2026/08/28 更新

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写真a

ハンダ　テツヤ
半田 哲也
HANDA TETSUYA
所属
生体防御医学研究所 学際生命科学部門 准教授
職名
准教授
外部リンク

経歴

  • 九州大学 生体防御医学研究所 准教授 

    2026年5月

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    国名：日本国

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

    2020年9月 - 2026年4月

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    国名：グレートブリテン・北アイルランド連合王国(英国)

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  • 東京工業大学 科学技術創成研究院 細胞制御工学研究センター 特任助教 

    2018年4月 - 2020年9月

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  • 東京工業大学 科学技術創成研究院 細胞制御工学研究センター 研究員 

    2016年4月 - 2018年3月

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  • 東京工業大学 生命理工学院 産学官連携研究員 

    2014年9月 - 2016年3月

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  • 大阪大学 大学院理学研究科 生物科学専攻 特任研究員 

    2012年10月 - 2014年8月

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  • 日本学術振興会特別研究員（DC2）   

    2009年4月 - 2011年3月

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学歴

  • 大阪大学   大学院 理学研究科   生物科学専攻

    2006年4月 - 2012年9月

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受賞

  • 手島精一記念研究賞

    2020年2月   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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論文

  • HMGA1 orchestrates chromatin compartmentalization and sequesters genes into 3D networks coordinating senescence heterogeneity 査読 国際共著 国際誌

    Olan, I; Ando-Kuri, M; Parry, AJ; Handa, T; Schoenfelder, S; Fraser, P; Ohkawa, Y; Kimura, H; Narita, M; Narita, M

    NATURE COMMUNICATIONS   15 ( 1 )   6891   2024年8月   （ ISSN:20411723 eISSN:2041-1723 ）

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    記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：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 査読

    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年8月   （ ISSN:0021-9525 ）

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    記述言語：英語   掲載種別：研究論文（学術雑誌）  

    DOI： 10.1083/jcb.202310084

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  • Transient Methionine DeprivationTriggers Histone Modification and Potentiates Differentiation of Induced Pluripotent Stem Cells 査読

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

    Stem Cells   41 ( 3 )   271 - 286   2023年3月   （ ISSN:1549-4918 ）

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    記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：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. and Handa, T. and Narita, M.

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

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    掲載種別：研究論文（学術雑誌）  

    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 査読

    Esquivel-Ch{\'a}vez, A. and Maki, T. and Tsubouchi, H. and Handa, T. and Kimura, H. and Haber, J.E. and Thon, G. and Iwasaki, H.

    Genes and Genetic Systems   97 ( 3 )   123 - 138   2022年6月   （ ISSN:1341-7568 eISSN:1880-5779 ）

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    掲載種別：研究論文（学術雑誌）   出版者・発行元：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 査読 国際誌

    Uchino S., Ito Y., Sato Y., Handa T., Ohkawa Y., Tokunaga M., Kimura H.

    Journal of Cell Biology   221 ( 2 )   2022年2月   （ ISSN:00219525 ）

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    記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：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 Ser2phmintbody 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) 査読

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

    Journal of Cell Biology   220 ( 12 )   2021年12月   （ ISSN:1540-8140 eISSN:1540-8140 ）

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    記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：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 査読

    Maehara, K. and Tomimatsu, K. and Harada, A. and Tanaka, K. and Sato, S. and Fukuoka, M. and Okada, S. and Handa, T. and Kurumizaka, H. and Saitoh, N. and Kimura, H. and Ohkawa, Y.

    Molecular Systems Biology   17 ( 11 )   e10323   2021年11月   （ ISSN:1744-4292 eISSN:1744-4292 ）

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    記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：EMBO  

    DOI： 10.15252/msb.202110323

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    その他リンク： 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 査読

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

    Nature Communications   12 ( 1 )   3158   2021年5月   （ ISSN:2041-1723 eISSN:2041-1723 ）

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    記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Springer Science and Business Media LLC  

    DOI： 10.1038/s41467-021-23417-0

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    その他リンク： 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 査読

    Tjalsma, S.J.D. and Hori, M. and Sato, Y. and Bousard, A. and Ohi, A. and Raposo, A.C. and Roensch, J. and Le Saux, A. and Nogami, J. and Maehara, K. and Kujirai, T. and Handa, T. and Bag{\'e}s-Arnal, S. and Ohkawa, Y. and Kurumizaka, H. and da Rocha, S.T. and ?ylicz, J.J. and Kimura, H. and Heard, E.

