2022/01/28 更新

写真a

チェン チャオ
曽 超
所属
理工学術院 理工学術院総合研究所
職名
次席研究員(研究院講師)
ホームページ

兼担

  • 理工学術院   先進理工学部

学歴

  • 2013年04月
    -
    2016年03月

    東京大学   新領域創成科学研究科   メディカル情報生命科学専攻  

  • 2011年04月
    -
    2013年03月

    京都大学   情報学研究科   (修士課程)  

学位

  • 東京大学   博士(科学)

  • 京都大学   修士(情報学)

経歴

  • 2021年04月
    -
    継続中

    早稲田大学   次席研究員

  • 2018年11月
    -
    2021年03月

    国立研究開発法人産業技術総合研究所 (産総研)   産総研・早大生体システムビッグデータ解析オープンイノベーションラボラトリ   特別研究員

  • 2018年05月
    -
    2018年10月

    早稲田大学   理工学術総合研究所   研究助手

  • 2016年12月
    -
    2018年04月

    国立研究開発法人産業技術総合研究所   産総研・早大 生体システムビッグデータ解析オープン・イノベーションラボラトリ   テクニカルスタッフ

  • 2016年04月
    -
    2016年11月

    東京大学   新領域創成科学研究科   特別研究員

所属学協会

  •  
     
     

    日本RNA学会

  •  
     
     

    日本バイオインフォマティクス学会

  •  
     
     

    日本分子生物学会

 

研究分野

  • 生命、健康、医療情報学

研究キーワード

  • lncRNA

論文

  • Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs (in press)

    Chao Zeng, Atsushi Takeda, Kotaro Sekine, Naoki Osato, Tsukasa Fukunaga, Michiaki Hamada

    Methods in Molecular Biology    2022年  [査読有り]  [招待有り]

    担当区分:筆頭著者, 責任著者

  • Impact of human gene annotations on RNA-seq differential expression analysis

    Yu Hamaguchi, Chao Zeng, Michiaki Hamada

    BMC Genomics   22   730  2021年10月  [査読有り]

  • Binding patterns of RNA-binding proteins to repeat-derived RNA sequences reveal putative functional RNA elements

    Masahiro Onoguchi, Chao Zeng, Ayako Matsumaru, Michiaki Hamada

    NAR Genomics and Bioinformatics   3 ( 3 )  2021年07月  [査読有り]

     概要を見る

    <jats:title>Abstract</jats:title>
    <jats:p>Recent reports have revealed that repeat-derived sequences embedded in introns or long noncoding RNAs (lncRNAs) are targets of RNA-binding proteins (RBPs) and contribute to biological processes such as RNA splicing or transcriptional regulation. These findings suggest that repeat-derived RNAs are important as scaffolds of RBPs and functional elements. However, the overall functional sequences of the repeat-derived RNAs are not fully understood. Here, we show the putative functional repeat-derived RNAs by analyzing the binding patterns of RBPs based on ENCODE eCLIP data. We mapped all eCLIP reads to repeat sequences and observed that 10.75 % and 7.04 % of reads on average were enriched (at least 2-fold over control) in the repeats in K562 and HepG2 cells, respectively. Using these data, we predicted functional RNA elements on the sense and antisense strands of long interspersed element 1 (LINE1) sequences. Furthermore, we found several new sets of RBPs on fragments derived from other transposable element (TE) families. Some of these fragments show specific and stable secondary structures and are found to be inserted into the introns of genes or lncRNAs. These results suggest that the repeat-derived RNA sequences are strong candidates for the functional RNA elements of endogenous noncoding RNAs.</jats:p>

    DOI

  • Long Non-Coding RNA CRNDE Is Involved in Resistance to EGFR Tyrosine Kinase Inhibitor in EGFR-Mutant Lung Cancer via eIF4A3/MUC1/EGFR Signaling

    Satoshi Takahashi, Rintaro Noro, Masahiro Seike, Chao Zeng, Masaru Matsumoto, Akiko Yoshikawa, Shinji Nakamichi, Teppei Sugano, Mariko Hirao, Kuniko Matsuda, Michiaki Hamada, Akihiko Gemma

    International Journal of Molecular Sciences   22 ( 8 ) 4005 - 4005  2021年04月  [査読有り]  [国際誌]

     概要を見る

    (1) Background: Acquired resistance to epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) is an intractable problem for many clinical oncologists. The mechanisms of resistance to EGFR-TKIs are complex. Long non-coding RNAs (lncRNAs) may play an important role in cancer development and metastasis. However, the biological process between lncRNAs and drug resistance to EGFR-mutated lung cancer remains largely unknown. (2) Methods: Osimertinib- and afatinib-resistant EGFR-mutated lung cancer cells were established using a stepwise method. A microarray analysis of non-coding and coding RNAs was performed using parental and resistant EGFR-mutant non-small cell lung cancer (NSCLC) cells and evaluated by bioinformatics analysis through medical-industrial collaboration. (3) Results: Colorectal neoplasia differentially expressed (CRNDE) and DiGeorge syndrome critical region gene 5 (DGCR5) lncRNAs were highly expressed in EGFR-TKI-resistant cells by microarray analysis. RNA-protein binding analysis revealed eukaryotic translation initiation factor 4A3 (eIF4A3) bound in an overlapping manner to CRNDE and DGCR5. The CRNDE downregulates the expression of eIF4A3, mucin 1 (MUC1), and phospho-EGFR. Inhibition of CRNDE activated the eIF4A3/MUC1/EGFR signaling pathway and apoptotic activity, and restored sensitivity to EGFR-TKIs. (4) Conclusions: The results showed that CRNDE is associated with the development of resistance to EGFR-TKIs. CRNDE may be a novel therapeutic target to conquer EGFR-mutant NSCLC.

