Updated on 2026/08/28

Information

 

写真a

 
HANDA TETSUYA
 
Organization
Medical Institute of Bioregulation Department of Multidisciplinary Life Science Associate Professor
Title
Associate Professor
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Research History

  • Kyushu University Medical Institute of Bioregulation Associate Professor 

    2026.5

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    Country：Japan

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  • Cancer Research UK Cambridge Institute, University of Cambridge  Research Associate 

    2020.9 - 2026.4

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    Country：United Kingdom

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  • Tokyo Institute of Technology Cell Biology Center, Institute of Innovative Research Specially Appointed Assistant Professor 

    2018.4 - 2020.9

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  • Tokyo Institute of Technology Cell Biology Center, Institute of Innovative Research Postdoctoral Fellow 

    2016.4 - 2018.3

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  • Tokyo Institute of Technology Graduate School of Bioscience and Biotechnology Postdoctoral Fellow 

    2014.9 - 2016.3

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  • Osaka University Department of Biological Sciences, Graduate School of Science Postdoctoral Fellow 

    2012.10 - 2014.8

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  • 日本学術振興会特別研究員（DC2）   

    2009.4 - 2011.3

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Education

  • Osaka University   Graduate School of Science   Department of Biological Sciences

    2006.4 - 2012.9

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Awards

  • 手島精一記念研究賞

    2020.2   東京工業大学  

    原田 哲仁, 前原 一満, 半田 哲也, 有村 泰宏, 野上 順平, 林-高中 陽子, 白髭 克彦, 胡桃坂 仁志, 木村 宏, 大川 恭行

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Papers

  • HMGA1 orchestrates chromatin compartmentalization and sequesters genes into 3D networks coordinating senescence heterogeneity Reviewed International coauthorship International journal

    Ioana Olan, Masami Ando-Kuri, Aled J. Parry, Tetsuya Handa, Stefan Schoenfelder, Peter Fraser, Yasuyuki Ohkawa, Hiroshi Kimura, Masako Narita, Masashi Narita

    Nature Communications   15 ( 1 )   6891   2024.8   （ ISSN:20411723 eISSN:2041-1723 ）

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

    HMGA1 is an abundant non-histone chromatin protein that has been implicated in embryonic development, cancer, and cellular senescence, but its specific role remains elusive. Here, we combine functional genomics approaches with graph theory to investigate how HMGA1 genomic deposition controls high-order chromatin networks in an oncogene-induced senescence model. While the direct role of HMGA1 in gene activation has been described previously, we find little evidence to support this. Instead, we show that the heterogeneous linear distribution of HMGA1 drives a specific 3D chromatin organization. HMGA1-dense loci form highly interactive networks, similar to, but independent of, constitutive heterochromatic loci. This, coupled with the exclusion of HMGA1-poor chromatin regions, leads to coordinated gene regulation through the repositioning of genes. In the absence of HMGA1, the whole process is largely reversed, but many regulatory interactions also emerge, amplifying the inflammatory senescence-associated secretory phenotype. Such HMGA1-mediated fine-tuning of gene expression contributes to the heterogeneous nature of senescence at the single-cell level. A similar ‘buffer’ effect of HMGA1 on inflammatory signalling is also detected in lung cancer cells. Our study reveals a mechanism through which HMGA1 modulates chromatin compartmentalization and gene regulation in senescence and beyond.

    DOI： 10.1038/s41467-024-51153-8

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  • ISWI chromatin remodeling complexes recruit NSD2 and H3K36me2 in pericentromeric heterochromatin Reviewed

    Goto, N., Suke, K., Yonezawa, N., Nishihara, H., Handa, T., Sato, Y., Kujirai, T., Kurumizaka, H., Yamagata, K., Kimura, H.

    Journal of Cell Biology   223 ( 8 )   2024.8   （ ISSN:0021-9525 ）

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    DOI： 10.1083/jcb.202310084

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  • Transient Methionine Deprivation Triggers Histone Modification and Potentiates Differentiation of Induced Pluripotent Stem Cells Reviewed

    Ozawa, H., Kambe, A., Hibi, K., Murakami, S., Oikawa, A., Handa, T., Fujiki, K., Nakato, R., Shirahige, K., Kimura, H., Shiraki, N., Kume, S.

