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Genome-wide analysis of transcriptional cascades using a statistical model

Research Project

Project/Area Number 16K00387
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Life / Health / Medical informatics
Research InstitutionWaseda University (2021-2022)
Osaka University (2016-2020)

Principal Investigator

Osato Naoki  早稲田大学, 理工学術院総合研究所(理工学研究所), 主任研究員 (50509536)

Project Period (FY) 2016-04-01 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2019: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2018: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2017: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2016: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Keywords遺伝子発現 / 転写制御 / 転写因子 / エンハンサー / クロマチン相互作用 / インシュレータ / エピゲノム / 深層学習 / ヒストン修飾・オープンクロマチン / CTCF / オープンクロマチン / エンハンサープロモーター相互作用 / 機能エンリッチメント / 遺伝子 / 発現制御 / ゲノム / 情報工学
Outline of Final Research Achievements

We used computational methods to predict transcription factors (DNA binding proteins) and DNA binding sequences involved in transcriptional regulation and control of gene expression. We developed an index to evaluate the criteria for selecting a gene whose expression is controlled by a transcription factor that binds at a distance from the gene (a transcriptional target gene). Using deep learning, we developed a method to predict transcription factors involved in the partitioning (insulator) function of the interaction between transcription factors and genes that bind at a distance from the gene. Unexpectedly, we predicted many transcription factors with the directional bias of their DNA binding sites, which would affect gene expression levels. The well-known transcription factor CTCF shows the directional bias of its DNA binding sites. The insulator function would be associated with phase separation.

Academic Significance and Societal Importance of the Research Achievements

インシュレータに関わる転写因子が多く予測され、既知の転写因子CTCFと同様に、DNA結合配列の向きの偏りがあり、遺伝子発現量に影響する傾向が示された。CTCFは相分離と関わることが論文で報告された。ループ形成で二量体形成によるDNA結合配列の向きの偏りが生じ、インシュレータ機能は相分離と関わると考えられる。情報解析により、このような特徴を発見でき、分子生物学実験では困難と思われる。またインシュレータを考慮した遺伝子発現量の予測を行った。分子的なメカニズムに基づき、より正確な予測法の開発や、新規の制御関係やメカニズムの発見に貢献する。疾患の原因や治療標的となる遺伝子発現制御の予測に貢献する。

Report

(8 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Research-status Report
  • 2020 Research-status Report
  • 2019 Research-status Report
  • 2018 Research-status Report
  • 2017 Research-status Report
  • 2016 Research-status Report
  • Research Products

    (55 results)

All 2023 2022 2021 2020 2019 2018 2017 2016 Other

All Journal Article (7 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 5 results,  Open Access: 7 results,  Acknowledgement Compliant: 1 results) Presentation (44 results) (of which Int'l Joint Research: 15 results,  Invited: 2 results) Book (3 results) Remarks (1 results)

  • [Journal Article] Long non-coding RNA 2310069B03Rik functions as a suppressor of Ucp1 expression under prolonged cold exposure in murine beige adipocytes2020

    • Author(s)
      Mari Iwase, Shoko Sakai, Shigeto Seno, Yu-Sheng Yeh, Tony Kuo, Haruya Takahashi, Wataru Nomura, Huei-Fen Jheng, Paul Horton, Naoki Osato, Hideo Matsuda, Kazuo Inoue, Teruo Kawada, Tsuyoshi Goto
    • Journal Title

      Bioscience, biotechnology, and biochemistry

      Volume: 84 Issue: 2 Pages: 305-313

    • DOI

      10.1080/09168451.2019.1677451

    • Related Report
      2020 Research-status Report 2019 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells2019

