Publications

HOMEPublications

Publications

2024

  • Murase Y, Yokogawa R, Yabuta Y, Nagano M, Katou Y, Mizuyama M, Kitamura A, Puangsricharoen P, Yamashiro C,
    Hu B, Mizuta K, Tsujimura T, Yamamoto T, Ogata K, Ishihama Y, Saitou M.
    In vitro reconstitution of epigenetic reprogramming in the human germ line.
    Nature. 2024 May 20. doi: 10.1038/s41586-024-07526-6. Epub ahead of print. PMID: 38768632.

2023

  • Gyobu-Motani S, Yabuta Y, Mizuta K, Katou Y, Okamoto I, Kawasaki M, Kitamura A, Tsukiyama T, Iwatani C, Tsuchiya H, Tsujimura T, Yamamoto T, Nakamura T, Saitou M.
    Induction of fetal meiotic oocytes from embryonic stem cells in cynomolgus monkeys.
    EMBO J. 2023 May 2;42(9):e112962. doi: 10.15252/embj.2022112962. Epub 2023 Mar 16. PMID: 36929479; PMCID: PMC10152148.

2022

  • Yamanaka Y, Hamidi S, Yoshioka-Kobayashi K, Munira S, Sunadome K, Zhang Y, Kurokawa Y, Ericsson R, Mieda A, Thompson JL, Kerwin J, Lisgo S, Yamamoto T, Moris N, Martinez-Arias A, Tsujimura T, Alev C.
    Reconstituting human somitogenesis in vitro.
    Nature. 2022 Dec 21. doi: 10.1038/s41586-022-05649-2. Epub ahead of print. PMID: 36543322.

Publications supported by SignAC

2024

  • Kitai Y, Toriu N, Yoshikawa T, Sahara Y, Kinjo S, Shimizu Y, Sato Y, Oguchi A, Yamada R, Kondo M, Uchino E,
    Taniguchi K, Arai H, Sasako T, Haga H, Fukuma S, Kubota N, Kadowaki T, Takasato M, Murakawa Y, Yanagita M.
    Female sex hormones inversely regulate acute kidney disease susceptibility throughout life.
    Kidney Int. 2024 Nov 1:S0085-2538(24)00712-9. doi: 10.1016/j.kint.2024.08.034. Epub ahead of print.
    PMID: 39503698.
  • Nakamuta S, Zhang Z, Nikaido M, Yokoyama T, Yamamoto Y, Nakamuta N.
    Type 2 vomeronasal receptor expression in the olfactory organ of African lungfish, Protopterus annectens.
    Cell Tissue Res. 2024 Sep 30. doi: 10.1007/s00441-024-03918-2. Epub ahead of print. PMID: 39347998.
  • Deguchi S, Kosugi K, Takeishi N, Watanabe Y, Morimoto S, Negoro R, Yokoi F, Futatsusako H, Nakajima-Koyama M, Iwasaki M, Yamamoto T, Kawaguchi Y, Torisawa YS, Takayama K.
    Construction of multilayered small intestine-like tissue by reproducing interstitial flow.
    Cell Stem Cell. 2024 Sep 5;31(9):1315-1326.e8. doi: 10.1016/j.stem.2024.06.012. Epub 2024 Jul 11. PMID: 38996472.
  • Oguchi A, Suzuki A, Komatsu S, Yoshitomi H, Bhagat S, Son R, Bonnal RJP, Kojima S, Koido M, Takeuchi K,
    Myouzen K, Inoue G, Hirai T, Sano H, Takegami Y, Kanemaru A, Yamaguchi I, Ishikawa Y, Tanaka N,Hirabayashi S,
    Konishi R, Sekito S, Inoue T, Kere J, Takeda S, Takaori-Kondo A, Endo I, Kawaoka S, Kawaji H, Ishigaki K,
    Ueno H, Hayashizaki Y, Pagani M, Carninci P, Yanagita M; ITEC Consortium‡; Parrish N, Terao C, Yamamoto K,
    Murakawa Y; ITEC Consortium Members.
    An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases.
    Science. 2024 Jul 5;385(6704):eadd8394. doi: 10.1126/science.add8394. Epub 2024 Jul 5. PMID: 38963856.
  • Murase Y, Yokogawa R, Yabuta Y, Nagano M, Katou Y, Mizuyama M, Kitamura A, Puangsricharoen P, Yamashiro C,
    Hu B, Mizuta K, Tsujimura T, Yamamoto T, Ogata K, Ishihama Y, Saitou M.
    In vitro reconstitution of epigenetic reprogramming in the human germ line.
    Nature. 2024 May 20. doi: 10.1038/s41586-024-07526-6. Epub ahead of print. PMID: 38768632.
  • Wang Z, Numada A, Wagai F, Oda Y, Ohgushi M, Maki K, Adachi T, Eiraku M.
    Spatial cell fate manipulation of human pluripotent stem cells by controlling the microenvironment using photocurable hydrogel.
    Development. 2024 Mar 15;151(6):dev201621. doi: 10.1242/dev.201621. Epub 2024 Mar 21. PMID: 38512805; PMCID: PMC11006369.
  • Seto Y, Ogihara R, Takizawa K, Eiraku M.
    In vitro induction of patterned branchial arch-like aggregate from human pluripotent stem cells.
    Nat Commun. 2024 Feb 14;15(1):1351. doi: 10.1038/s41467-024-45285-0. PMID: 38355589.

