Updated on 2026/01/28

写真b

 
YANO Koichi
 
*Items subject to periodic update by Rikkyo University (The rest are reprinted from information registered on researchmap.)
Affiliation*
College of Science
Title*
Assistant Professor
Campus Career*
  • 10 2022 - Present 
    College of Science   Assistant Professor
 

Research Areas

  • Life Science / Molecular biology

Papers

  • Involvement of the inner surface residues of bacterial SMC protein MukB in the ssDNA binding in vitro Peer-reviewed

    Koichiro Akiyama, Koichi Yano, Hironori Niki

    Communications Biology9 ( 1 )   16 12 2025

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

    DOI： 10.1038/s42003-025-09345-5

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    Other Link： https://www.nature.com/articles/s42003-025-09345-5

  • The Ty1 retrotransposon harbors a DNA region that performs dual functions as both a gene silencing and chromatin insulator. Peer-reviewed International journal

    Hiroshi Masumoto, Hideki Muto, Koichi Yano, Yohei Kurosaki, Hironori Niki

    Scientific reports14 ( 1 ) 16641 - 16641   18 7 2024

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

    In various eukaryotic kingdoms, long terminal repeat (LTR) retrotransposons repress transcription by infiltrating heterochromatin generated within their elements. In contrast, the budding yeast LTR retrotransposon Ty1 does not itself undergo transcriptional repression, although it is capable of repressing the transcription of the inserted genes within it. In this study, we identified a DNA region within Ty1 that exerts its silencing effect via sequence orientation. We identified a DNA region within the Ty1 group-specific antigen (GAG) gene that causes gene silencing, termed GAG silencing (GAGsi), in which the silent chromatin in the GAGsi region is created by euchromatin-specific histone modifications. A characteristic inverted repeat (IR) sequence is present at the 5' end of this region, forming a chromatin boundary between promoter-specific chromatin upstream of the IR sequence and silent chromatin downstream of the IR sequence. In addition, Esc2 and Rad57, which are involved in DNA repair, were required for GAGsi silencing. Finally, the chromatin boundary was required for the transcription of Ty1 itself. Thus, the GAGsi sequence contributes to the creation of a chromatin environment that promotes Ty1 transcription.

    DOI： 10.1038/s41598-024-67242-z

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  • Amino acid residues for specific binding to ssDNA facilitate topological loading of bacterial condensin MukB

    Koichiro Akiyama, Koichi Yano, Hironori Niki

        21 9 2023

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    Publisher：Cold Spring Harbor Laboratory  

    ABSTRACT

    The bacterial condensin MukB facilitates proper chromosome segregation inEscherichia coli. A portion of the MukB proteins localize at a specific chromosome region, binding to DNA in a non-sequence-specific manner. However, it is unclear how MukB localizes at a particular site without sequence specificity. Like other structural maintenance of chromosome (SMC) proteins, MukB topologically loads onto DNA, and It has an intrinsic property of preferential topological loading onto the single-stranded DNA (ssDNA). We consider it crucial for the localization of a specific region. To investigate the property of MukB, we attempted to identify positively charged amino acid residues responsible for ssDNA binding. We created a series of mutated MukB proteins in which a single positively charged amino acid was replaced with a negatively charged one. The results showed that some substitutions located on the inner surface of the MukB head domain impacted ssDNA-binding activity, leading to deficiencies in cell growth and nucleoid segregation. The efficiency of topological loading onto ssDNA was also decreased when the positive charges were replaced with negative ones. These amino acid residues align with and bind to ssDNA when the MukB dimer secures ssDNA within its ring, thereby likely strengthening the ssDNA-binding ability of MukB.

    DOI： 10.1101/2023.09.21.558748

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  • Profiling a single-stranded DNA region within an rDNA segment that affects the loading of bacterial condensin Peer-reviewed

    Koichi Yano, Hideki Noguchi, Hironori Niki

    iScience25 ( 12 ) 105504 - 105504   12 2022

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    Authorship：Lead author   Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

    DOI： 10.1016/j.isci.2022.105504

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  • Profiling a single-stranded DNA region within an rDNA segment that is a loading site for bacterial condensin

    Koichi Yano, Hideki Noguchi, Hironori Niki

        18 6 2021

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    Publisher：Cold Spring Harbor Laboratory  