    • Author(s)
      Nakato R, Wada Y, Nakaki R, Nagae G, Katou Y, Tsutsumi S, Nakajima N, Fukuhara H, Iguchi A, Kohro T, Kanki Y, Saito Y, Kobayashi M, Izumi-Taguchi A, Osato N, Tatsuno K, Kamio A, Hayashi-Takanaka Y, Wada H, Ohta S, Aikawa M, Nakajima H, Nakamura M, McGee RC, Heppner KW, Kawakatsu T, Genno M, Yanase H, Kume H, et al.
    • Journal Title

      Epigenetics & Chromatin

      Volume: 12 Issue: 1 Pages: 77-77

    • DOI

      10.1186/s13072-019-0319-0

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Common genetic variants associated with Parkinson’s disease display widespread signature of epigenetic plasticity2019

    • Author(s)
      Sharma Amit、Osato Naoki、Liu Hongde、Asthana Shailendra、Dakal Tikam Chand、Ambrosini Giovanna、Bucher Philipp、Schmitt Ina、W?llner Ullrich
    • Journal Title

      Scientific Reports

      Volume: 9 Issue: 1

    • DOI

      10.1038/s41598-019-54865-w

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Improvement of detection performance of fusion genes from RNA-seq data by clustering short reads2019

    • Author(s)
      Sota Yoshiaki、Seno Shigeto、Shigeta Hironori、Osato Naoki、Shimoda Masafumi、Noguchi Shinzaburo、Matsuda Hideo
    • Journal Title

      Journal of Bioinformatics and Computational Biology

      Volume: 17 Issue: 03 Pages: 1940008-1940008

    • DOI

      10.1142/s0219720019400080

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Discovery of biased orientation of human DNA motif sequences affecting enhancer-promoter interactions and transcription of genes2018

    • Author(s)
      Naoki Osato
    • Journal Title

      bioRxiv

      Volume: -

    • DOI

      10.1101/290825

    • Related Report
      2020 Research-status Report 2019 Research-status Report 2018 Research-status Report 2017 Research-status Report
    • Open Access
  • [Journal Article] Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes2018

    • Author(s)
      Naoki Osato
    • Journal Title

      BMC Genomics

      Volume: 29(Supple 1) Issue: S1

    • DOI

      10.1186/s12864-017-4339-5

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes2016

    • Author(s)
      Naoki Osato
    • Journal Title

      bioRxiv

      Volume: -

    • DOI

      10.1101/085654

    • Related Report
      2016 Research-status Report
    • Open Access / Acknowledgement Compliant
  • [Presentation] Systematic discovery of regulatory motifs associated with an insulator function for human enhancer-promoter interactions2023

    • Author(s)
      Naoki Osato, Michiaki Hamada
    • Organizer
      ERATO International Symposium on Chromatin Architecture: Structure and Function
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Systematic discovery of regulatory motifs associated with the insulator function of human enhancer-promoter interactions2022

    • Author(s)
      Naoki Osato, Michiaki Hamada
    • Organizer
      Intelligent Systems for Molecular Biology (ISMB)
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] ヒト遺伝子発現制御のインシュレータ機能に関わる転写因子の予測と発見2022

    • Author(s)
      大里直樹, 浜田道昭
    • Organizer
      第45回日本分子生物学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] ヒト遺伝子発現制御のインシュレータ機能に関わる転写因子の予測と発見2022

    • Author(s)
      大里直樹, 浜田道昭
    • Organizer
      日本遺伝学会第94回大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] ヒトのクロマチン相互作用のインシュレータ機能と関わる転写因子の網羅的な解析と発見2022

    • Author(s)
      大里直樹, 浜田道昭
    • Organizer
      第11回生命医薬情報学連合大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 深層学習を用いた、ヒトのエンハンサー・遺伝子相互作用に影響する転写因子の解析2021

    • Author(s)
      大里直樹・浜田道昭
    • Organizer
      JST CREST 「データ駆動・AI駆動を中心としたデジタルトランスフォーメーションによる生命科学研究の革新[バイオDX]」 キックオフシンポジウム「バイオDXの最前線」
    • Related Report
      2021 Research-status Report
  • [Presentation] ヒトのエンハンサーと遺伝子相互作用や転写制御に影響する、方向性のある転写因子DNA結合配列の解析法の開発2021