    EMBO Reports   22 ( 3 )   e51989   2021年2月   （ ISSN:1469-221X eISSN:1469-3178 ）

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    記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：EMBO  

    DOI： 10.15252/embr.202051989

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    その他リンク： https://onlinelibrary.wiley.com/doi/full-xml/10.15252/embr.202051989

  • Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input 査読 国際誌

    Handa, T. and Harada, A. and Maehara, K. and Sato, S. and Nakao, M. and Goto, N. and Kurumizaka, H. and Ohkawa, Y. and Kimura, H.

    Nature Protocols   15 ( 10 )   3334 - 3360   2020年8月   （ ISSN:1754-2189 eISSN:1750-2799 ）

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    担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：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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    その他リンク： 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. 査読 国際誌

    Yamagata, K. and Nagai, K. and Miyamoto, H. and Anzai, M. and Kato, H. and Miyamoto, K. and Kurosaka, S. and Azuma, R. and Kolodeznikov, I.I. and Protopopov, A.V. and Plotnikov, V.V. and Kobayashi, H. and Kawahara-Miki, R. and Kono, T. and Uchida, M. and Shibata, Y. and Handa, T. and Kimura, H. and Hosoi, Y. and Mitani, T. and Matsumoto, K. and Iritani, A.

    Scientific reports   9 ( 1 )   4050 - 4050   2019年3月   （ ISSN:20452322 ）

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    記述言語：英語   掲載種別：研究論文（学術雑誌）  

    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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    その他リンク： http://orcid.org/0000-0001-7707-0195

  • A chromatin integration labelling method enables epigenomic profiling with lower input. 査読 国際誌

    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年2月   （ ISSN:1465-7392 ）

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    記述言語：英語   掲載種別：研究論文（学術雑誌）  

    DOI： 10.1038/s41556-018-0248-3

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  • Shelterin promotes tethering of late replication origins to telomeres for replication-timing control. 査読 国際誌

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

    The EMBO journal   37 ( 15 )   2018年8月   （ ISSN:0261-4189 ）

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    記述言語：英語   掲載種別：研究論文（学術雑誌）  

    DOI： 10.15252/embj.201898997

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

    Yamazaki, T. and Hatano, Y. and Handa, T. and Kato, S. and Hoida, K. and Yamamura, R. and Fukuyama, T. and Uematsu, T. and Kobayashi, N. and Kimura, H. and Yamagata, K.

    PLoS ONE   12 ( 5 )   e0177764   2017年5月   （ ISSN:1932-6203 ）

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    記述言語：英語   掲載種別：研究論文（学術雑誌）  

    DOI： 10.1371/journal.pone.0177764

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    その他リンク： http://orcid.org/0000-0001-7707-0195

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

    Tashiro, S. and Handa, T. and Matsuda, A. and Ban, T. and Takigawa, T. and Miyasato, K. and Ishii, K. and Kugou, K. and Ohta, K. and Hiraoka, Y. and Masukata, H. and Kanoh, J.

    Nature Communications   7   10393   2016年1月   （ ISSN:2041-1723 ）

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    記述言語：英語   掲載種別：研究論文（学術雑誌）  

    DOI： 10.1038/ncomms10393

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    その他リンク： 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. 査読

    Handa, T. and Kanke, M. and Takahashi, T.S. and Nakagawa, T. and Masukata, H.

    Molecular biology of the cell   23 ( 16 )   3240 - 3253   2012年8月   （ ISSN:1059-1524 eISSN:1939-4586 ）

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    担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

    DOI： 10.1091/mbc.E12-05-0339

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    その他リンク： 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年12月

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    記述言語：日本語  

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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年1月   （ ISSN:1343-0971 ）

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    記述言語：日本語   出版者・発行元：(株)メディカルドゥ  

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