2023

  • Ishikawa M, Sugino S, Masuda Y, Tarumoto Y, Seto Y, Taniyama N, Wagai F, Yamauchi Y, Kojima Y, Kiryu H, Yusa K, Eiraku M, Mochizuki A.
    RENGE infers gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations.
    Commun Biol. 2023 Dec 28;6(1):1290. doi: 10.1038/s42003-023-05594-4. PMID: 38155269; PMCID: PMC10754834.
  • Okubo T, Rivron N, Kabata M, Masaki H, Kishimoto K, Semi K, Nakajima-Koyama M, Kunitomi H, Kaswandy B, Sato H, Nakauchi H, Woltjen K, Saitou M, Sasaki E, Yamamoto T, Takashima Y.
    Hypoblast from human pluripotent stem cells regulates epiblast development.
    Nature. 2023 Dec 5. doi: 10.1038/s41586-023-06871-2. Epub ahead of print. PMID: 38052228.
  • Zhao Z, Ito A, Kuroki H, Aoyama T.
    Analysis of Molecular Changes and Features in Rat Knee Osteoarthritis Cartilage: Progress From Cellular Changes to Structural Damage.
    Cartilage. 2023 Nov 17:19476035231213174. doi: 10.1177/19476035231213174.Epub ahead of print. PMID: 37978830.
  • Kanatsu-Shinohara M, Shiromoto Y, Ogonuki N, Inoue K, Hattori S, Miura K, Watanabe N, Hasegawa A, Mochida K, Yamamoto T, Miyakawa T, Ogura A, Shinohara T.
    Intracytoplasmic sperm injection induces transgenerational abnormalities in mice.
    J Clin Invest. 2023 Nov 15;133(22):e170140. doi: 10.1172/JCI170140. PMID: 37966118; PMCID: PMC10645388.
  • Aoki K, Hyuga M, Tarumoto Y, Nishibuchi G, Ueda A, Ochi Y, Sugino S, Mikami T, Kobushi H, Kato I, Akahane K, Inukai T, Takaori-Kondo A, Takita J, Ogawa S, Yusa K.
    Canonical BAF complex regulates the oncogenic program in human T-cell acute lymphoblastic leukemia.
    Blood. 2023 Nov 3:blood.2023020857. doi: 10.1182/blood.2023020857. Epub ahead of print. PMID: 37922452.
  • Yoshikawa T, Oguchi A, Toriu N, Sato Y, Kobayashi T, Ogawa O, Haga H, Sakurai S, Yamamoto T, Murakawa Y,
    Yanagita M.
    Tertiary Lymphoid Tissues Are Microenvironments with Intensive Interactions between Immune Cells and Proinflammatory Parenchymal Cells in Aged Kidneys.
    J Am Soc Nephrol. 2023 Oct 1;34(10):1687-1708. doi: 10.1681/ASN.0000000000000202. Epub 2023 Aug 7. PMID: 37548710; PMCID: PMC10561819.
  • Ikeda H, Miyao S, Nagaoka S, Takashima T, Law SM, Yamamoto T, Kurimoto K.
    High-quality single-cell transcriptomics from ovarian histological sections during folliculogenesis.
    Life Sci Alliance. 2023 Sep 18;6(11):e202301929. doi: 10.26508/lsa.202301929. PMID: 37722727; PMCID: PMC10507249.
  • Sunadome K, Erickson AG, Kah D, Fabry B, Adori C, Kameneva P, Faure L, Kanatani S, Kaucka M, Dehnisch Ellström I, Tesarova M, Zikmund T,Kaiser J, Edwards S, Maki K, Adachi T, Yamamoto T, Fried K, Adameyko I.
    Directionality of developing skeletal muscles is set by mechanical forces.
    Nat Commun. 2023 May 27;14(1):3060. doi: 10.1038/s41467-023-38647-7. PMID: 37244931; PMCID: PMC10224984.
  • Gyobu-Motani S, Yabuta Y, Mizuta K, Katou Y, Okamoto I, Kawasaki M, Kitamura A, Tsukiyama T, Iwatani C, Tsuchiya H, Tsujimura T, Yamamoto T, Nakamura T, Saitou M.
    Induction of fetal meiotic oocytes from embryonic stem cells in cynomolgus monkeys.
    EMBO J. 2023 May 2;42(9):e112962. doi: 10.15252/embj.2022112962. Epub 2023 Mar 16. PMID: 36929479; PMCID: PMC10152148.