    Stem cells (Dayton, Ohio)   41 ( 3 )   271 - 286   2023.3   （ ISSN:1549-4918 ）

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press ({OUP})  

    DOI： 10.1093/stmcls/sxac082

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  • Beyond SAHF: An integrative view of chromatin compartmentalization during senescence

    Olan, I., Handa, T., Narita, M.

    Current Opinion in Cell Biology   83   2023   （ ISSN:1879-0410 ）

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    Publishing type：Research paper (scientific journal)  

    DOI： 10.1016/j.ceb.2023.102206

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  • Euchromatin factors HULC and Set1C affect heterochromatin organization and mating-type switching in fission yeast Schizosaccharomyces pombe Reviewed

    Alfredo Esquivel-Chávez, Takahisa Maki, Hideo Tsubouchi, Testuya Handa, Hiroshi Kimura, James E. Haber, Geneviève Thon, Hiroshi Iwasaki

    Genes & Genetic Systems   97 ( 3 )   123 - 138   2022.6   （ ISSN:1341-7568 eISSN:1880-5779 ）

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    Publishing type：Research paper (scientific journal)   Publisher：Genetics Society of Japan  

    DOI： 10.1266/ggs.22-00012

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  • Live imaging of transcription sites using an elongating RNA polymerase II-specific probe. Reviewed International journal

    Satoshi Uchino, Yuma Ito, Yuko Sato, Tetsuya Handa, Yasuyuki Ohkawa, Makio Tokunaga, Hiroshi Kimura

    The Journal of cell biology   221 ( 2 )   2022.2   （ ISSN:00219525 ）

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Journal of Cell Biology  

    In eukaryotic nuclei, most genes are transcribed by RNA polymerase II (RNAP2), whose regulation is a key to understanding the genome and cell function. RNAP2 has a long heptapeptide repeat (Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7), and Ser2 is phosphorylated on an elongation form. To detect RNAP2 Ser2 phosphorylation (RNAP2 Ser2ph) in living cells, we developed a genetically encoded modification-specific intracellular antibody (mintbody) probe. The RNAP2 Ser2ph-mintbody exhibited numerous foci, possibly representing transcription "factories," and foci were diminished during mitosis and in a Ser2 kinase inhibitor. An in vitro binding assay using phosphopeptides confirmed the mintbody's specificity. RNAP2 Ser2ph-mintbody foci were colocalized with proteins associated with elongating RNAP2 compared with factors involved in the initiation. These results support the view that mintbody localization represents the sites of RNAP2 Ser2ph in living cells. RNAP2 Ser2ph-mintbody foci showed constrained diffusional motion like chromatin, but they were more mobile than DNA replication domains and p300-enriched foci, suggesting that the elongating RNAP2 complexes are separated from more confined chromatin domains.

    DOI： 10.1083/jcb.202104134

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  • High-throughput single-cell epigenomic profiling by targeted insertion of promoters (Tip-seq) Reviewed

    Bartlett, D.A., Dileep, V., Handa, T., Ohkawa, Y., Kimura, H., Henikoff, S., Gilbert, D.M.

    Journal of Cell Biology   220 ( 12 )   2021.12   （ ISSN:1540-8140 eISSN:1540-8140 ）

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Rockefeller University Press  

    DOI： 10.1083/jcb.202103078

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  • Modeling population size independent tissue epigenomes by ChIL‐seq with single thin sections Reviewed

    Kazumitsu Maehara, Kosuke Tomimatsu, Akihito Harada, Kaori Tanaka, Shoko Sato, Megumi Fukuoka, Seiji Okada, Tetsuya Handa, Hitoshi Kurumizaka, Noriko Saitoh, Hiroshi Kimura, Yasuyuki Ohkawa

    Molecular Systems Biology   17 ( 11 )   e10323   2021.11   （ ISSN:1744-4292 eISSN:1744-4292 ）

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

    DOI： 10.15252/msb.202110323

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    Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.15252/msb.202110323

  • Live-cell imaging reveals the spatiotemporal organization of endogenous RNA polymerase II phosphorylation at a single gene Reviewed

    Forero-Quintero, L.S., Raymond, W., Handa, T., Saxton, M.N., Morisaki, T., Kimura, H., Bertr, , E., Munsky, B., Stasevich, T.J.

