Updated on 2022/05/25

写真a

 
KAKUI, Yasutaka
 
Affiliation
Affiliated organization, Waseda Institute for Advanced Study
Job title
Assistant Professor(without tenure)
 

Papers

  • Tracheal motile cilia in mice require CAMSAP3 for formation of central microtubule pair and coordinated beating.

    Saito H, Matsukawa-Usami F, Fujimori T, Kimura T, Ide T, Yamamoto T, Shibata T, Onoue K, Okayama S, Yonemura S, Misaki K, Soba Y, Kakui Y, Sato M, Takeichi M

    Molecular biology of the cell    2021.07  [Refereed]

    DOI PubMed

  • Tell the Difference Between Mitosis and Meiosis: Interplay Between Chromosomes, Cytoskeleton, and Cell Cycle Regulation.

    Sato M, Kakui Y, Toya M

    Frontiers in cell and developmental biology    2021.04  [Refereed]

    DOI PubMed

  • Comparison of loop extrusion and diffusion capture as mitotic chromosome formation pathways in fission yeast

    Tereza Gerguri, Xiao Fu, Yasutaka Kakui, Bhavin S Khatri, Christopher Barrington, Paul A Bates, Frank Uhlmann

    Nucleic Acids Research   49 ( 3 ) 1294 - 1312  2021.02  [Refereed]

    Authorship:Lead author

     View Summary

    <title>Abstract</title>
    Underlying higher order chromatin organization are Structural Maintenance of Chromosomes (SMC) complexes, large protein rings that entrap DNA. The molecular mechanism by which SMC complexes organize chromatin is as yet incompletely understood. Two prominent models posit that SMC complexes actively extrude DNA loops (loop extrusion), or that they sequentially entrap two DNAs that come into proximity by Brownian motion (diffusion capture). To explore the implications of these two mechanisms, we perform biophysical simulations of a 3.76 Mb-long chromatin chain, the size of the long Schizosaccharomyces pombe chromosome I left arm. On it, the SMC complex condensin is modeled to perform loop extrusion or diffusion capture. We then compare computational to experimental observations of mitotic chromosome formation. Both loop extrusion and diffusion capture can result in native-like contact probability distributions. In addition, the diffusion capture model more readily recapitulates mitotic chromosome axis shortening and chromatin compaction. Diffusion capture can also explain why mitotic chromatin shows reduced, as well as more anisotropic, movements, features that lack support from loop extrusion. The condensin distribution within mitotic chromosomes, visualized by stochastic optical reconstruction microscopy (STORM), shows clustering predicted from diffusion capture. Our results inform the evaluation of current models of mitotic chromosome formation.

    DOI PubMed

  • Fission yeast condensin contributes to interphase chromatin organization and prevents transcription-coupled DNA damage

    Yasutaka Kakui, Christopher Barrington, David J. Barry, Tereza Gerguri, Xiao Fu, Paul A. Bates, Bhavin S. Khatri, Frank Uhlmann

    Genome Biology   21 ( 1 )  2020.12  [Refereed]

    Authorship:Lead author, Corresponding author

     View Summary

    <title>Abstract</title>
    <sec>
    <title>Background</title>
    Structural maintenance of chromosomes (SMC) complexes are central organizers of chromatin architecture throughout the cell cycle. The SMC family member condensin is best known for establishing long-range chromatin interactions in mitosis. These compact chromatin and create mechanically stable chromosomes. How condensin contributes to chromatin organization in interphase is less well understood.


    </sec>
    <sec>
    <title>Results</title>
    Here, we use efficient conditional depletion of fission yeast condensin to determine its contribution to interphase chromatin organization. We deplete condensin in G2-arrested cells to preempt confounding effects from cell cycle progression without condensin. Genome-wide chromatin interaction mapping, using Hi-C, reveals condensin-mediated chromatin interactions in interphase that are qualitatively similar to those observed in mitosis, but quantitatively far less prevalent. Despite their low abundance, chromatin mobility tracking shows that condensin markedly confines interphase chromatin movements. Without condensin, chromatin behaves as an unconstrained Rouse polymer with excluded volume, while condensin constrains its mobility. Unexpectedly, we find that condensin is required during interphase to prevent ongoing transcription from eliciting a DNA damage response.


    </sec>
    <sec>
    <title>Conclusions</title>
    In addition to establishing mitotic chromosome architecture, condensin-mediated long-range chromatin interactions contribute to shaping chromatin organization in interphase. The resulting structure confines chromatin mobility and protects the genome from transcription-induced DNA damage. This adds to the important roles of condensin in maintaining chromosome stability.