    <title>Abstract</title>Bacterial condensin preferentially loads to single-stranded DNA (ssDNA) in vitro and loads onto rDNA in vivo to support proper chromosome compaction. Thus, the actively transcribing rDNA would provide the ssDNA region for the topological loading of bacterial condensin. We attempted to detect the ssDNA region in the <italic>rrnI</italic> gene in situ. Non-denaturing sodium bisulfite treatment catalyzed the conversion of cytosines to thymines via uracils (CT-conversion) at locally melted DNA of a bacterial genome. Using next-generation sequencing, we generated an average of 11,000 reads covering each cytosine on the PCR-amplified rDNA segment to obtain the actual CT-conversion rate. In principle, the CT-conversion rate is an accurate guide to detect the formation of the ssDNA segment. We expected that an increment of the CT-conversion rate would reflect a trend toward ssDNA accumulation at a given site within the rDNA. We detected multiple ssDNA segments throughout the rDNA. The deletion mutations of the rDNA that affect the bacterial-condensin loading hindered the ssDNA formation only at the 100–500 bp segment downstream of the promoter. These data support the idea that the ssDNA segment plays a crucial role as the bacterial condensin-loading site and suggest the mechanism of condensin loading onto rDNA.

    DOI： 10.1101/2021.06.17.448897

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  • In Vivo and In Vitro Assay for Monitoring the Topological Loading of Bacterial Condensins on DNA

    Koichi Yano, Koichiro Akiyama, Hironori Niki

    Methods in Molecular Biology   181 - 196   5 2019

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    Authorship：Lead author   Publishing type：Part of collection (book)   Publisher：Springer New York  

    DOI： 10.1007/978-1-4939-9520-2_14

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  • Multiple cis-Acting rDNAs Contribute to Nucleoid Separation and Recruit the Bacterial Condensin Smc-ScpAB Peer-reviewed

    Koichi Yano, Hironori Niki

    CELL REPORTS21 ( 5 ) 1347 - 1360   10 2017

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

    DOI： 10.1016/j.celrep.2017.10.014

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  • In vitro topological loading of bacterial condensin MukB on DNA, preferentially single-stranded DNA rather than double-stranded DNA Peer-reviewed

    Hironori Niki, Koichi Yano

    SCIENTIFIC REPORTS6   29469   7 2016

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

    DOI： 10.1038/srep29469

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  • Ribosome dimerization is essential for the efficient regrowth of Bacillus subtilis Peer-reviewed

    Genki Akanuma, Yuka Kazo, Kazumi Tagami, Hirona Hiraoka, Koichi Yano, Shota Suzuki, Ryo Hanai, Hideaki Nanamiya, Yasuyuki Kato-Yamada, Fujio Kawamura

    MICROBIOLOGY-SGM162 ( 3 ) 448 - 458   3 2016

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

    DOI： 10.1099/mic.0.000234

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  • Growth and sporulation defects in Bacillus subtilis mutants with a single rrn operon can be suppressed by amplification of the rrn operon Peer-reviewed

    Koichi Yano, Kenta Masuda, Genki Akanuma, Tetsuya Wada, Takashi Matsumoto, Yuh Shiwa, Taichiro Ishige, Hirofumi Yoshikawa, Hironori Niki, Takashi Inaoka, Fujio Kawamura

    MICROBIOLOGY-SGM162 ( 1 ) 35 - 45   1 2016

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

    DOI： 10.1099/mic.0.000207

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  • Multiple rRNA operons are essential for efficient cell growth and sporulation as well as outgrowth in Bacillus subtilis Peer-reviewed

    Koichi Yano, Tetsuya Wada, Shota Suzuki, Kazumi Tagami, Takashi Matsumoto, Yuh Shiwa, Taichiro Ishige, Yasuhiro Kawaguchi, Kenta Masuda, Genki Akanuma, Hideaki Nanamiya, Hironori Niki, Hirofumi Yoshikawa, Fujio Kawamura

    MICROBIOLOGY-SGM159   2225 - 2236   11 2013

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

    DOI： 10.1099/mic.0.067025-0

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  • rRNA (rrn) operon-engineered Bacillus subtilis as a feasible test organism for antibiotic discovery Peer-reviewed

    Yukinori Tanaka, Hideaki Nanamiya, Koichi Yano, Koji Kakugawa, Fujio Kawamura, Kozo Ochi

