Updated on 2025/06/17

Information

 

写真a

 
NOJIMA TAKAYUKI
 
Organization
Medical Institute of Bioregulation Research Center for Systems Immunology Associate Professor
Medical Institute of Bioregulation Research Center for Systems Immunology(Concurrent)
Title
Associate Professor
Contact information
メールアドレス
Tel
0926426295
Profile
生体防御医学研究所で腫瘍防御学分野を担当しています。できたばかりのRNA(新生RNA)を解析し、ゲノム作動原理を解き明かすことを目標としています。がんなどの病気のクロマチン環境での転写やRNAプロセシング制御を調べ、革新的な治療法開発に貢献します。
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Research Areas

  • Life Science / Genome biology

  • Life Science / Molecular biology

Degree

  • Ph.D. ( 2006.4 Tokyo Medical and Dental University )

Research History

  • Kyushu University Medical Institute of Bioregulation Research Center for Systems Immunology  Associate Professor 

    2021.2 - Present

  • Tokyo Medical and Dental University  Specially Appointed Assistant Professor 

Education

  • Tokyo Medical and Dental University   生命情報科学教育部  

    2003.4 - 2006.3

  • Kitasato University   薬学研究科  

    2001.4 - 2003.3

  • Kitasato University   薬学部   薬学科

    1997.4 - 2001.3

Research Interests・Research Keywords

  • Research theme: Cell cycle controled by transcription-replication conflict

    Keyword: Transcription, DNA replication, cell cycle

    Research period: 2021.4 - Present

  • Research theme: 1. Mechanism of transcription termination 2. Mechanism of premature transcription termination and function of its long noncoding RNA 3. Regulation of RNA splicing 4. Noncoding genome transcription under cellular senescence and cancer chromatin

    Keyword: RNA splicing

    Research period: 2021.2 - Present

  • Research theme: Mechanism of premature transcription termination and function of its long noncoding RNA

    Keyword: RNA polymerase II, splicing, transcription termination, cancer

    Research period: 2021.2 - Present

  • Research theme: Noncoding genome transcription under cellular senescence and cancer chromatin

    Keyword: RNA polymerase II, noncoding RNAs, cancer, cellular senescence

    Research period: 2021.2 - Present

  • Research theme: Mechanism of transcription termination

    Keyword: RNA polymerase II, splicing, transcription termination, cancer, cellular senescence

    Research period: 2021.2 - Present

Awards

  • ISPF International Collaborating Award UK-JAPAN

    2024.3   The Royal Society   Dissecting transcription termination addiction in cancer

    Michael Tellier and Takayuki Nojima

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    Country:United Kingdom

  • 令和5年度科学技術分野の文部科学大臣表彰科学技術賞(科学技術振興部門)

    2023.4   文部科学省   超高解像度新生RNA解析法の開発とゲノム転写制御の研究

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    『超高解像度新生RNA 解析法の開発とゲノム転写制御の研究』

  • ベストポスター賞

    2018.1   RNA society UK  

  • Exceptional Achievement Award

    2014.9   University of Oxford  

  • 海外リサーチアワード

    2013.9   かなえ医薬振興財団  

  • 海外留学リサーチフェローシップ

    2010.9   上原記念生命科学財団  

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Papers

  • NELF coordinates Pol II transcription termination and DNA replication initiation International journal

    #Chihiro Nakayama, @Yasukazu Daigaku, @Yuki Aoi, Qi Fang, @Hiroshi Kimura, @Ali Shilatifard, @Michael Tellier, Takayuki Nojima

    BioRxiv [Preprint]   2024.1

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: https://doi.org/10.1101/2024.01.31.578294

    Other Link: https://www.biorxiv.org/content/10.1101/2024.01.31.578294v1

  • Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics Invited Reviewed International journal

    Nojima, Takayuki; @Proudfoot, Nick J.

    NATURE REVIEWS MOLECULAR CELL BIOLOGY   23 ( 6 )   389 - 406   2022.6   ISSN:1471-0072 eISSN:1471-0080

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    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:Nature Reviews Molecular Cell Biology  

    Mammalian genomes express two principal gene categories through RNA polymerase II-mediated transcription: protein-coding transcription units and non-coding RNA transcription units. Non-coding RNAs are further divided into relatively abundant structural RNAs, such as small nuclear RNAs, and into a myriad of long non-coding RNAs (lncRNAs) of often low abundance and low stability. Although at least some lncRNA synthesis may reflect transcriptional ‘noise’, recent studies define unique functions for either specific lncRNAs or for the process of lncRNA synthesis. Notably, the transcription, processing and metabolism of lncRNAs are regulated differently from protein-coding genes. In this Review, we provide insight into the regulation of lncRNA transcription and processing gleaned from the application of recently devised nascent transcriptomics technology. We first compare and contrast different methodologies for studying nascent transcription. We then discuss the molecular mechanisms regulating lncRNA transcription, especially transcription initiation and termination, which emphasize fundamental differences in their expression as compared with protein-coding genes. When perturbed, lncRNA misregulation leads to genomic stress such as transcription–replication conflict and R-loop-mediated DNA damage. We discuss many unresolved but important questions about the synthesis and potential functions of lncRNAs.