    • Author(s)
      大里直樹・浜田道昭
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Research-status Report
  • [Presentation] ヒトのエンハンサーと遺伝子相互作用や転写制御に影響する、方向性のある転写因子DNA結合配列の解析法の開発2021

    • Author(s)
      大里直樹・浜田道昭
    • Organizer
      第68回バイオ情報学研究会
    • Related Report
      2021 Research-status Report
  • [Presentation] 深層学習の予測結果に寄与する因子の大規模な解析に伴うノイズの影響の低減2021

    • Author(s)
      大里直樹・浜田道昭
    • Organizer
      第24回情報論的学習理論ワークショップ
    • Related Report
      2021 Research-status Report
  • [Presentation] ヒトのエンハンサーと遺伝子相互作用や転写制御に影響する、方向性のある転写因子DNA結合配列の解析法の開発2021

    • Author(s)
      大里直樹・浜田道昭
    • Organizer
      第67回バイオ情報学研究会
    • Related Report
      2021 Research-status Report
  • [Presentation] ヒトのエンハンサーと遺伝子相互作用や転写制御に影響する、方向性のある転写因子DNA結合配列の発見2021

    • Author(s)
      大里直樹・浜田道昭
    • Organizer
      第10回生命医薬情報学連合大会
    • Related Report
      2021 Research-status Report
  • [Presentation] Systematic discovery of directional chromatin-associated regulatory motifs affecting human gene transcription2021

    • Author(s)
      Naoki Osato
    • Organizer
      Intelligent Systems for Molecular Biology (ISMB)
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] Systematic discovery of directional chromatin-associated regulatory motifs affecting human gene transcription2021

    • Author(s)
      Naoki Osato
    • Organizer
      CSHL meeting, Mechanisms of Eukaryotic Transcription
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] ヒト転写因子の標的遺伝子の特徴とエンハンサー・遺伝子相互作用に影響する転写因子の発見2020

    • Author(s)
      大里直樹
    • Organizer
      第43回日本分子生物学会年会
    • Related Report
      2020 Research-status Report
  • [Presentation] 脂肪細胞におけるSTAT3を介したUCP1発現制御機構の解明2020

    • Author(s)
      疋田菜光・岩瀬麻里・川原崎聡子・酒井章子・坂本智弥・大里直樹・瀬尾茂人・野村亘・高橋春弥・松田秀雄・井上和生・河田照雄・後藤剛
    • Organizer
      日本栄養・食料学会近畿支部大会
    • Related Report
      2020 Research-status Report
  • [Presentation] ヒトのオープンクロマチン領域に存在する転写因子DNA結合配列の網羅的な解析2020

    • Author(s)
      大里直樹
    • Organizer
      日本遺伝学会第92回大会
    • Related Report
      2020 Research-status Report
  • [Presentation] ヒト転写因子の標的遺伝子の特徴とエンハンサー・遺伝子相互作用に関わる転写因子解析2020

    • Author(s)
      大里直樹
    • Organizer
      第9回生命医薬情報学連合大会
    • Related Report
      2020 Research-status Report
  • [Presentation] ヒト転写因子の標的遺伝子の特徴とインシュレータ機能に関わるDNA配列の発見2020

    • Author(s)
      大里直樹
    • Organizer
      遺伝学会春季分科会
    • Related Report
      2020 Research-status Report
  • [Presentation] Discovery of directional chromatin-associated regulatory motifs affecting human gene transcription2020

    • Author(s)
      Naoki Osato
    • Organizer
      RECOMB/ISCB conference on regulatory & systems genomics with dream challenges 2020.
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research
  • [Presentation] Discovery of biased orientations of regulatory motifs affecting transcription of human genes and including known insulators2020