    </sec>

    DOI PubMed

  • Computational and experimental analyses of mitotic chromosome formation pathways in fission yeast

    Tereza Gerguri, Xiao Fu, Yasutaka Kakui, Bhavin S. Khatri, Christopher Barrington, Paul A. Bates, Frank Uhlmann

       2020.10

    Authorship:Lead author

     View Summary

    <title>Abstract</title>Underlying higher order chromatin organization are Structural Maintenance of Chromosomes (SMC) complexes, large protein rings that entrap DNA. The molecular mechanism by which SMC complexes organize chromatin is as yet incompletely understood. Two prominent models posit that SMC complexes actively extrude DNA loops (loop extrusion), or that they sequentially entrap two DNAs that come into proximity by Brownian motion (diffusion capture). To explore the implications of these two mechanisms, we perform biophysical simulations of a 3.76 Mb-long chromatin chain, the size of the long <italic>S. pombe</italic> chromosome I left arm. On it, the SMC complex condensin is modeled to perform loop extrusion or diffusion capture. We then compare computational to experimental observations of mitotic chromosome formation. Both loop extrusion and diffusion capture can result in native-like contact probability distributions. In addition, the diffusion capture model more readily recapitulates mitotic chromosome axis shortening and chromatin density enrichment. Diffusion capture can also explain why mitotic chromatin shows reduced, as well as more anisotropic, movements, features that lack support from loop extrusion. The condensin distribution within mitotic chromosomes, visualized by stochastic optical reconstruction microscopy (STORM), shows clustering predicted from diffusion capture. Our results inform the evaluation of current models of mitotic chromosome formation.

    DOI

  • CSynth: an interactive modelling and visualization tool for 3D chromatin structure

    Stephen Todd, Peter Todd, Simon J McGowan, James R Hughes, Yasutaka Kakui, Frederic Fol Leymarie, William Latham, Stephen Taylor

    Bioinformatics    2020.08  [Refereed]

     View Summary

    <title>Abstract</title>
    <sec>
    <title>Motivation</title>
    The 3D structure of chromatin in the nucleus is important for gene expression and regulation. Chromosome conformation capture techniques, such as Hi-C, generate large amounts of data showing interaction points on the genome but these are hard to interpret using standard tools.


    </sec>
    <sec>
    <title>Results</title>
    We have developed CSynth, an interactive 3D genome browser and real-time chromatin restraint-based modeller to visualize models of any chromosome conformation capture (3C) data. Unlike other modelling systems, CSynth allows dynamic interaction with the modelling parameters to allow experimentation and effects on the model. It also allows comparison of models generated from data in different tissues/cell states and the results of third-party 3D modelling outputs. In addition, we include an option to view and manipulate these complicated structures using Virtual Reality (VR) so scientists can immerse themselves in the models for further understanding. This VR component has also proven to be a valuable teaching and a public engagement tool.


    </sec>
    <sec>
    <title>Availabilityand implementation</title>
    CSynth is web based and available to use at https://csynth.org.


    </sec>
    <sec>
    <title>Supplementary information</title>
    Supplementary data are available at Bioinformatics online.


    </sec>

    DOI

  • Division of Labor between PCNA Loaders in DNA Replication and Sister Chromatid Cohesion Establishment

    Hon Wing Liu, Céline Bouchoux, Mélanie Panarotto, Yasutaka Kakui, Harshil Patel, Frank Uhlmann

    Molecular Cell   78 ( 4 ) 725 - 738.e4  2020.05  [Refereed]

    DOI

  • Efficient Depletion of Fission Yeast Condensin by Combined Transcriptional Repression and Auxin-Induced Degradation

    Yasutaka Kakui, Frank Uhlmann

    Methods in Molecular Biology     25 - 33  2019  [Refereed]

    Authorship:Lead author

    DOI

  • SMC complexes orchestrate the mitotic chromatin interaction landscape

    Yasutaka Kakui, Frank Uhlmann

    Current Genetics   64 ( 2 ) 335 - 339  2018.04  [Refereed]

    Authorship:Lead author, Corresponding author

    DOI PubMed

  • Condensin-mediated remodeling of the mitotic chromatin landscape in fission yeast

    Yasutaka Kakui, Adam Rabinowitz, David J Barry, Frank Uhlmann

    Nature Genetics   49 ( 10 ) 1553 - 1557  2017.10  [Refereed]

    Authorship:Lead author

    DOI PubMed

  • Building chromosomes without bricks

    Yasutaka Kakui, Frank Uhlmann

    Science   356 ( 6344 ) 1233 - 1234  2017.06

    Authorship:Lead author

    DOI PubMed

  • Differentiating the roles of microtubule-associated proteins at meiotic kinetochores during chromosome segregation

    Yasutaka Kakui, Masamitsu Sato

    Chromosoma   125 ( 2 ) 309 - 320  2016.06  [Refereed]