    DOI: 10.1038/s41580-021-00447-6

    Web of Science

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  • POINT technology illuminates the processing of polymerase-associated intact nascent transcripts Reviewed International journal

    @Rui Sousa-Luís, @Gwendal Dujardin, @Inna Zukher, @Hiroshi Kimura, @Carika Weldon, @Maria Carmo-Fonseca, @Nick J.Proudfoot, and Takayuki Nojima

    Molecular Cell   2021.5

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    Language:English   Publishing type:Research paper (scientific journal)  

    Mammalian chromatin is the site of both RNA polymerase II (Pol II) transcription and coupled RNA processing. However, molecular details of such co-transcriptional mechanisms remain obscure, partly because of technical limitations in purifying authentic nascent transcripts. We present a new approach to characterize nascent RNA, called polymerase intact nascent transcript (POINT) technology. This three-pronged methodology maps nascent RNA 5' ends (POINT-5), establishes the kinetics of co-transcriptional splicing patterns (POINT-nano), and profiles whole transcription units (POINT-seq). In particular, we show by depletion of the nuclear exonuclease Xrn2 that this activity acts selectively on cleaved 5' P-RNA at polyadenylation sites. Furthermore, POINT-nano reveals that co-transcriptional splicing either occurs immediately after splice site transcription or is delayed until Pol II transcribes downstream sequences. Finally, we connect RNA cleavage and splicing with either premature or full-length transcript termination. We anticipate that POINT technology will afford full dissection of the complexity of co-transcriptional RNA processing.

    DOI: https://doi.org/10.1101/2020.11.09.374108

    Other Link: https://www.sciencedirect.com/science/article/pii/S1097276521001441?via%3Dihub

  • Deregulated expression of lncRNA through loss of SPT6 induces R-loop, DNA replication stress and cellular senescence Reviewed International coauthorship

    Nojima T, Tellier M, Foxwell J, Rebeiro de Almeida C, Tan-Wong SM, Dhir S, Dhir A, Murphy S, and Proudfoot NJ.

    Molecular Cell   2018.12

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    Authorship:Lead author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.molcel.2018.10.011

  • RNA polymerase II phosphorylated on CTD serine 5 interacts with the spliceosome during co-transcriptional splicing Reviewed International coauthorship

    Nojima T, Rebelo K, Gomes T, Fialho Grosso AR, Proudfoot NJ, and Carmo-Fonseca M.

    Molecular Cell   2018.10

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.molcel.2018.09.004

  • Distinctive patterns of transcription and RNA processing for human lincRNA Reviewed International coauthorship

    Schlackow M, Nojima T, Gomes T, Dhir A, Carmo-Fonseca M, and Proudfoot NJ.

    Molecular Cell   2017.1

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    Authorship:Lead author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.molcel.2016.11.029

  • Mammalian NET-seq reveals genome-wide nascent transcription coupled to RNA processing. International coauthorship

    Nojima T, Gomes T, Fialho Grosso AR, Kimura H, Dye MJ, Dhir S, Carmo-Fonseca M, and Proudfoot NJ

    Cell   2015.4

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.cell.2015.03.027

  • Single-molecule multimodal timing of in vivo mRNA synthesis International coauthorship

    A.J. Sethi, Marco Guarnacci, Muhammad Bilal, Karthik Subramanian Krishnan, Azusa Hayashi, Madhu Kanchi, Takayuki Nojima, Thomas Preiss, Eduardo Eyras, and Rippei Hayashi

    BioRxiv   2025.4

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: https://doi.org/10.1101/2025.04.27.650906

  • DNA-directed termination of mammalian RNA polymerase II.

    Davidson L, Rouvière JO, Sousa-Luís R, Nojima T, Proudfoot NJ, Jensen TH, West S

    Genes & development   38 ( 21-24 )   998 - 1019   2024.11   ISSN:0890-9369 eISSN:1549-5477

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    Language:English   Publisher:Genes and Development  

    The best-studied mechanism of eukaryotic RNA polymerase II (RNAPII) transcriptional termination involves polyadenylation site-directed cleavage of the nascent RNA. The RNAPII-associated cleavage product is then degraded by XRN2, dislodging RNAPII from the DNA template. In contrast, prokaryotic RNAP and eukaryotic RNAPIII often terminate directly at T-tracts in the coding DNA strand. Here, we demonstrate a similar and omnipresent capability for mammalian RNAPII. Importantly, this termination mechanism does not require upstream RNA cleavage. Accordingly, T-tract-dependent termination can take place when XRN2 cannot be engaged. We show that T-tracts can terminate snRNA transcription independently of RNA cleavage by the Integrator complex. Importantly, we found genome-wide termination at T-tracts in promoter-proximal regions but not within protein-coding gene bodies. XRN2-dependent termination dominates downstream from protein-coding genes, but the T-tract process is sometimes used. Overall, we demonstrate global DNA-directed attrition of RNAPII transcription, suggesting that RNAPs retain the potential to terminate over T-rich sequences throughout evolution.