    • Author(s)
      Naoki Osato
    • Organizer
      Conference on Intelligent Systems for Molecular Biology (ISMB)
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research
  • [Presentation] Characteristics of human putative transcriptional target genes and discovery of biased orientation of DNA motifs affecting transcription of genes.2019

    • Author(s)
      Naoki Osasto
    • Organizer
      Intelligent Systems for Molecular Biology (ISMB)
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] A method for inferring gene regulatory networks based on pseudo time-series gene expression profiles from single-cell RNA-seq data.2019

    • Author(s)
      Kaito Uemura, Naoki Osato, Hironori Shigeta, Shigeto Seno, Hideo Matsuda
    • Organizer
      Intelligent Systems for Molecular Biology (ISMB)
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Characteristic of human putative transcriptional target genes and discovery of biased orientation of DNA moitfs affecting transcription of genes.2019

    • Author(s)
      Naoki Osato
    • Organizer
      The 13th International Workshop on Advanced Genomics
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Characteristic of human putative transcriptional target genes and discovery of biased orientations of DNA motifs affecting transcription of genes2019

    • Author(s)
      大里直樹
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2019 Research-status Report
  • [Presentation] ヒト転写因子の標的遺伝子の特徴とエンハンサー・遺伝子相互作用に関わる転写因子解析2019

    • Author(s)
      大里直樹
    • Organizer
      第8回生命医薬情報学連合大会年会
    • Related Report
      2019 Research-status Report
  • [Presentation] ヒト転写因子の標的遺伝子の特徴とエンハンサー・遺伝子相互作用に関わる転写因子解析2019

    • Author(s)
      大里直樹
    • Organizer
      日本遺伝学会第91回大会
    • Related Report
      2019 Research-status Report
  • [Presentation] ヒト転写因子の標的遺伝子の特徴とエンハンサー・遺伝子相互作用に関わる転写因子解析2019

    • Author(s)
      大里直樹
    • Organizer
      遺伝学会春季分科会
    • Related Report
      2018 Research-status Report
  • [Presentation] ヒトのエンハンサーと遺伝子相互作用や転写制御に影響する、方向性のある転写因子DNA結合配列の発見2018

    • Author(s)
      大里直樹
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Research-status Report
  • [Presentation] ヒトのエンハンサーと遺伝子相互作用や転写制御に影響する、方向性のある転写因子DNA結合配列の発見2018

    • Author(s)
      大里直樹
    • Organizer
      日本遺伝学会第90回大会
    • Related Report
      2018 Research-status Report
  • [Presentation] ヒトのエンハンサーと遺伝子相互作用や転写制御に影響する、方向性のある転写因子DNA結合配列の発見2018

    • Author(s)
      大里直樹
    • Organizer
      第7回生命医薬情報学連合大会年会
    • Related Report
      2018 Research-status Report
  • [Presentation] Discovery of biased orientation of DNA motif sequences affecting enhancer-promoter interactions and transcription of genes2018

    • Author(s)
      Naoki Osato
    • Organizer
      RECOMB/ISCB conference on regulatory & systems genomics with dream challenges
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] Discovery of biased orientation of DNA motif sequences affecting enhancer-promoter interactions and transcription of genes2018

    • Author(s)
      Naoki Osato
    • Organizer
      Conference on Intelligent Systems for Molecular Biology (ISMB)
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] Discovery of biased orientation of DNA motif sequences affecting human gene expression for prediction of enhancer-promoter interactions2018

    • Author(s)
      Naoki Osato
    • Organizer
      Human Genome Meeting
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Chromatin accessibility dynamics reveal decrease of DNA motif sequences of transcription factors during macrophage aging2018

    • Author(s)
      Naoki Osato
    • Organizer
      International Meeting on RECQ Helicases and Related Diseases
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes2017

    • Author(s)
      Naoki Osato
    • Organizer
      The 12th International Workshop on Advanced Genomics
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Methylation diversity among human vascular endothelial cells2017