    Antimicrobial Agents and Chemotherapy57 ( 4 ) 1948 - 1951   4 2013

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：4  

    DOI： 10.1128/AAC.02604-12

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  • Single mutations introduced in the essential ribosomal proteins L3 and S10 cause a sporulation defect in Bacillus subtilis Peer-reviewed

    Genki Akanuma, Shota Suzuki, Koichi Yano, Hideaki Nanamiya, Yousuke Natori, Eri Namba, Kazuya Watanabe, Kazumi Tagami, Takuya Takeda, Yuka Iizuka, Ako Kobayashi, Morio Ishizuka, Hirofumi Yoshikawa, Fujio Kawamura

    JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY59 ( 2 ) 105 - 117   2013

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

    DOI： 10.2323/jgam.59.105

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  • Inactivation of Ribosomal Protein Genes in Bacillus subtilis Reveals Importance of Each Ribosomal Protein for Cell Proliferation and Cell Differentiation Peer-reviewed

    Genki Akanuma, Hideaki Nanamiya, Yousuke Natori, Koichi Yano, Shota Suzuki, Shuya Omata, Morio Ishizuka, Yasuhiko Sekine, Fujio Kawamura

    JOURNAL OF BACTERIOLOGY194 ( 22 ) 6282 - 6291   11 2012

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

    DOI： 10.1128/JB.01544-12

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  • Bacillus subtilis RNA polymerase incorporates digoxigenin-labeled nucleotide in vitro Peer-reviewed

    Koichi Yano, Yee Lii Mien, Yoshito Sadaie, Kei Asai

    JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY57 ( 3 ) 153 - 157   6 2011

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

    DOI： 10.2323/jgam.57.153

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  • The Genome of Bacillus subtilis Phage SP10: A Comparative Analysis with Phage SPO1 Peer-reviewed

    Lii Mien Yee, Takashi Matsumoto, Koichi Yano, Satoshi Matsuoka, Yoshito Sadaie, Hirofumi Yoshikawa, Kei Asai

    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY75 ( 5 ) 944 - 952   5 2011

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

    DOI： 10.1271/bbb.100921

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  • Heterologous Expression of the Oceanobacillus iheyensis SigW and Its Anti-Protein RsiW in Bacillus subtilis Peer-reviewed

    Koichi Yano, Hiromi Inoue, Hirokazu Mori, Lii Mien Yee, Satoshi Matsuoka, Yoshito Sadaie, Kei Asai

    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY75 ( 5 ) 966 - 975   5 2011

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

    DOI： 10.1271/bbb.110035

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  • Inhibitory effect of prophage SP beta fragments on phage SP10 ribonucleotide reductase function and its multiplication in Bacillus subtilis Peer-reviewed

    Lii Mien Yee, Satoshi Matsuoka, Koichi Yano, Yoshito Sadaie, Kei Asai

    GENES & GENETIC SYSTEMS86 ( 1 ) 7 - 18   2 2011

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

    DOI： 10.1266/ggs.86.7

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Misc.

  • Gene silencing of budding yeast retrotransposon regulated by DNA repair factors

    増本博司, 武藤秀樹, 黒崎陽平, 矢野晃一, 仁木宏典

    日本分子生物学会年会プログラム・要旨集(Web)44th   2021

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  • バクテリアコンデンシンがロードするrDNAに生じる一本鎖DNA領域の1塩基レベルでの同定

    矢野晃一, 野口英樹, 仁木宏典

    日本分子生物学会年会プログラム・要旨集(Web)42nd   2019

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  • A new aspect of rRNA genes; involvement in origin resolution by DNA condensation

    Hironori Niki, Koichi Yano

    GENES & GENETIC SYSTEMS90 ( 6 ) 403 - 403   12 2015

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    Language：English   Publishing type：Research paper, summary (international conference)  

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  • Molecular genetic analysis of the function of rRNA in Bacillus subtilis

    Koichi Yano, Eri Namba, Rie Sekine, Shota Suzuki, Kazumi Tagami, Fujio Kawamura

    GENES & GENETIC SYSTEMS87 ( 6 ) 410 - 410   12 2012

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    Language：English   Publishing type：Research paper, summary (international conference)  

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  • Development of high expression Bacillus subtilis system using a ribosome possessing an altered Shine-Dalgarno sequence

    Takuya Takeda, Koichi Yano, Shota Suzuki, Eri Nanba, Fujio Kawamura

    GENES & GENETIC SYSTEMS87 ( 6 ) 432 - 432   12 2012

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    Language：English   Publishing type：Research paper, summary (international conference)  