    DOI: 10.1101/gad.351978.124

    Web of Science

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  • Pro-inflammatory polarization and colorectal cancer modulate alternative and intronic polyadenylation in primary human macrophages

    Wilton, J; de Mendonca, FL; Pereira-Castro, I; Tellier, M; Nojima, T; Costa, AM; Freitas, J; Murphy, S; Oliveira, MJ; Proudfoot, NJ; Moreira, A

    FRONTIERS IN IMMUNOLOGY   14   2023.6   ISSN:1664-3224

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    Publisher:Frontiers in Immunology  

    Introduction: Macrophages are essential cells of the immune system that alter their inflammatory profile depending on their microenvironment. Alternative polyadenylation in the 3’UTR (3’UTR-APA) and intronic polyadenylation (IPA) are mechanisms that modulate gene expression, particularly in cancer and activated immune cells. Yet, how polarization and colorectal cancer (CRC) cells affect 3’UTR-APA and IPA in primary human macrophages was unclear. Methods: In this study, we isolated primary human monocytes from healthy donors, differentiated and polarized them into a pro-inflammatory state and performed indirect co-cultures with CRC cells. ChrRNA-Seq and 3’RNA-Seq was performed to quantify gene expression and characterize new 3’UTR-APA and IPA mRNA isoforms. Results: Our results show that polarization of human macrophages from naïve to a pro-inflammatory state causes a marked increase of proximal polyA site selection in the 3’UTR and IPA events in genes relevant to macrophage functions. Additionally, we found a negative correlation between differential gene expression and IPA during pro-inflammatory polarization of primary human macrophages. As macrophages are abundant immune cells in the CRC microenvironment that either promote or abrogate cancer progression, we investigated how indirect exposure to CRC cells affects macrophage gene expression and 3’UTR-APA and IPA events. Co-culture with CRC cells alters the inflammatory phenotype of macrophages, increases the expression of pro-tumoral genes and induces 3’UTR-APA alterations. Notably, some of these gene expression differences were also found in tumor-associated macrophages of CRC patients, indicating that they are physiologically relevant. Upon macrophage pro-inflammatory polarization, SRSF12 is the pre-mRNA processing gene that is most upregulated. After SRSF12 knockdown in M1 macrophages there is a global downregulation of gene expression, in particular in genes involved in gene expression regulation and in immune responses. Discussion: Our results reveal new 3’UTR-APA and IPA mRNA isoforms produced during pro-inflammatory polarization of primary human macrophages and CRC co-culture that may be used in the future as diagnostic or therapeutic tools. Furthermore, our results highlight a function for SRSF12 in pro-inflammatory macrophages, key cells in the tumor response.

    DOI: 10.3389/fimmu.2023.1182525

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  • PTBP1-activated co-transcriptional splicing controls epigenetic status of pluripotent stem cells Invited Reviewed International journal

    @Iannone Camilla, @Kainov Yaroslav; @Zhuravskaya Anna, @Hamid Fursham, Nojima, Takayuki, @Makeyev Eugene V

    MOLECULAR CELL   83 ( 2 )   203 - +   2023.1   ISSN:1097-2765 eISSN:1097-4164

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    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:Molecular Cell  

    Many spliceosomal introns are excised from nascent transcripts emerging from RNA polymerase II (RNA Pol II). The extent of cell-type-specific regulation and possible functions of such co-transcriptional events remain poorly understood. We examined the role of the RNA-binding protein PTBP1 in this process using an acute depletion approach followed by the analysis of chromatin- and RNA Pol II-associated transcripts. We show that PTBP1 activates the co-transcriptional excision of hundreds of introns, a surprising effect given that this protein is known to promote intron retention. Importantly, some co-transcriptionally activated introns fail to complete their splicing without PTBP1. In a striking example, retention of a PTBP1-dependent intron triggers nonsense-mediated decay of transcripts encoding DNA methyltransferase DNMT3B. We provide evidence that this regulation facilitates the natural decline in DNMT3B levels in developing neurons and protects differentiation-specific genes from ectopic methylation. Thus, PTBP1-activated co-transcriptional splicing is a widespread phenomenon mediating epigenetic control of cellular identity.

    DOI: 10.1016/j.molcel.2022.12.014

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  • CDK9 and PP2A regulate RNA polymerase II transcription termination and coupled RNA maturation Invited Reviewed International journal

    @Tellier, Michael; @Zaborowska, Justyna; @Neve, Jonathan; @Nojima, Takayuki; @Hester, Svenja; @Fournier, Marjorie; @Furger, Andre; @Murphy, Shona

    EMBO REPORTS   23 ( 10 )   e54520   2022.10   ISSN:1469-221X eISSN:1469-3178

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:EMBO Reports  

    CDK9 is a kinase critical for the productive transcription of protein-coding genes by RNA polymerase II (pol II). As part of P-TEFb, CDK9 phosphorylates the carboxyl-terminal domain (CTD) of pol II and elongation factors, which allows pol II to elongate past the early elongation checkpoint (EEC) encountered soon after initiation. We show that, in addition to halting pol II at the EEC, loss of CDK9 activity causes premature termination of transcription across the last exon, loss of polyadenylation factors from chromatin, and loss of polyadenylation of nascent transcripts. Inhibition of the phosphatase PP2A abrogates the premature termination and loss of polyadenylation caused by CDK9 inhibition, indicating that this kinase/phosphatase pair regulates transcription elongation and RNA processing at the end of protein-coding genes. We also confirm the splicing factor SF3B1 as a target of CDK9 and show that SF3B1 in complex with polyadenylation factors is lost from chromatin after CDK9 inhibition. These results emphasize the important roles that CDK9 plays in coupling transcription elongation and termination to RNA maturation downstream of the EEC.

