Shoji Laboratory庄司研究室
Tokyo Univ. of Agriculture and TechnologyLaboratory of RNA Bioinformatics (graduate school)
Laboratory of Nucleic Acid Bioinformatics (undergraduate)日本語

Publications

34 papers

* Co-first author† Corresponding author

2026

  1. Complete transition from chromosomal to cytoplasmic sex determination during prolonged Wolbachia symbiosis

    Takahiro Fukui, Tomohiro Muro, Noriko Matsuda-Imai, Tatsunori Kaneda, Hidetaka Kosako, Hideaki Hiraki, Keisuke Shoji, Takeshi Fujii, Yutaka Suzuki, Atsushi Toyoda, Takehiko Itoh, Takashi Kiuchi, Susumu Katsuma

    Nature Communications 17(1): 104

2025

  1. The Masc-PSI complex directly induces male-type doublesex splicing in silkworms

    Tatsunori Kaneda, Noriko Matsuda-Imai, Hidetaka Kosako, Keisuke Shoji, Masataka G Suzuki, Yutaka Suzuki, Takashi Kiuchi, Susumu Katsuma

    Communications Biology 8(1): 927

  2. Autonomous shaping of the piRNA sequence repertoire by competition between adjacent ping-pong sites

    Jie Yu, Fumiko Kawasaki, Natsuko Izumi, Takashi Kiuchi, Susumu Katsuma, Yukihide Tomari, Keisuke Shoji

    Molecular Cell 85(6): 1134–1146.e4

  3. A novel rhabdovirus persistently infects lepidopteran cell lines

    Takeo Fukushima, Shohei Takamura, Keisuke Shoji, Tomoyo Touguchi, Susumu Katsuma, Masashi Iwanaga

    Virus Research 354: 199548

  4. Transposon–host arms race: a saga of genome evolution

    Yuka W Iwasaki, Keisuke Shoji, Shinichi Nakagawa, Tomoichiro Miyoshi, Yukihide Tomari

    Trends in Genetics 41(5): 369–389Review

2024

  1. The dual role of Spn-E in supporting heterotypic ping-pong piRNA amplification in silkworms

    Natsuko Izumi*, Keisuke Shoji*, Lumi Negishi, Yukihide Tomari

    EMBO Reports 25(5): 11

  2. A potential role of inefficient and non-specific piRNA production from the whole transcriptome cells

    Keisuke Shoji, Yukihide Tomari

    bioRxivPreprint

2023

  1. Non-gonadal somatic piRNA pathways ensure sexual differentiation, larval growth, and wing development in silkworms

    Takashi Kiuchi, Keisuke Shoji, Natsuko Izumi, Yukihide Tomari, Susumu Katsuma

    PLoS Genetics 19(9): e1010912

  2. Masculinizer is not post-transcriptionally regulated by female-specific piRNAs during sex determination in the Asian corn borer, Ostrinia furnacalis

    Takahiro Fukui, Keisuke Shoji, Takashi Kiuchi, Yutaka Suzuki, Susumu Katsuma

    Insect Biochemistry and Molecular Biology 156: 103946

  3. The piRNA cluster torimochi is an expanding transposon in cultured silkworm cells

    Keisuke Shoji, Yusuke Umemura, Susumu Katsuma, Yukihide Tomari

    PLoS Genetics 19(2): e1010632

2022

  1. The mechanisms of siRNA selection by plant Argonaute proteins triggering DNA methylation

    Wei Liu, Keisuke Shoji, Masahiro Naganuma, Yukihide Tomari, Hiro-Oki Iwakawa

    Nucleic Acids Research 50(22): 12997–13010

  2. The two Gtsf paralogs in silkworms orthogonally activate their partner PIWI proteins for target cleavage

    Natsuko Izumi, Keisuke Shoji, Takashi Kiuchi, Susumu Katsuma, Yukihide Tomari

    RNA 29(1): 18–29

  3. A Wolbachia factor for male killing in lepidopteran insects

    Susumu Katsuma, Kanako Hirota, Noriko Matsuda-Imai, Takahiro Fukui, Tomohiro Muro, Kohei Nishino, Hidetaka Kosako, Keisuke Shoji, Hideki Takanashi, Takeshi Fujii, Shin-Ichi Arimura, Takashi Kiuchi

    Nature Communications 13(1): 6764

2021

  1. Cell-free reconstitution reveals the molecular mechanisms for the initiation of secondary siRNA biogenesis in plants

    Yuriki Sakurai, Kyungmin Baeg, Andy Y W Lam, Keisuke Shoji, Yukihide Tomari, Hiro-Oki Iwakawa

    Proc. Natl. Acad. Sci. USA 118(31): e2102889118

  2. H3K4me3 histone modification in baculovirus-infected silkworm cells

    Keisuke Shoji, Ryuhei Kokusho, Munetaka Kawamoto, Yutaka Suzuki, Susumu Katsuma

    Virus Genes 57(5): 459–463

  3. Dynamic subcellular compartmentalization ensures fidelity of piRNA biogenesis in silkworms

    Pui Yuen Chung, Keisuke Shoji, Natsuko Izumi, Yukihide Tomari

    EMBO Reports 22(7): EMBR202051342

  4. Potential for small RNA production against Bombyx mori latent virus in Bombyx mori ovaries

    Susumu Katsuma, Keisuke Shoji, Yutaka Suzuki, Masashi Iwanaga

    Archives of Insect Biochemistry and Physiology 106(2): e21761

  5. CRISPR/Cas9-mediated mutagenesis of Ago2 and Siwi in silkworm cultured cells

    Susumu Katsuma, Keisuke Shoji, Yutaka Suzuki, Takashi Kiuchi

    Gene 768: 145314

2020

  1. Whole-genome sequencing and comparative transcriptome analysis of Bombyx mori nucleopolyhedrovirus La strain

    Shota Fujimoto, Munetaka Kawamoto, Keisuke Shoji, Yutaka Suzuki, Susumu Katsuma, Masashi Iwanaga