    • Author(s)
      Genta Nagae, Youichiro Wada, Ryuichiro Nakato, Takayoshi Umeda, Yuki Katou, Shuichi Tsutsumi, Naoki Osato, Yasuharu Kanki, Mika Kobayashi, Akashi Izumi-Taguchi, Yutaka Saito, Toutai Mitsuyma, Hiroshi Kimura, Katsuhiko Shirahige, Hiroyuki Aburatani
    • Organizer
      The 12 th International Workshop on Advanced Genomics. Japan
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] ヒト転写標的遺伝子の機能エンリッチメントの特徴とクロマチン相互作用に関わるタンパク質のDNA結合配列解析への応用2017

    • Author(s)
      大里直樹
    • Organizer
      第40回日本分子生物学会年会
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] Ucp1発現を制御するnon-coding RNAの探索と機能解析2017

    • Author(s)
      岩瀬麻里、酒井章子、高橋春弥、野村亘、Jheng Huie-Fen、荒武、瀬尾茂人、大里直樹、松田秀雄、河田照雄、後藤剛
    • Organizer
      農芸化学学会年会
    • Related Report
      2017 Research-status Report
  • [Presentation] UCP1発現制御に関するmiRNAの探索及び機能解析2017

    • Author(s)
      酒井章子、大久保麻里、高橋春弥、野村亘、Jheng Huie-Fen、荒武、瀬尾茂人、大里直樹、松田秀雄、河田照雄、後藤剛
    • Organizer
      第56回日本栄養・食糧学会年会
    • Related Report
      2017 Research-status Report
  • [Presentation] Characteristic of functional enrichments of putative transcriptional target genes and its application2017

    • Author(s)
      Naoki Osato
    • Organizer
      第52回バイオ情報学研究会
    • Related Report
      2017 Research-status Report
  • [Presentation] Characteristic of functional enrichments of human putative transcriptional target genes2017

    • Author(s)
      Naoki Osato
    • Organizer
      第6回生命医薬情報学連合大会年会
    • Related Report
      2017 Research-status Report
  • [Presentation] 1細胞RNA-seqの特性を考慮した遺伝子発現差解析手法の検討2017

    • Author(s)
      大里直樹、繁田浩功、瀬尾茂人、松田秀雄
    • Organizer
      NGS現場の会第五回研究会
    • Related Report
      2017 Research-status Report
  • [Presentation] ヒト転写標的遺伝子予測と転写標的遺伝子機能の偏り2016

    • Author(s)
      大里直樹
    • Organizer
      第39回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2016-12-01
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] Prediction of transcriptional target genes and its association with their functional enrichments2016

    • Author(s)
      Naoki Osato
    • Organizer
      第5回生命医薬情報学連合大会
    • Place of Presentation
      東京国際交流会館プラザ平成
    • Year and Date
      2016-09-29
    • Related Report
      2016 Research-status Report
  • [Book] 月刊細胞11月号 Topics 機械学習による遺伝子転写制御に関わる因子の探索2022

    • Author(s)
      大里直樹, 浜田道昭
    • Total Pages
      3
    • Publisher
      ニューサイエンス社
    • Related Report
      2022 Annual Research Report
  • [Book] 月刊細胞12月号 Topics データ解析と機械学習による転写制御因子の探索2021

    • Author(s)
      大里直樹, 浜田道昭
    • Total Pages
      5
    • Publisher
      ニューサイエンス社
    • Related Report
      2021 Research-status Report
  • [Book] 月刊細胞7月号 Topics データ解析による転写制御因子の探索2021

    • Author(s)
      大里直樹
    • Total Pages
      4
    • Publisher
      ニューサイエンス社
    • Related Report
      2021 Research-status Report
  • [Remarks] researchmap 大里直樹

    • URL

      https://researchmap.jp/naokiosato

    • Related Report
      2019 Research-status Report 2018 Research-status Report

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Published: 2016-04-21   Modified: 2025-01-30  

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