    DOI: 10.15252/embr.202154520

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  • Simultaneous studies of gene expression and alternative polyadenylation in primary human immune cells Reviewed International journal

    @Joana Wilton, @Michael Tellier, @Takayuki Nojima, @Angela M Costa, @Maria Jose Oliveira, Alexandra Moreira

    Methods in Enzymology   2021.6

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/bs.mie.2021.04.004

    Other Link: https://www.sciencedirect.com/science/article/abs/pii/S0076687921001397?via%3Dihub

  • Enhancers predominantly regulate gene expression during differentiation via transcription initiation Reviewed International coauthorship

    Larke MSC, Schwessinger R, Nojima T, Telenius J, Beagrie RA, Downes DJ, Oudelaar AM, Truch J, Graham B, Bender MA, Proudfoot NJ, Higgs DR, and Hughes JR

    Molecular Cell   2021.3

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.molcel.2021.01.002

    DOI: 10.1016/j.molcel.2021.01.002

  • SCAF4 and SCAF8, mRNA Anti-terminator Proteins Reviewed International coauthorship

    Gregersen LH, Mitter R, Ugalde AP, Nojima T, Proudfoot NJ, Agami R, Stewart A, and Svejstrup JQ

    Cell   2019.6

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.cell.2019.04.038

    DOI: 10.1016/j.cell.2019.04.038

  • Selective roles of vertebrate PCF11 in premature and full-length transcript termination. Reviewed International coauthorship

    Kamieniarz-Gdula K, Gdula MR, Panser K, Nojima T, Monks J, Wiśniewski JR, Riepsaame J, Brockdorff N, Pauli A and Proudfoot NJ

    Molecular Cell   2019.4

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.molcel.2019.01.027

    DOI: 10.1016/j.molcel.2019.01.027

  • Mitochondrial double stranded RNA triggers antiviral signalling in humans. Reviewed International coauthorship

    Dhir A, Dhir S, Borowski L, Jimenez L, Teitell M, Rötig A, Crow YJ, Rice GI, Duffy D, Tamby C, Nojima T, Munnich A, Schiff M, Ribeiro de Almeida C, Rehwinkel J, Dziembowski A, Szczesny R, and Proudfoot NJ.

    Nature   2018.7

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: https://doi.org/10.1038/s41586-018-0363-0

    DOI: https://doi.org/10.1038/s41586-018-0363-0

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Presentations

  • The end of RNA synthesis Invited

    野島孝之

    RNAフロンティアミーティング2022  2023.10 

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    Event date: 2023.10

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Venue:大阪大学 銀杏会館   Country:Japan  

  • POINTing towards transcription termination Invited International conference

    Takayuki Nojima

    第30回 Hot Spring Harbor Symposium、クロマチン潜在能 合同国際シンポジウム  2022.1 

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    Event date: 2022.1

    Language:English   Presentation type:Symposium, workshop panel (public)  

    Venue:zoom   Country:Japan  

    Transcription is terminated in appropriate region to prevent genome stresses such as transcription-replication conflict and RNA-DNA hybrid caused in extragenic region of eukaryote cells. Biochemical and genetic approaches identified several trans-factors and cis-elements involved in transcription termination. However, the mechanism and the rule remain largely unclear due to technical limitation and complexity created by other co-transcriptional events.
    In order to investigate precise mechanisms of transcription, we developed a nascent RNA technology named mammalian native elongating transcript-sequencing (mNET-seq) method that reveals Pol II pausing and RNA processing intermediates with the phosphorylation states at single nucleotide resolution. In mNET-seq analysis, RNA polymerase II (Pol II) machinery was specifically detected at termination region of protein coding genes with the CTD phosphorylation at threonine 4 position (T4P). Our group substantially extended mNET-seq method to dissect intact nascent RNA associated with elongating Pol II machinery. This new method was termed Polymerase Intact Nascent Transcript (POINT) technology. The POINT technology is applied to a template switching based 5’RACE method, resulting in detection of nascent transcript 5’ends at single nucleotide resolution (POINT-5) in illumina platform. Therefore POINT-5 method precisely profiles transcription start sites and co-transcriptional RNA cleavage sites. Notably rapid depletion of nuclear 5’-3’ exonuclease Xrn2 significantly induced a termination defect with increased RNA cleavage peaks only on polyadenylation sites of pre-mRNA genes, but not on other cleavage sites. This analysis revealed specificity of Xrn2-dependent RNA turnover.
    In conclusion, mNET and POINT technology variants will prove invaluable to dissect the termination mechanism not only for pre-mRNA gene, but also other gene category such as noncoding genes.

