDNMT3LのADDドメインの協調的役割2023
- Author(s)
  久保直樹
- Organizer
  全能性プログラム第5回公開シンポジウム
- Data Source
  KAKENHI-PUBLICLY-22H04675
[Presentation] KMT2C/KMT2D (MLL3/MLL4) histone methyltranferase activity dependent chromatin organization at enhancers during embryonic stem cell differentiation2022
- Author(s)
  久保直樹
- Organizer
  The International Symposium on Totipotency and Germ Cell Development
- Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-22H04675
[Presentation] KMT2C/KMT2D (MLL3/MLL4) histone methyltranferase activity dependent chromatin organization at enhancers during embryonic stem cell differentiation2022
- Author(s)
  久保直樹
- Organizer
  The International Symposium on Totipotency and Germ Cell Development
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K15037
[Presentation] KMT2C/KMT2D (MLL3/MLL4) histone methyltranferase activity dependent chromatin organization at enhancers during embryonic stem cell differentiation2022
- Author(s)
  久保直樹
- Organizer
  Cold Spring Habor Laboratory Meetings（epigenetics & chromatin)
- Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-22H04675
[Presentation] 細胞分化におけるエンハンサー・プロモーター相互作用のダイナミクス2022
- Author(s)
  久保直樹
- Organizer
  第67回日本人類遺伝学会
- Invited
- Data Source
  KAKENHI-PROJECT-22K15037
[Presentation] Dynamics of enhancer-promoter contacts during cell differentiation2022
- Author(s)
  久保直樹
- Organizer
  第95回日本生化学会大会
- Invited
- Data Source
  KAKENHI-PUBLICLY-22H04675
[Presentation] Dynamics of CTCF-dependent and -independent enhancer-promoter contacts during cell differentiation2022
- Author(s)
  久保直樹
- Organizer
  The 29th Federation of Asian and Oceanian Biochemists and Molecular Biologists Conference & the 2022 Chinese Society of Biochemistry and Molecular Biology Conference
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K15037
[Presentation] 細胞分化におけるエンハンサー・プロモーター相互作用のダイナミクス2022
- Author(s)
  久保直樹
- Organizer
  第67回日本人類遺伝学会
- Invited
- Data Source
  KAKENHI-PUBLICLY-22H04675
[Presentation] Dynamics of CTCF-dependent and -independent enhancer-promoter contacts during cell differentiation2022
- Author(s)
  久保直樹
- Organizer
  The 29th Federation of Asian and Oceanian Biochemists and Molecular Biologists Conference & the 2022 Chinese Society of Biochemistry and Molecular Biology Conference
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-22H04675
[Presentation] KMT2C/KMT2D (MLL3/MLL4) histone methyltranferase activity dependent chromatin organization at enhancers during embryonic stem cell differentiation2022
- Author(s)
  久保直樹
- Organizer
  Cold Spring Habor Laboratory Meetings（epigenetics & chromatin)
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K15037
[Presentation] Dynamics of enhancer-promoter contacts during cell differentiation2022
- Author(s)
  久保直樹
- Organizer
  第95回日本生化学会大会
- Invited
- Data Source
  KAKENHI-PROJECT-22K15037

Kubo Naoki 久保 直樹

KUBO Naoki 久保 直樹

Research Projects

Research Products

多生物エピゲノム情報統合による初期胚エンハンサー制御予測モデルの開発Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

精子形成過程のDNAメチル化と３Dゲノム変化が織りなす遺伝子制御ネットワークの解明Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Exploring CTCF-Mediated 3D Genome Dynamics and Gene Regulation in Early Embryonic DevelopmentPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

初期胚の全能性獲得と消失で起こるエンハンサー・プロモーター相互作用のダイナミクスPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

[Book] 月間『細胞』、 Vol 56 (3) 2024、ゲノム３次元構造が司る遺伝子制御2024

Author(s)

Total Pages

Publisher

Data Source

[Book] 月間『細胞』、 Vol 56 (3) 2024、ゲノム３次元構造が司る遺伝子制御2024

Author(s)

Total Pages

Publisher

Data Source

[Book] 月間『細胞』, Vol 56 (3)、2024、ゲノム３次元構造が司る遺伝子制御2024

Author(s)

Total Pages

Publisher

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[Book] Medical Science Digest、Vol 49 (2)、2023、ゲノム３次元構造が司る遺伝子制御2024

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[Book] Medical Science Digest、Vol 49 (2)、2023、ゲノム３次元構造が司る遺伝子制御2023

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[Journal Article] Combined and differential roles of ADD domains of DNMT3A and DNMT3L on DNA methylation landscapes in mouse germ cells2024

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[Journal Article] H3K4me1 facilitates promoter-enhancer interactions and gene activation during embryonic stem cell differentiation2024

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[Journal Article] Combined and differential roles of ADD domains of DNMT3A and DNMT3L on DNA methylation landscapes in mouse germ cells2024

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[Journal Article] Combined and differential roles of ADD domains of DNMT3A and DNMT3L on DNA methylation landscapes in mouse germ cells2024

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[Journal Article] ゲノム３次元構造が司る遺伝子制御2023

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[Journal Article] The DNMT3A ADD domain is required for efficient de novo DNA methylation and maternal imprinting in mouse oocytes2023

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Kubo Naoki 久保直樹

KUBO Naoki 久保直樹

[Presentation] エピゲノム・3Dゲノム解析で迫る細胞分化過程の転写制御機構2024

[Presentation] エピゲノム・3Dゲノム解析で迫る細胞分化過程の転写制御機構2024