    Authorship:Lead author, Corresponding author

     View Summary

    Meiosis is a specialised cell division process for generating gametes. In contrast to mitosis, meiosis involves recombination followed by two consecutive rounds of cell division, meiosis I and II. A vast field of research has been devoted to understanding the differences between mitotic and meiotic cell divisions from the viewpoint of chromosome behaviour. For faithful inheritance of paternal and maternal genetic information to offspring, two events are indispensable: meiotic recombination, which generates a physical link between homologous chromosomes, and reductional segregation, in which homologous chromosomes move towards opposite poles, thereby halving the ploidy. The cytoskeleton and its regulators play specialised roles in meiosis to accomplish these divisions. Recent studies have shown that microtubule-associated proteins (MAPs), including tumour overexpressed gene (TOG), play unique roles during meiosis. Furthermore, the conserved mitotic protein kinase Polo modulates MAP localisation in meiosis I. As Polo is a well-known regulator of reductional segregation in meiosis, the evidence suggests that Polo constitutes a plausible link between meiosis-specific MAP functions and reductional segregation. Here, we review the latest findings on how the localisation and regulation of MAPs in meiosis differ from those in mitosis, and we discuss conservation of the system between yeast and higher eukaryotes.

    DOI PubMed

  • Module-based construction of plasmids for chromosomal integration of the fission yeast Schizosaccharomyces pombe

    Yasutaka Kakui, Tomonari Sunaga, Kunio Arai, James Dodgson, Liang Ji, Attila Csikasz-Nagy, Rafael Carazo-Salas, Masamitsu Sato

    OPEN BIOLOGY   5 ( 6 )  2015.06  [Refereed]

    Authorship:Lead author, Corresponding author

     View Summary

    Integration of an external gene into a fission yeast chromosome is useful to investigate the effect of the gene product. An easy way to knock-in a gene construct is use of an integration plasmid, which can be targeted and inserted to a chromosome through homologous recombination. Despite the advantage of integration, construction of integration plasmids is energy-and time-consuming, because there is no systematic library of integration plasmids with various promoters, fluorescent protein tags, terminators and selection markers; therefore, researchers are often forced to make appropriate ones through multiple rounds of cloning procedures. Here, we establish materials and methods to easily construct integration plasmids. We introduce a convenient cloning system based on Golden Gate DNA shuffling, which enables the connection of multiple DNA fragments at once: any kind of promoters and terminators, the gene of interest, in combination with any fluorescent protein tag genes and any selection markers. Each of those DNA fragments, called a 'module', can be tandemly ligated in the order we desire in a single reaction, which yields a circular plasmid in a one-step manner. The resulting plasmids can be integrated through standard methods for transformation. Thus, these materials and methods help easy construction of knock-in strains, and this will further increase the value of fission yeast as a model organism.

    DOI PubMed

  • Microtubules and Alp7-Alp14 (TACC-TOG) reposition chromosomes before meiotic segregation

    Yasutaka Kakui, Masamitsu Sato, Naoyuki Okada, Takashi Toda, Masayuki Yamamoto

    Nature Cell Biology   15 ( 7 ) 786 - 796  2013.07  [Refereed]

    Authorship:Lead author

     View Summary

    Tethering kinetochores at spindle poles facilitates their efficient capture and segregation by microtubules at mitotic onset in yeast. During meiotic prophase of fission yeast, however, kinetochores are detached from the poles, which facilitates meiotic recombination but may cause a risk of chromosome mis-segregation during meiosis. How cells circumvent this dilemma remains unclear. Here we show that an extensive microtubule array assembles from the poles at meiosis I onset and retrieves scattered kinetochores towards the poles to prevent chromosome drift. Moreover, the microtubule-associated protein complex Alp7-Alp14 (the fission yeast orthologues of mammalian TACC-TOG) is phosphorylated by Polo kinase, which promotes its meiosis-specific association to the outer kinetochore complex Nuf2-Ndc80 of scattered kinetochores, thereby assisting in capturing remote kinetochores. Although TOG was recently characterized as a microtubule polymerase, Dis1 (the other TOG orthologue in fission yeast), together with the Dam1 complex, plays a role in microtubule shortening to pull kinetochores polewards. Thus, microtubules and their binding proteins uniquely reconstitute chromosome configuration during meiosis. © 2013 Macmillan Publishers Limited. All rights reserved.

