2022/06/28 更新

写真a

オノグチ マサヒロ
小野口 真広
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)

学位

  • 東京大学   博士(生命科学)

経歴

  • 2021年04月
    -
    継続中

    早稲田大学   理工学術院   次席研究員

 

研究キーワード

  • lncRNA

  • トランスポゾン

  • noncoding RNA

論文

  • 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 ) lqab055  2021年07月  [査読有り]  [国際誌]

    担当区分:筆頭著者

     概要を見る

    <title>Abstract</title>
    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.

    DOI PubMed

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

    Chao Zeng, Masahiro Onoguchi, Michiaki Hamada

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

     概要を見る

    <title>Abstract</title><sec>
    <title>Background</title>
    Although recent studies have revealed the genome-wide distribution of R-loops, our understanding of R-loop formation is still limited. Genomes are known to have a large number of repetitive elements. Emerging evidence suggests that these sequences may play an important regulatory role. However, few studies have investigated the effect of repetitive elements on R-loop formation.


    </sec><sec>
    <title>Results</title>
    We found different repetitive elements related to R-loop formation in various species. By controlling length and genomic distributions, we observed that satellite, long interspersed nuclear elements (LINEs), and DNA transposons were each specifically enriched for R-loops in humans, fruit flies, and Arabidopsis thaliana, respectively. R-loops also tended to arise in regions of low-complexity or simple repeats across species. We also found that the repetitive elements associated with R-loop formation differ according to developmental stage. For instance, LINEs and long terminal repeat retrotransposons (LTRs) are more likely to contain R-loops in embryos (fruit fly) and then turn out to be low-complexity and simple repeats in post-developmental S2 cells.


    </sec><sec>
    <title>Conclusions</title>
    Our results indicate that repetitive elements may have species-specific or development-specific regulatory effects on R-loop formation. This work advances our understanding of repetitive elements and R-loop biology.


    </sec>

    DOI PubMed

  • The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders

    Cheen Euong Ang, Qing Ma, Orly L Wapinski, ShengHua Fan, Ryan A Flynn, Qian Yi Lee, Bradley Coe, Masahiro Onoguchi, Victor Hipolito Olmos, Brian T Do, Lynn Dukes-Rimsky, Jin Xu, Koji Tanabe, LiangJiang Wang, Ulrich Elling, Josef M Penninger, Yang Zhao, Kun Qu, Evan E Eichler, Ana, d Srivastava, Marius Wernig, Howard Y Chang

    eLIFE   DOI: 10.7554/eLife.41770  2019年01月  [査読有り]

  • A noncoding RNA regulates the neurogenin1 gene locus during mouse neocortical development

    Masahiro Onoguchi, Yusuke Hirabayashi, Haruhiko Koseki, Yukiko Gotoh

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   109 ( 42 ) 16939 - 16944  2012年10月  [査読有り]

    担当区分:筆頭著者

     概要を見る

    The proneural basic helix-loop-helix (bHLH) transcription factor neurogenin1 (Neurog1) plays a pivotal role in neuronal differentiation during mammalian development. The spatiotemporal control of the Neurog1 gene expression is mediated by several specific enhancer elements, although how these elements regulate the Neurog1 locus has remained largely unclear. Recently it has been shown that a large number of enhancer elements are transcribed, but the regulation and function of the resulting transcripts have been investigated for only several such elements. We now show that an enhancer element located 5.8-7.0 kb upstream of the mouse Neurog1 locus is transcribed. The production of this transcript, designated utNgn1, is highly correlated with that of Neurog1 mRNA during neuronal differentiation. Moreover, knockdown of utNgn1 by a corresponding short interfering RNA inhibits the production of Neurog1 mRNA in response to induction of neuronal differentiation. We also found that production of utNgn1 is suppressed by polycomb group (PcG) proteins, which inhibit the expression of Neurog1. Our results thus suggest that a noncoding RNA transcribed from an enhancer element positively regulates transcription at the Neurog1 locus.

    DOI

  • Formation of cytochrome C-apatite composite layer on NaOH- and heat-treated titanium

    Yu Sogo, Atsuo Ito, Masahiro Onoguchi, Xia Li, Ayako Oyane, Noboru Ichinose

    MATERIALS SCIENCE & ENGINEERING C-BIOMIMETIC AND SUPRAMOLECULAR SYSTEMS   29 ( 3 ) 766 - 770  2009年04月  [査読有り]

     概要を見る

    A cytochrome C (cyt C) and apatite composite layer was formed on a NaOH- and heat-treated titanium substrate (Ti substrate) by immersing the Ti substrate for one day at 25 degrees C in supersaturated calcium phosphate solutions obtained by mixing infusion fluids. When the initial supersaturation level of the calcium phosphate solution was increased, the total amount of cyt C and apatite deposited on the Ti substrate increased. On the other hand, the cyt C content in the composite layer decreased with an increase in initial supersaturation level. The morphology of the composite layer markedly changed depending on the initial supersaturation level. Therefore, the initial supersaturation level affected the formation of the cyt C and apatite composite layer. It is expected that fibroblast growth factor-2 can be immobilized on NaOH- and heat-treated titanium Substrates using the same method. (C) 2008 Elsevier B.V. All rights reserved.