    DOI PubMed

  • Association analysis of repetitive elements and R-loop formation across species

    Chao Zeng, Masahiro Onoguchi, Michiaki Hamada

    Mobile DNA   12 ( 3 )  2021年01月  [査読有り]

    担当区分:筆頭著者, 責任著者

  • Detection and Characterization of Ribosome-Associated Long Noncoding RNAs

    Chao Zeng, Michiaki Hamada

    Methods in Molecular Biology   2254   179 - 194  2021年  [査読有り]  [招待有り]  [国際誌]

     概要を見る

    Ribosome profiling shows potential for studying the function of long noncoding RNAs (lncRNAs). We introduce a bioinformatics pipeline for detecting ribosome-associated lncRNAs (ribo-lncRNAs) from ribosome profiling data. Further, we describe a machine-learning approach for the characterization of ribo-lncRNAs based on their sequence features. Scripts for ribo-lncRNA analysis can be accessed at ( https://ribolnc.hamadalab.com/ ).

    DOI PubMed

  • RNA-Seq Analysis Reveals Localization-Associated Alternative Splicing across 13 Cell Lines

    Chao Zeng, Michiaki Hamada

    Genes   11 ( 7 ) 820  2020年07月  [査読有り]  [国際誌]

    担当区分:筆頭著者, 責任著者

    DOI PubMed

  • Identifying sequence features that drive ribosomal association for lncRNA.

    Chao Zeng, Michiaki Hamada

    BMC genomics   19 ( Suppl 10 ) 906 - 906  2018年12月  [査読有り]  [国際誌]

     概要を見る

    BACKGROUND: With the increasing number of annotated long noncoding RNAs (lncRNAs) from the genome, researchers are continually updating their understanding of lncRNAs. Recently, thousands of lncRNAs have been reported to be associated with ribosomes in mammals. However, their biological functions or mechanisms are still unclear. RESULTS: In this study, we tried to investigate the sequence features involved in the ribosomal association of lncRNA. We have extracted ninety-nine sequence features corresponding to different biological mechanisms (i.e., RNA splicing, putative ORF, k-mer frequency, RNA modification, RNA secondary structure, and repeat element). An [Formula: see text]-regularized logistic regression model was applied to screen these features. Finally, we obtained fifteen and nine important features for the ribosomal association of human and mouse lncRNAs, respectively. CONCLUSION: To our knowledge, this is the first study to characterize ribosome-associated lncRNAs and ribosome-free lncRNAs from the perspective of sequence features. These sequence features that were identified in this study may shed light on the biological mechanism of the ribosomal association and provide important clues for functional analysis of lncRNAs.

    DOI PubMed

  • Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

    Chao Zeng, Tsukasa Fukunaga, Michiaki Hamada

    BMC Genomics   19 ( 414 )  2018年05月  [査読有り]

    担当区分:筆頭著者, 責任著者

  • Obstacle Avoidance and Path Planning Based on S-Type Double-Arc Insertion Method

    Xiao-tong Hu, Chao Zeng

       2010年09月  [査読有り]

    担当区分:責任著者

    DOI

▼全件表示

受賞

  • 生命医薬情報学連合大会研究奨励賞

    2017年07月   日本バイオインフォマティクス学会  

    受賞者: 曽超

共同研究・競争的資金等の研究課題

  • RNA品質管理機構によるイントロン-エクソン化RNA生成と癌維持機構への関与

    日本学術振興会  科学研究費助成事業 挑戦的研究(萌芽)

    研究期間:

    2021年07月
    -
    2023年03月
     

    谷上 賢瑞

  • Identification and characterization of lncRNAs involved in genetic compensation

    日本学術振興会  科学研究費助成事業 若手研究

    研究期間:

    2020年04月
    -
    2022年03月
     

    曽 超

講演・口頭発表等

  • Bioinformatic approaches for understanding RNA reincarnation

    Chao Zeng, Masahiro Onoguchi, Michiaki Hamada

    第43回日本分子生物学会  

    発表年月: 2020年12月

    開催年月:
    2020年12月
     
     
  • Identification and characterisation of ribosome-associated lncRNAs in human and mouse

    Chao Zeng, Michiaki Hamada

    RNA bioinformatics  

    発表年月: 2019年09月

  • Identifying sequence features that drive ribosomal association for lncRNA

    Chao Zeng, Michiaki Hamada

    The 29th International Conference on Genome Informatics(GIW2018)  

    発表年月: 2018年12月

  • A comprehensive analysis of the effects of alternative splicing on RNA localization in human

    Chao Zeng, Michiaki Hamada

    第7回生命医薬情報学連合大会(IIBMP2018)  

    発表年月: 2018年09月

  • Integrative analysis of multiple ribosome profiling datasets reveals widespread lncRNA-ribosome interaction in mammals

    Chao Zeng, Michiaki Hamada

    第6回生命医薬情報学連合大会(IIBMP2017)  

    発表年月: 2017年09月

  • Mapping and Aligning PacBio RNA-seq Data

    Chao Zeng, Hiroaki Iwata, Natsuhiro Ichinose, Tetsushi Yada, Osamu Gotoh

    The Asian Young Researchers Conference on Computational and Omics Biology (AYRCOB)  

    発表年月: 2012年12月

▼全件表示

 

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