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  • Analysis of the degradation of rRNA during an early stage of sporulation in Bacillus subtilis

    Kazuya Watanabe, Koichi Yano, Kazumi Tagami, Eri Namba, Fujio Kawamura

    GENES & GENETIC SYSTEMS87 ( 6 ) 432 - 432   12 2012

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    Language：English   Publishing type：Research paper, summary (international conference)  

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  • Regulatory for the dimerization of ribosome by a small (p) ppGpp synthetase, YwaC, in Delta relA Delta yjbM Delta ywaC triple mutant of Bacillus subtilis

    Kazumi Tagami, Koichi Yano, Yuka Kazo, Masahiro Hoshiya, Yoshiaki Ohashi, Hideaki Nanamiya, Yasuo Onishi, Fujio Kawamura

    GENES & GENETIC SYSTEMS86 ( 6 ) 419 - 419   12 2011

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  • Functional analysis of mutants deleting the 16S rRNA helix 9 in Bacillus subtilis

    Shota Suzuki, Eri Namba, Takuya Takeda, Koichi Yano, Yasuhiko Sekine, Fujio Kawamura

    GENES & GENETIC SYSTEMS86 ( 6 ) 420 - 420   12 2011

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    Language：English   Publishing type：Research paper, summary (international conference)  

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  • Comparative analysis of SigW-YbbM system between Bacillus subtilis and Oceanobacillus iheyensis

    Koichi Yano, Kei Asai

    GENES & GENETIC SYSTEMS85 ( 6 ) 424 - 424   12 2010

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    Language：English   Publishing type：Research paper, summary (international conference)  

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  • Comparative analysis of extracytoplasmic function sigma factor among genus Bacillus

    Koichi Yano, Hirokazu Mori, Kei Asai

    GENES & GENETIC SYSTEMS84 ( 6 ) 453 - 453   12 2009

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Books and Other Publications

  • In Vivo and In Vitro Assay for Monitoring the Topological Loading of Bacterial Condensins on DNA

    Koichi Yano（ Role： Joint author）

    2019 

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Presentations

  • The cruciform-centered region inside budding yeast Ty1 retrotransposon manages two distinct transcriptional modes: the gene silencing and the activation of Ty1 transcription

    Hiroshi Masumoto, Miki Hanasaki, Hideki Muto, Koichi Yano, Hironori Niki

    Cold Spring Harbor Symposium  6 10 2020 

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    Event date： 6 10 2020 - 9 10 2020

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  • レトロトランスポゾンTy1中のDNAのcruciform構造を中心とした遺伝子サイレンシング機構

    鼻崎美紀, 武藤秀樹, 矢野晃一, 仁木宏典, 増本博司

    酵母遺伝学フォーラム  7 9 2020 

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    Event date： 7 9 2020 - 9 9 2020

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  • Profiling of single-stranded DNA segments at single base resolution in a rDNA region loaded by bacterial condensin

    Koichi Yano, Hideki Noguchi, Hironori Niki

    The 42nd Annual Meeting of the Molecular Biology Society of Japan  3 12 2019 

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    Language：Japanese   Presentation type：Poster presentation  

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  • コンデンシンがロードするrDNA領域に生じる一本鎖DNAの1塩基レベルでの検出

    矢野晃一, 野口英樹, 仁木宏典

    第２５回DNA複製・組換え・修復ワークショップ  9 11 2019 

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    Event date： 9 11 2019 - 11 11 2019

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  • Cis-acting rDNA acts as a loading site for Smc-ScpAB during nucleoid separation in Bacillus subtilis

    Koichi Yano, Hironori Niki

    11 6 2017 

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    Event date： 11 6 2017 - 16 6 2017

    Language：English   Presentation type：Oral presentation (general)  

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  • Multiple cis-acting rDNAs contribute to nucleoid separation by loading of condensin, Smc-ScpAB

    Koichi Yano, Hironori Niki

    Gordon Research Conferences  21 5 2017 

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    Event date： 21 5 2017 - 26 5 2017

    Language：English   Presentation type：Oral presentation (general)  

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Research Projects

  • 一本鎖rDNAを介したコンデンシンの染色体結合機構の解明

    国立遺伝学研究所  科研費（若手研究） 

    矢野晃一

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    4 2018 - 3 2021

    Authorship：Principal investigator  Grant type：Competitive

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