    Other Link: http://hshis30.umin.ne.jp/

  • Mechanism of Co-transcriptional RNA splicing Invited

    Takayuki Nojima

    第16回生命医科学研究所ネットワーク国際シンポジウム& KEY FORUM 2021  2021.11 

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    Event date: 2021.11

    Language:English   Presentation type:Symposium, workshop panel (public)  

    Venue:zoom   Country:Japan  

    In mammalian cells, transcripts synthesised by RNA polymerase II (Pol II) are largely co-transcriptionally (co-T) spliced. The exact timing of intron excision after transcription may influence splice site usage, thus shaping the alternatively spliced transcriptome. However, the underlying splicing kinetics is still poorly understood due to technical limitations in the purification of authentic newly synthesized transcripts (nascent RNA). To overcome this issue, our group have developed mammalian native elongating transcript-sequencing (mNET-seq) technology to analyse nascent RNAs with Pol II phosphorylation states (Nojima et al., Cell 2015). mNET-seq method revealed Pol II pausing on exon and phosphorylated Pol II specific spliceosome assembly (Nojima et al., Mol Cell 2018). Furthermore, we recently developed a new technology to dissect intact nascent RNAs directly purified from all Pol II transcribing states, called Polymerase Intact Nascent Transcript (POINT) (Sousa-Luis et al., Mol Cell 2021). By combining Illumina and Nanopore technologies, we took advantage of the high coverage of the former and the long read lengths of the latter. POINT single-molecule long-read data in human cells revealed the presence of different classes of splicing kinetics. ~40% of analysed introns are immediately excised as soon as the downstream exon emerges from Pol II, whereas many other introns progressively undergo delayed co-T splicing while Pol II transcribes the next intron. Moreover, we found that splicing dynamics relate to the distance between the intron and the 3’ end of the gene. Using engineered cell-lines with auxin-inducible degradation of the endogenous cleavage factor CPSF73 gene, we detected higher levels of splicing in cleavage-deficient cells. Most likely, this is because the transcriptional read-through increased the time available for delayed co-T splicing. Taken together, our novel POINT technology is able to show variation in co-T processing splicing dynamics, suggesting the presence of both immediate and delayed co-T splicing mechanisms.

    Other Link: https://www.keyforum2021.org/

  • End of RNA synthesis Invited International conference

    Takayuki Nojima

    日本生化学会  2021.10 

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    Event date: 2021.10

    Language:English   Presentation type:Symposium, workshop panel (public)  

    Venue:zoom   Country:Japan  

    Transcription is terminated in appropriate region to prevent genome stresses such as transcription-replication conflict and RNA-DNA hybrid caused in extragenic region of eukaryote cells. Biochemical and genetic approaches identified several trans-factors and cis-elements involved in transcription termination. However, the mechanism and the rule remain largely unclear due to technical limitation and complexity created by other co-transcriptional events.
    In order to investigate precise mechanisms of transcription, we developed a nascent RNA technology named mammalian native elongating transcript-sequencing (mNET-seq) method that reveals Pol II pausing and RNA processing intermediates with the phosphorylation states at single nucleotide resolution. In mNET-seq analysis, RNA polymerase II (Pol II) machinery was specifically detected at termination region of protein coding genes with the CTD phosphorylation at threonine 4 position (T4P). On the other hand, the T4P CTD mark is distributed throughout long noncoding RNA (lncRNA) gene units, suggesting transcription termination signals are embedded in lncRNA genes to fine tune lncRNA expression.
    We substantially extended mNET-seq method to dissect intact nascent RNA associated with elongating Pol II machinery. This new method was termed Polymerase Intact Nascent Transcript (POINT) technology. The POINT technology is applied to a template switching based 5’RACE method, resulting in detection of nascent transcript 5’ends at single nucleotide resolution (POINT-5) in illumina platform. Therefore POINT-5 method precisely profiles transcription start sites and co-transcriptional RNA cleavage sites. Notably rapid depletion of nuclear 5’-3’ exonuclease Xrn2 significantly induced a termination defect with increased RNA cleavage peaks only on polyadenylation sites of pre-mRNA genes, but not on other cleavage sites. This analysis revealed specificity of Xrn2-dependent RNA turnover.
    In conclusion, mNET and POINT technology variants will prove invaluable to dissect the termination mechanism not only for pre-mRNA gene, but also other gene category such as noncoding genes.

  • 新生RNA解析で理解するゲノム作動 Invited

    野島孝之

    染色体安定維持研究会  2023.7 

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    Event date: 2023.7

    Language:Japanese   Presentation type:Symposium, workshop panel (public)  

    Venue:国立遺伝学研究所   Country:Japan  

  • Mechanism of RNA transcription termination and its biological role

    野島孝之

    JST創発研究者による自発的な融合の場 「第1回分子生命反応創発討論会」  2022.2 

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    Event date: 2023.2

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:金沢大学角間キャンパス   Country:Japan  

  • Transcription termination: Forgotten mechanism in RNA synthesis cycle Invited

    野島孝之

    熊本大学リエゾンラボ/HIGO最先端研究セミナー  2022.7 

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    Event date: 2022.7

    Language:English   Presentation type:Oral presentation (general)  

    Venue:オンライン   Country:Japan  

  • 新生RNAライフサイクルを理解する Invited

    野島孝之

    金沢創発数理セミナー  2022.4 

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    Event date: 2022.4

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  • 新生RNA解析で理解するゲノム転写 Invited

    野島孝之

    金沢大学がん進展制御研究所 異分野融合セミナー  2022.1 

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    Event date: 2022.1

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:zoom   Country:Japan  

  • ゲノム転写と新生RNAライフサイクル Invited

    野島孝之

    大阪大学 生命機能セミナー  2021.4 

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    Event date: 2021.4

    Language:Japanese   Presentation type:Public lecture, seminar, tutorial, course, or other speech  