    Nature Communications   12 ( 1 )   3158   2021.5   （ ISSN:2041-1723 eISSN:2041-1723 ）

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

    DOI： 10.1038/s41467-021-23417-0

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    Other Link： http://www.nature.com/articles/s41467-021-23417-0

  • H4K20me1 and H3K27me3 are concurrently loaded onto the inactive X chromosome but dispensable for inducing gene silencing Reviewed

    Sjoerd J D Tjalsma, Mayako Hori, Yuko Sato, Aurelie Bousard, Akito Ohi, Ana Cláudia Raposo, Julia Roensch, Agnes Le Saux, Jumpei Nogami, Kazumitsu Maehara, Tomoya Kujirai, Tetsuya Handa, Sandra Bagés‐Arnal, Yasuyuki Ohkawa, Hitoshi Kurumizaka, Simão Teixeira da Rocha, Jan J Żylicz, Hiroshi Kimura, Edith Heard

    EMBO reports   22 ( 3 )   e51989   2021.2   （ ISSN:1469-221X eISSN:1469-3178 ）

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

    DOI： 10.15252/embr.202051989

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    Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.15252/embr.202051989

  • Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input Reviewed International journal

    Tetsuya Handa, Akihito Harada, Kazumitsu Maehara, Shoko Sato, Masaru Nakao, Naoki Goto, Hitoshi Kurumizaka, Yasuyuki Ohkawa, Hiroshi Kimura

    Nature Protocols   15 ( 10 )   3334 - 3360   2020.8   （ ISSN:1754-2189 eISSN:1750-2799 ）

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

    Cell identity is determined by the selective activation or silencing of specific genes via transcription factor binding and epigenetic modifications on the genome. Chromatin immunoprecipitation (ChIP) has been the standard technique for mapping the sites of transcription factor binding and histone modification. Recently, alternative methods to ChIP have been developed for addressing the increasing demands for low-input epigenomic profiling. Chromatin integration labeling (ChIL) followed by sequencing (ChIL-seq) has been demonstrated to be particularly useful for epigenomic profiling of low-input samples or even single cells because the technique amplifies the target genomic sequence before cell lysis. After labeling the target protein or modification in situ with an oligonucleotide-conjugated antibody (ChIL probe), the nearby genome sequence is amplified by Tn5 transposase-mediated transposition followed by T7 RNA polymerase-mediated transcription. ChIL-seq enables the detection of the antibody target localization under a fluorescence microscope and at the genomic level. Here we describe the detailed protocol of ChIL-seq with assessment methods for the key steps, including ChIL probe reaction, transposition, in situ transcription and sequencing library preparation. The protocol usually takes 3 d to prepare the sequencing library, including overnight incubations for the ChIL probe reaction and in situ transcription. The ChIL probe can be separately prepared and stored for several months, and its preparation and evaluation protocols are also documented in detail. An optional analysis for multiple targets (multitarget ChIL-seq) is also described. We anticipate that the protocol presented here will make the ChIL technique more widely accessible for analyzing precious samples and facilitate further applications.

    DOI： 10.1038/s41596-020-0375-8

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    Other Link： http://www.nature.com/articles/s41596-020-0375-8

  • Signs of biological activities of 28,000-year-old mammoth nuclei in mouse oocytes visualized by live-cell imaging. Reviewed International journal

    Kazuo Yamagata, Kouhei Nagai, Hiroshi Miyamoto, Masayuki Anzai, Hiromi Kato, Kei Miyamoto, Satoshi Kurosaka, Rika Azuma, Igor I Kolodeznikov, Albert V Protopopov, Valerii V Plotnikov, Hisato Kobayashi, Ryouka Kawahara-Miki, Tomohiro Kono, Masao Uchida, Yasuyuki Shibata, Tetsuya Handa, Hiroshi Kimura, Yoshihiko Hosoi, Tasuku Mitani, Kazuya Matsumoto, Akira Iritani