    DOI PubMed

  • A novel fission yeast mei4 mutant that allows efficient synchronization of telomere dispersal and the first meiotic division

    Yasutaka Kakui, Masamitsu Sato, Kayoko Tanaka, Masayuki Yamamoto

    Yeast   28 ( 6 ) 467 - 479  2011.06  [Refereed]

    Authorship:Lead author

    DOI PubMed

  • Protein disulfide isomerase-P5, down-regulated in the final stage of boar epididymal sperm maturation, catalyzes disulfide formation to inhibit protein function in oxidative refolding of reduced denatured lysozyme

    Kuniko Akama, Tomoe Horikoshi, Atsushi Sugiyama, Satoko Nakahata, Aoi Akitsu, Nobuyoshi Niwa, Atsushi Intoh, Yasutaka Kakui, Michiko Sugaya, Kazuo Takei, Noriaki Imaizumi, Takaya Sato, Rena Matsumoto, Hitoshi Iwahashi, Shin-ichi Kashiwabara, Tadashi Baba, Megumi Nakamura, Tosifusa Toda

    Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics   1804 ( 6 ) 1272 - 1284  2010.06  [Refereed]

    DOI PubMed

  • Nucleocytoplasmic transport of Alp7/TACC organizes spatiotemporal microtubule formation in fission yeast

    Masamitsu Sato, Naoyuki Okada, Yasutaka Kakui, Masayuki Yamamoto, Minoru Yoshida, Takashi Toda

    EMBO reports   10 ( 10 ) 1161 - 1167  2009.10  [Refereed]

    DOI PubMed

▼display all

Misc

  • コンデンシンはクロマチンの空間配置を再構築することにより分裂期における染色体の凝縮を担う

    角井康貢

       2017

    Authorship:Lead author, Corresponding author

    Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media)  

  • 微小管とTACC-TOG複合体は染色体の配置を変換することにより減数分裂における組換えと正確な染色体分配の連携を制御する

    角井康貢, 佐藤政充

       2013

    Authorship:Lead author, Corresponding author

    Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media)  

Research Projects

  • 染色体構造に基づく卵子劣化の分子基盤の解明

    日本学術振興会  科学研究費助成事業 研究活動スタート支援

    Project Year :

    2020.09
    -
    2022.03
     

    角井 康貢

Presentations

  • 生物進化における染色体構造の制御機構

    角井康貢  [Invited]

    第 200 回 酵母細胞研究会例会 

    Presentation date: 2022.02

  • 真核生物におけるクロマチン相互作用と分裂期染色体形成メカニズム

    第39回染色体ワークショップ・ 第20回核ダイナミクス研究会 

    Presentation date: 2021.12

  • What determines the right size of chromosomes in the cells?

     [Invited]

    Presentation date: 2021.12

  • クロマチン相互作用で可視化する分裂期染色体形成

     [Invited]

    第94回日本生化学会大会 

    Presentation date: 2021.11

Specific Research

  • 減数分裂においてゲノムDNAの半減を制御するクロマチン構造基盤

    2021  

     View Summary

    減数分裂では、遺伝情報をもつゲノムDNAを半減させるために、DNA交換反応により二価染色体が形成される。そこで本研究は、二価染色体の三次元構造を分子レベルで可視化し、減数分裂における染色体構造制御に関わる分子基盤の解明を目的とした。DNAシークエンス解析により染色体構造を決定するために、減数分裂の各ステージに細胞を同調する実験システムを構築した。これにより減数分裂の任意のステージの細胞を効率よく回収できるようになり、染色体の三次元構造解析の基盤を確立することができた。また、二価染色体を形成するためのDNA交換反応を人工的に誘導する実験も立ち上げており、二価染色体の構造制御メカニズムを解明する実験基盤が構築できた。

  • 染色体構造の制御基盤から探る高齢不妊の分子実体

    2021  

     View Summary

    本研究課題は、高齢不妊の背後に潜む生物学的原因探究のため、配偶子形成を担う減数分裂における染色体の三次元構造の制御メカニズムの解明を目的とした。DNAシークエンス解析(Hi-C)により、染色体の三次元構造は、顕微鏡を超えた高解像度の立体情報が得られる。これまで大多数の細胞を用いて行われてきたHi-Cを利用して、細胞ごとに異なる染色体構造を明らかとするために、1細胞から回収した染色体ゲノムDNA由来のDNAシークエンスライブラリーの作成を行なった。本手法の開発により各細胞の染色体構造を1細胞レベルで可視化できるようになるため、本研究成果は、高齢不妊と染色体構造の繋がりを明らかとするための礎を構築したといえる。

  • 減数分裂におけるクロマチン三次元構造の制御機構

    2020  

     View Summary

    本研究課題は、染色体構造を分子レベルで解き明かすことにより、配偶子(卵・精子)を形成するための減数分裂を理解することを目的とした。「Hi−C」による染色体構造の高解像度での可視化には、均一な細胞集団を用いてビッグデータを取得する必要がある。そこで本研究では、シンプルなゲノム構造を持つ分裂酵母を利用して、減数分裂を同調的に誘導する実験システムを確立した。本研究の成果は、減数分裂の進行に伴う染色体構造の時間変化を決定するための実験基盤であり、今後Hi−Cによって染色体の内部構造を分子レベルで解き明かすための礎となる成果といえる。