    Venue:大阪大学   Country:Japan  

  • 細胞内外環境を感知するゲノム作動ネットワークの新局面 リードスルーRNA転写による細胞周期の停止

    野島 孝之, Qi Fang, 大学 保一, 中山 千尋, Yuki Aoi, Ali Shilatifard, Michael Tellier

    日本生化学会大会プログラム・講演要旨集  2023.10  (公社)日本生化学会

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    Language:Japanese  

  • SETD2によるRNA転写終結制御機構の解明

    中山 千尋, Kopczynska Magda, Kamieniarz-Gdula Kinga, 野島 孝之

    日本生化学会大会プログラム・講演要旨集  2023.10  (公社)日本生化学会

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    Language:Japanese  

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MISC

  • Mechanism of lncRNA biogenesis as revealed by nascent transcriptomics Reviewed

    Takayuki Nojima, @Nicholas J Proudfoot

    Nature Reviews Molecular Cell Biology   2022.3

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    Language:English   Publishing type:Article, review, commentary, editorial, etc. (scientific journal)  

    Mammalian genomes express two principal gene categories through RNA polymerase II-mediated transcription: protein-coding transcription units and non-coding RNA transcription units. Non-coding RNAs are further divided into relatively abundant structural RNAs, such as small nuclear RNAs, and into a myriad of long non-coding RNAs (lncRNAs) of often low abundance and low stability. Although at least some lncRNA synthesis may reflect transcriptional ‘noise’, recent studies define unique functions for either specific lncRNAs or for the process of lncRNA synthesis. Notably, the transcription, processing and metabolism of lncRNAs are regulated differently from protein-coding genes. In this Review, we provide insight into the regulation of lncRNA transcription and processing gleaned from the application of recently devised nascent transcriptomics technology. We first compare and contrast different methodologies for studying nascent transcription. We then discuss the molecular mechanisms regulating lncRNA transcription, especially transcription initiation and termination, which emphasize fundamental differences in their expression as compared with protein-coding genes. When perturbed, lncRNA misregulation leads to genomic stress such as transcription–replication conflict and R-loop-mediated DNA damage. We discuss many unresolved but important questions about the synthesis and potential functions of lncRNAs.

    DOI: https://doi.org/10.1038/s41580-021-00447-6

    Other Link: https://www.nature.com/articles/s41580-021-00447-6

  • Defining gene ends: RNA polymerase II CTD threonine 4 phosphorylation marks transcription termination regions genome-wide Invited Reviewed

    Kopczyńska M, Saha U, Romanenko A, Nojima T, Gdula M.R. and, Kamieniarz-Gdula K

    Nucleic Acid Research   2025.1

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    Language:English   Publishing type:Article, review, commentary, editorial, etc. (scientific journal)  

    DOI: https://doi.org/10.1093/nar/gkae1240

  • 【情報からマテリアルへ ノンコーディングRNA研究 機能分子としてのRNAを見つけ、知り、創薬に使う新時代】(第1章)ncRNAを"見つける" 新たな解析手法と見出された分子 新生RNA解析技術からわかるncRNAの転写反応

    中山 千尋, 野島 孝之

    実験医学   42 ( 15 )   2276 - 2282   2024.9   ISSN:0288-5514

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    Language:Japanese   Publisher:(株)羊土社  

    近年,転写されたばかりのRNA(新生RNA)を解析する技術が次々に開発されたことで,ヒトゲノムのほとんどの領域で転写が起きていることがわかってきた.われわれのゲノムは,タンパク質をコードする領域とそうでない領域(非コードDNA)の2つに分類される.それら2つのゲノム領域から転写されるRNAの質は同じであろうか.本稿では,単なる転写のノイズであると考えられてきた多くの長鎖非コードRNA(lncRNA)の発現解析方法,それによって明らかになったlncRNA転写制御と安定性制御機構について紹介する.(著者抄録)

  • Author Correction: Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics (Nature Reviews Molecular Cell Biology, (2022), 23, 6, (389-406), 10.1038/s41580-021-00447-6)

    Nojima T., Proudfoot N.J.

    Nature Reviews Molecular Cell Biology   23 ( 12 )   853   2022.12   ISSN:14710072

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    Language:English   Publisher:Nature Reviews Molecular Cell Biology  

    In the version of this article initially published, the technique fastGRO was presented in Fig. 2 and the main text as a chromatin- based run- on technique when in fact it is a nuclear run- on technique. Accordingly, in Fig. 2, right- hand “Techniques” section, the third balloon has been edited to include “fastGRO” and the seventh balloon edited to remove “fastGRO,” and the eighth sentence of the Fig. 2 legend has been amended to include fastGRO, as follows: “Nucleus: transcription run- on (TRO) analyses are performed in biochemically isolated nuclei using 5-bromouridine 5′-triphosphate (BrUTP) in GRO-seq37, 4- thiouridine (4sU) in fastGRO40 or biotin- labelled NTPs (biotin- NTP) in PRO- seq38.” Further, the penultimate sentence of the “In vitro RNA labelling” section has been amended to read “Finally, a variation on genomic TRO called fastGRO also employs 4- thiouridine (4sU) in the NRO reaction” (from the original “Finally, a variation on genomic TRO called fastGRO also employs the use of chromatin fractions as starting material but the nascent transcript is tagged with 4- thiouridine (4sU)….”). The changes are reflected in the HTML and PDF versions of the article.