    DOI

  • Formation of a FGF-2 and calcium phosphate composite layer on a hydroxyapatite ceramic for promoting bone formation

    Yu Sogo, Atsuo Ito, Masahiro Onoguchi, Ayako Oyane, Hideo Tsurushima, Noboru Ichinose

    BIOMEDICAL MATERIALS   2 ( 3 ) S175 - S180  2007年09月  [査読有り]

     概要を見る

    Fibroblast growth factor-2 (FGF-2) was immobilized on a hydroxyapatite (HAP) ceramic in supersaturated calcium phosphate solution prepared using solutions corresponding to clinically approved infusion fluids. To avoid the risk of FGF-2 denaturation, FGF-2 immobilization was carried out at 25 degrees C. FGF-2 was successfully immobilized on HAP ceramic surfaces by deposition with calcium phosphate to form a FGF-2 and calcium phosphate composite layer. A maximum of 2.72 +/- 0.01 mu g cm(-2) of FGF-2 was immobilized in the composite layer formed on the HAP ceramic under the optimum condition. A FGF-2-immobilized HAP ceramic is likely to have the ability to release a sufficient amount of FGF-2 to promote bone formation. FGF-2 released from a FGF-2-immobilized HAP ceramic maintained its biological activity, since the proliferation of fibroblastic NIH3T3 was promoted. Therefore, the FGF-2-immobilized HAP ceramic is expected to be a useful material for promoting new bone formation.

    DOI

  • Formation of an ascorbate-apatite composite layer on titanium

    Atsuo Ito, Yu Sogo, Yuko Ebihara, Masahiro Onoguchi, Ayako Oyane, Noboru Ichinose

    BIOMEDICAL MATERIALS   2 ( 3 ) S181 - S185  2007年09月  [査読有り]

     概要を見る

    An ascorbate - apatite composite layer was successfully formed on NaOH- and heat-treated titanium by coprecipitating L-ascorbic acid phosphate and low-crystalline apatite in a supersaturated calcium phosphate solution at 37 degrees C for 48 h. The supersaturated calcium phosphate solutions used have chemical compositions attainable by mixing infusion fluids officially approved for clinical use. The amount of immobilized L-ascorbic acid phosphate ranged from 1.0 to 2.3 mu g mm(-2), which is most likely to be sufficient for the in vitro osteogenic differentiation of mesenchymal stem cells on titanium. Since ascorbate is important for the collagen synthesis and subsequent osteogenesis of mesenchymal stem cells, titanium coated with the ascorbate - apatite composite layer would be useful as a scaffold in bone tissue engineering and as a bone substitute.

    DOI

▼全件表示

書籍等出版物

  • エピジェネティクス実験スタンダード

    牛島俊和, 眞貝洋一, 塩見春彦, 編, 小野口真広, 他, 著( 担当: 分担執筆,  担当範囲: 274-286)

    羊土社  2017年

共同研究・競争的資金等の研究課題

  • eCLIPデータを用いた機能性RNA反復配列の探索

    日本学術振興会  科学研究費助成事業 基盤研究(C)

    研究期間:

    2021年04月
    -
    2024年03月
     

    小野口 真広

  • リピート要素のde novo発見に基づく長鎖ノンコーディングRNAの機能の解明

    日本学術振興会  科学研究費助成事業 基盤研究(A)

    研究期間:

    2020年04月
    -
    2023年03月
     

    浜田 道昭, 小野口 真広, 福永 津嵩

  • 選択的なpiRNA生合成経路の包括的解析

    日本学術振興会  科研費若手(B)

    研究期間:

    2017年04月
    -
    2019年03月
     

    小野口真広

  • エンハンサーによるlncRNAを介した新しい遺伝子発現制御機構の解析

    日本学術振興会  科研費若手(B)

    研究期間:

    2013年04月
    -
    2014年03月
     

    小野口真広

講演・口頭発表等

  • Binding Patterns of RNA Binding Proteins To Repeat-Derived RNA Sequences Reveal Putative Functional RNA Elements

    小野口真広, 曽超, 松丸綾子, 浜田道昭

    日本R N A学会年会  

    発表年月: 2021年07月

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

    Masahiro Onoguchi, Chao Zeng, Ayako Matsumaru, Michiaki Hamada

    2021 Keystone Symposia Conference, Non-Coding RNAs: Biology and Applications  

    発表年月: 2021年05月

    開催年月:
    2021年05月
     
     
  • LINE1配列に結合するRNA結合タンパク質の同定とRNA機能エレメントの推定

    小野口真広, 浜田道昭

    第43回日本分子生物学会年会  

    発表年月: 2020年12月

    開催年月:
    2020年12月
     
     
  • RNAリインカネーション

    曽超, 小野口真広, 浜田道昭

    第43回日本分子生物学会年会  

    発表年月: 2020年12月

    開催年月:
    2020年12月
     
     
  • Analysis and estimation of functional domains of lncRNAs using eCLIP data

    Masahiro Onoguchi, Chao Zeng, Yukiteru Ono, Michiaki Hamada

    2020 Keystone Symposia Conference, Noncoding RNAs: Mechanism, Function and Therapies  

    発表年月: 2020年01月

    開催年月:
    2020年01月
     
     
  • eCLIPデータを用いた機能性RNA反復配列の推定

    小野口真広, 曽超, 松丸綾子, 浜田道昭

    第42回日本分子生物学会年会  

    発表年月: 2019年12月

    開催年月:
    2019年12月
     
     

▼全件表示