    Virus Genes 56(2): 249–259

  2. Zucchini consensus motifs determine the mechanism of pre-piRNA production

    Natsuko Izumi, Keisuke Shoji, Yutaka Suzuki, Susumu Katsuma, Yukihide Tomari

    Nature 578(7794): 311–316

2019

  1. Masc-induced dosage compensation in silkworm cultured cells

    Susumu Katsuma, Keisuke Shoji, Yudai Sugano, Yutaka Suzuki, Takashi Kiuchi

    FEBS Open Bio 9(9): 1573–1579

  2. VCP machinery mediates autophagic degradation of empty Argonaute

    Hotaka Kobayashi, Keisuke Shoji, Kaori Kiyokawa, Lumi Negishi, Yukihide Tomari

    Cell Reports 28(5): 1144–1153.e4

  3. Iruka eliminates dysfunctional Argonaute by selective ubiquitination of its empty state

    Hotaka Kobayashi, Keisuke Shoji, Kaori Kiyokawa, Lumi Negishi, Yukihide Tomari

    Molecular Cell 73(1): 119–129.e5

2018

  1. In vivo masculinizing function of the Ostrinia furnacalis Masculinizer gene

    Takahiro Fukui, Takashi Kiuchi, Keisuke Shoji, Munetaka Kawamoto, Toru Shimada, Susumu Katsuma

    Biochem. Biophys. Res. Commun. 503(3): 1768–1772

  2. Transcriptome profiling reveals infection strategy of an insect maculavirus

    Susumu Katsuma, Munetaka Kawamoto, Keisuke Shoji, Takahiro Aizawa, Takashi Kiuchi, Natsuko Izumi, Moe Ogawa, Takaaki Mashiko, Hideki Kawasaki, Sumio Sugano, Yukihide Tomari, Yutaka Suzuki, Masashi Iwanaga

    DNA Research 25(3): 277–286

2017

  1. Artificial “ping-pong” cascade of PIWI-interacting RNA in silkworm cells

    Keisuke Shoji, Yutaka Suzuki, Sumio Sugano, Toru Shimada, Susumu Katsuma

    RNA 23(1): 86–97

2016

  1. Identification and functional analysis of the pre-piRNA 3′ trimmer in silkworms

    Natsuko Izumi, Keisuke Shoji, Yuriko Sakaguchi, Shozo Honda, Yohei Kirino, Tsutomu Suzuki, Susumu Katsuma, Yukihide Tomari

    Cell 164(5): 962–973

2015

  1. Is the expression of sense and antisense transgenes really sufficient for artificial piRNA production?

    Keisuke Shoji, Susumu Katsuma

    Current Biology 25(16): R708–R710

  2. The endosymbiotic bacterium Wolbachia selectively kills male hosts by targeting the masculinizing gene

    Takahiro Fukui, Munetaka Kawamoto, Keisuke Shoji, Takashi Kiuchi, Sumio Sugano, Toru Shimada, Yutaka Suzuki, Susumu Katsuma

    PLoS Pathogens 11(7): e1005048

  3. Sexually biased transcripts at early embryonic stages of the silkworm depend on the sex chromosome constitution

    Munetaka Kawamoto, Hikaru Koga, Takashi Kiuchi, Keisuke Shoji, Sumio Sugano, Toru Shimada, Yutaka Suzuki, Susumu Katsuma

    Gene 560(1): 50–56

  4. Silkworm HP1a transcriptionally enhances highly expressed euchromatic genes via association with their transcription start sites

    Keisuke Shoji, Kahori Hara, Munetaka Kawamoto, Takashi Kiuchi, Shinpei Kawaoka, Sumio Sugano, Toru Shimada, Yutaka Suzuki, Susumu Katsuma

    Nucleic Acids Research 42(18): 11462–11471

2014

  1. A single female-specific piRNA is the primary determiner of sex in the silkworm

    Takashi Kiuchi, Hikaru Koga, Munetaka Kawamoto, Keisuke Shoji, Hiroki Sakai, Yuji Arai, Genki Ishihara, Shinpei Kawaoka, Sumio Sugano, Toru Shimada, Yutaka Suzuki, Masataka G Suzuki, Susumu Katsuma

    Nature 509(7502): 633–636

2013

  1. Characterization of a novel chromodomain-containing gene from the silkworm, Bombyx mori

    Keisuke Shoji, Takashi Kiuchi, Kahori Hara, Munetaka Kawamoto, Shinpei Kawaoka, Shin-Ichi Arimura, Nobuhiro Tsutsumi, Sumio Sugano, Yutaka Suzuki, Toru Shimada, Susumu Katsuma

    Gene 527(2): 649–654

  2. The comprehensive epigenome map of piRNA clusters

    Shinpei Kawaoka, Kahori Hara, Keisuke Shoji, Maki Kobayashi, Toru Shimada, Sumio Sugano, Yukihide Tomari, Yutaka Suzuki, Susumu Katsuma

    Nucleic Acids Research 41(3): 1581–1590