    DOI: 10.1038/s41580-022-00551-1

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Professional Memberships

  • 日本生化学会

  • 日本RNA学会

Committee Memberships

  • 九州大学   障害者支援推進委員会  

    2022.4 - Present   

Academic Activities

  • 世話人

    日本生化学会  ( Japan ) 2023.11

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    Type:Competition, symposium, etc. 

    Number of participants:50

  • 世話人

    RNAフロンティアミーティング2023  ( Japan ) 2023.10

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    Type:Competition, symposium, etc. 

    Number of participants:50

Other

  • 転写研究会

    2025.2 - Present

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    転写研究者のネットワーク作り

  • Fukuoka RNA commons

    2023.6 - Present

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    Fukuoka RNA commons は、生物現象を支える最も重要な分子の一つである 「RNA」の研究者を日本国内外からお招きし、九州大学学内のみならず、福岡エリアを中心に RNA研究の普及、さらには研究者・学生たちのネットワーク作りへの貢献を目指しています。

Research Projects

  • DNA複製・RNA転写コンフリクトのゲノム科学的解析

    2024 - 2026

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

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    Authorship:Coinvestigator(s)  Grant type:Scientific research funding

  • Mechanism of transcription termination defect caused by cellular stresses

    Grant number:24K01957  2024 - 2026

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    野島 孝之

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    Authorship:Principal investigator  Grant type:Scientific research funding

    ゲノム作動と安定化の両者に重要な反応である転写終結がどのように制御されているのか、細胞ストレスによるその破綻がどのような生物学的インパクトをもたらすのであろうか。ポリA付加配列がタンパク質コード遺伝子の重要な転写終結シグナルであることは間違い無いが、クロマチン環境、タンパク質修飾、転写スピード、DNA配列や構造なども関与すると考えられる。しかしながら、技術的な制約があったため、転写終結の全体像は今のところよく分かっていない。本研究では、独自に開発した新生RNA解析法を駆使して、新規の転写終結機構と、その制御破綻やそれによって産生される非コードRNAが細胞に与える影響を明らかにする。

    CiNii Research

  • DNA損傷により惹起されるゲノム変異非依存的な新規ネオアンチゲン発生機構の解明

    2024 - 2025

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Challenging Research(Exploratory)

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    Authorship:Coinvestigator(s)  Grant type:Scientific research funding

  • Elucidation of the mechanisms underlying neoantigen production independent of genomic mutation induced by DNA damage

    Grant number:23K18232  2023.6 - 2025.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Challenging Research (Exploratory)

    柴田 淳史, 野島 孝之

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    Grant type:Scientific research funding

    我々のこれまでの研究成果から、DNA損傷後のシグナル伝達が、転写及び翻訳の変化を引き起こし、非自己となる抗原(ネオアンチゲン)を産生しているという新たなモデルを考案している。そこで本研究では、「ゲノム変異非依存的なネオアンチゲン産生機構」の立証およびその分子機構解明を目的として、DNA損傷依存的な転写および翻訳開始点の変化を検出および解析する。DNA損傷という細胞に過度なストレスを与えた環境においては、従来の定説とは異なる抗原産生メカニズムが働くという新しい生命応答を示すことができ、当該分野における新たな概念を世界に先駆けて発信することができると考えている。

    CiNii Research

  • DNA複製・RNA転写コンフリクトのゲノム科学的解析

    Grant number:23K27156  2023.4 - 2026.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    大学 保一, 野島 孝之

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    Grant type:Scientific research funding

    真核生物では、複製開始点が染色体上に多数存在し、周辺の遺伝子上では複製フォークと転写装置間の衝突・干渉(複製・転写コンフリクト)を完全に回避する事はできない。複製フォークとRNAポリメラーゼの相互干渉は、ゲノム不安定性の要素の1つとして着目されてきたが、現在までの知見からは、複製・転写コンフリクトが起きやすい領域がゲノム上にどのように分布するかは明らかになっておらず、該当領域を探索する解析方法も確立されていない。本研究では、その領域で複製・転写コンフリクトの生成・解消に関わる因子の解析を進めつつ、染色体不安定を誘引する複製・転写コンフリクトの特徴を明らかにする。

    CiNii Research

  • がん機能性⾮コードRNAの発現を左右する転写終結機構の分⼦解剖と医学的応⽤

    2023

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    Grant type:Donation

  • がんクロマチン環境における非コードRNA産生機構の解明

    2022 - 2024

    金沢大学がん進展制御研究所 共同研究助成

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    Authorship:Principal investigator  Grant type:Contract research