    Scientific reports   9 ( 1 )   4050 - 4050   2019.3   （ ISSN:20452322 ）

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    The 28,000-year-old remains of a woolly mammoth, named 'Yuka', were found in Siberian permafrost. Here we recovered the less-damaged nucleus-like structures from the remains and visualised their dynamics in living mouse oocytes after nuclear transfer. Proteomic analyses demonstrated the presence of nuclear components in the remains. Nucleus-like structures found in the tissue homogenate were histone- and lamin-positive by immunostaining. In the reconstructed oocytes, the mammoth nuclei showed the spindle assembly, histone incorporation and partial nuclear formation; however, the full activation of nuclei for cleavage was not confirmed. DNA damage levels, which varied among the nuclei, were comparable to those of frozen-thawed mouse sperm and were reduced in some reconstructed oocytes. Our work provides a platform to evaluate the biological activities of nuclei in extinct animal species.

    DOI： 10.1038/s41598-019-40546-1

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    Other Link： http://orcid.org/0000-0001-7707-0195

  • A chromatin integration labelling method enables epigenomic profiling with lower input. Reviewed International journal

    Harada A, Maehara K, Handa T, Arimura Y, Nogami J, Hayashi-Takanaka Y, Shirahige K, Kurumizaka H, Kimura H, Ohkawa Y

    Nature cell biology   21 ( 2 )   287 - 296   2019.2   （ ISSN:1465-7392 ）

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

    DOI： 10.1038/s41556-018-0248-3

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  • Shelterin promotes tethering of late replication origins to telomeres for replication-timing control. Reviewed International journal

    Ogawa S, Kido S, Handa T, Ogawa H, Asakawa H, Takahashi TS, Nakagawa T, Hiraoka Y, Masukata H

    The EMBO journal   37 ( 15 )   2018.8   （ ISSN:0261-4189 ）

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

    DOI： 10.15252/embj.201898997

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  • Targeted DNA methylation in pericentromeres with genome editing-based artificial DNA methyltransferase Reviewed

    Taiga Yamazaki, Yu Hatano, Tetsuya Handa, Sakiko Kato, Kensuke Hoida, Rui Yamamura, Takashi Fukuyama, Takayuki Uematsu, Noritada Kobayashi, Hiroshi Kimura, Kazuo Yamagata

    PLOS ONE   12 ( 5 )   e0177764   2017.5   （ ISSN:1932-6203 ）

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

    DOI： 10.1371/journal.pone.0177764

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    Other Link： http://orcid.org/0000-0001-7707-0195

  • Shugoshin forms a specialized chromatin domain at subtelomeres that regulates transcription and replication timing Reviewed

    Sanki Tashiro, Tetsuya Handa, Atsushi Matsuda, Takuto Ban, Toru Takigawa, Kazumi Miyasato, Kojiro Ishii, Kazuto Kugou, Kunihiro Ohta, Yasushi Hiraoka, Hisao Masukata, Junko Kanoh

    NATURE COMMUNICATIONS   7   10393   2016.1   （ ISSN:2041-1723 ）

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

    DOI： 10.1038/ncomms10393

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    Other Link： http://orcid.org/0000-0001-7707-0195

  • DNA polymerization-independent functions of DNA polymerase epsilon in assembly and progression of the replisome in fission yeast Reviewed

    Tetsuya Handa, Mai Kanke, Tatsuro S. Takahashi, Takuro Nakagawa, Hisao Masukata

    MOLECULAR BIOLOGY OF THE CELL   23 ( 16 )   3240 - 3253   2012.8   （ ISSN:1059-1524 eISSN:1939-4586 ）

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

    DOI： 10.1091/mbc.E12-05-0339

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    Other Link： http://orcid.org/0000-0001-7707-0195

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MISC

  • 1細胞レベルで転写因子やヒストン修飾のゲノム上の局在を特定するーChIL-seq

    半田 哲也

    実験医学別冊 - エピゲノムをもっと見るための クロマチン解析実践プロトコール (分担執筆)   2020.12

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    Language：Japanese  

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  • ヒストン修飾解析の最前線

    半田 哲也, 木村 宏

    遺伝子医学 通巻31号(復刊6号) 特集/エピゲノム医療 (分担執筆)   10 ( 1 )   124 - 129   2020.1   （ ISSN:1343-0971 ）

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    Language：Japanese   Publisher：(株)メディカルドゥ  

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