  • 研究助成/非コードRNAを創出するがん特異的な転写終結機構の解明

    2022

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    Grant type:Donation

  • 自然研究科学助成/非コードRNA産生を制御する転写終結機構の解明

    2022

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    Grant type:Donation

  • 生命科学研究助成/非コードRNA機能を調節する転写終結機構の解明

    2022

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    Grant type:Donation

  • PIセットアップ研究助成/非コードRNA発現をON/OFFにする転写終結機構の解明とその医学的応用

    2022

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    Grant type:Donation

  • 基礎医学医療研究助成金/未成熟転写終結を介する非コードRNA代謝物の産生機構と生物学的機能の解明

    2022

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    Grant type:Donation

  • 基礎科学研究助成/遺伝子代謝産物の長さを決定する未成熟転写終結機構の解明

    2022

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    Grant type:Donation

  • 研究助成/転写終結機構の解明とそれ由来代謝物の医学的応用

    2022

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    Grant type:Donation

  • 研究助成/非コードRNA異常産生を防ぐ転写終結機構の解明

    2022

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    Grant type:Donation

  • 研究助成/スプライシング阻害が引き起こす未成熟転写終結機構とそれ由来非コードRNA代謝物の細胞機能の解明

    2022

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    Grant type:Donation

  • 非コードゲノム転写とRNAプロセシング

    2021.2 - 2025.1

    九州大学 

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    Authorship:Principal investigator 

  • 新生RNAライフサイクルを制御する転写終結機構の解明

    2021 - 2027

    JST

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    Authorship:Principal investigator  Grant type:Contract research

  • Mechanism of transcription coupled to RNA processing and its defect

    Grant number:19K24692  2021 - 2023

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Home-Returning Researcher Development Research

    Nojima Takayuki

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    Authorship:Principal investigator  Grant type:Scientific research funding

    This research aimed to understand a gene transcription and its coupled RNA processing, which are important regulatory steps in eukaryotic gene expression, and to develop necessary analytical methods and gain medical insights. Firstly, we successfully established the POINT method, which allows analysis of newly transcribed RNA. My POINT method reveals precise transcription start sites, RNA cleavage sites, and kinetics of co-transcriptional splicing. We also demonstrates the importance of alternative splicing during developmental stages. Additionally, the mechanisms of transcription termination defect in colorectal cancer and kidney cancer are revealed. The findings of this research contribute to the advancement of basic biology and also the development of treatment methods for diseases such as cancer.

    CiNii Research

  • クロマチンコンパクション機構の解明

    2021 - 2022

    QRプログラム (わかばチャレンジ)

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    Authorship:Principal investigator  Grant type:On-campus funds, funds, etc.

  • 研究助成/ゲノム転写終結が制御する非コードRNA産生機構の解明とその医学的応用

    2021

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    Grant type:Donation

  • 研究助成/抗がん化合物で誘導される“未成熟”転写終結制御機構とそれ由来長鎖非コードRNAの生理学的機能解析

    2021

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    Grant type:Donation

  • ヘルペスウイルス感染による宿主選択的スプライシング制御と免疫回避機構

    Grant number:20790353  2008 - 2009

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Young Scientists (B)

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    Authorship:Principal investigator  Grant type:Scientific research funding

  • 悪性腫瘍特異的なRNA選択的スプライシングを制御する抗がん剤の開発

    Grant number:21200074  2008 - 2009

    Japan Society for the Promotion of Science・Ministry of Education, Culture, Sports, Science and Technology  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

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    Authorship:Principal investigator  Grant type:Scientific research funding

  • ヘルペスウイルスRNAの核外輸送制御機構の解明

    2008 - 2009

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research on Priority Areas

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    Authorship:Coinvestigator(s)  Grant type:Scientific research funding

  • イントロンレスRNAの核外輸送の分子メカニズム

    2007 - 2008

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

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    Authorship:Coinvestigator(s)  Grant type:Scientific research funding

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Educational Activities

  • 医学部ウォーミングアップ講義
    医学部生命科学イントロダクションコース

Class subject

  • 医学部ウォーミングアッププログラム

    2022.10 - 2023.3   Second semester

  • 医学部生命科学入門

    2022.10 - 2023.3   Second semester

  • 医学部生命科学入門

    2021.10 - 2022.3   Second semester

FD Participation

  • 2022.3   Role:Panelist   Title:令和3年度馬出地区4部局合同男女共同参画FD

    Organizer:[Undergraduate school/graduate school/graduate faculty]

  • 2021.12   Role:Participation   Title:教養科目としての統合科学:ビッグヒストリーで紡ぐ社会と自然科学

    Organizer:University-wide

Teaching Student Awards

  • JSPS DC2

    Year and month of award:2025.4

    Classification of award-winning students:JSPS Research Fellow (DC, PD)   Name of award-winning student:中山千尋

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  • JST未来創造コース 次世代研究者挑戦的研究プログラム K2-SPRING

    Year and month of award:2024.4

    Classification of award-winning students:Doctoral student   Name of award-winning student:Yue Dong

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Other educational activity and Special note

  • 2024  Lecture at Education Method and Practice  転写研究会

  • 2024  Special Affairs  Fukuoka RNA commons

  • 2023  Special Affairs  Fukuoka RNA commons

Acceptance of Foreign Researchers, etc.

  • 九州大学

    Acceptance period: 2022.6 - 2023.3   (Period):1 month or more

    Nationality:Canada

    Business entity:On-campus funds

  • Australian National University

    (Period):2weeks to less than 1 month

    Nationality:Australia

    Business entity:Foreign governments, foreign research institutes, international organizations

  • Center for Advanced Technologies, Adam Mickiewicz University

    (Period):2weeks to less than 1 month

    Nationality:Poland

    Business entity:Foreign governments, foreign research institutes, international organizations

Travel Abroad

  • 2010.9 - 2021.1

    Staying countory name 1:United Kingdom   Staying institution name 1:University of Oxford