2022

  • Yamanaka Y, Hamidi S, Yoshioka-Kobayashi K, Munira S, Sunadome K, Zhang Y, Kurokawa Y, Ericsson R, Mieda A, Thompson JL, Kerwin J, Lisgo S, Yamamoto T, Moris N, Martinez-Arias A, Tsujimura T, Alev C.
    Reconstituting human somitogenesis in vitro.
    Nature. 2022 Dec 21. doi: 10.1038/s41586-022-05649-2. Epub ahead of print. PMID: 36543322.
  • Yoshinaga M, Han K, Morgens DW, Horii T, Kobayashi R, Tsuruyama T, Hia F, Yasukura S, Kajiya A, Cai T, Cruz PHC, Vandenbon A, Suzuki Y, Kawahara Y, Hatada I, Bassik MC, Takeuchi O.
    The N6-methyladenosine methyltransferase METTL16 enables erythropoiesis through safeguarding genome integrity.
    Nat Commun. 2022 Oct 28;13(1):6435. doi: 10.1038/s41467-022-34078-y. PMID: 36307435; PMCID: PMC9616860.
  • Hashimoto R, Takahashi J, Shirakura K, Funatsu R, Kosugi K, Deguchi S, Yamamoto M, Tsunoda Y, Morita M, Muraoka K, Tanaka M, Kanbara T, Tanaka S, Tamiya S, Tokunoh N, Kawai A, Ikawa M, Ono C, Tachibana K, Kondoh M, Obana M, Matsuura Y, Ohsumi A, Noda T, Yamamoto T, Yoshioka Y, Torisawa YS, Date H, Fujio Y, Nagao M, Takayama K, Okada Y.
    SARS-CoV-2 disrupts respiratory vascular barriers by suppressing Claudin-5 expression.
    Sci Adv. 2022 Sep 23;8(38):eabo6783. doi: 10.1126/sciadv.abo6783. Epub 2022 Sep 21. PMID: 36129989; PMCID: PMC9491726.
  • Imoto Y, Nakamura T, Escolar EG, Yoshiwaki M, Kojima Y, Yabuta Y, Katou Y, Yamamoto T, Hiraoka Y, Saitou M.
    Resolution of the curse of dimensionality in single-cell RNA sequencing data analysis.
    Life Sci Alliance. 2022 Aug 9;5(12):e202201591. doi: 10.26508/lsa.202201591. PMID: 35944930; PMCID: PMC9363502.
  • Mizuta K, Katou Y, Nakakita B, Kishine A, Nosaka Y, Saito S, Iwatani C, Tsuchiya H, Kawamoto I, Nakaya M, Tsukiyama T, Nagano M, Kojima Y, Nakamura T, Yabuta Y, Horie A, Mandai M, Ohta H, Saitou M.
    Ex vivo reconstitution of fetal oocyte development in humans and cynomolgus monkeys.
    EMBO J. 2022 Aug 1:e110815. doi: 10.15252/embj.2022110815. Epub ahead of print. PMID: 35912849.
  • Ichijo R, Maki K, Kabata M, Murata T, Nagasaka A, Ishihara S, Haga H, Honda T, Adachi T, Yamamoto T, Toyoshima F.
    Vasculature atrophy causes a stiffened microenvironment that augments epidermal stem cell differentiation in aged skin.
    Nat Aging. 2022 July 11; 2(7):592–600. doi: 10.1038/s43587-022-00244-6.
  • Ohgushi M, Taniyama N, Vandenbon A, Eiraku M.
    Delamination of trophoblast-like syncytia from the amniotic ectodermal analogue in human primed embryonic stem cell-based differentiation model.
    Cell Rep. 2022 Jun 21;39(12):110973. doi: 10.1016/j.celrep.2022.110973. PMID: 35732132.
  • Nagano M, Hu B, Yokobayashi S, Yamamura A, Umemura F, Coradin M, Ohta H, Yabuta Y, Ishikura Y, Okamoto I, Ikeda H, Kawahira N, Nosaka Y, Shimizu S, Kojima Y, Mizuta K, Kasahara T, Imoto Y, Meehan K, Stocsits R, Wutz G, Hiraoka Y, Murakawa Y, Yamamoto T, Tachibana K, Peters JM, Mirny LA, Garcia BA, Majewski J, Saitou M.
    Nucleome programming is required for the foundation of totipotency in mammalian germline development.
    EMBO J. 2022 Jul 4;41(13):e110600. doi: 10.15252/embj.2022110600. Epub 2022 Jun 15. PMID: 35703121; PMCID: PMC9251848.
  • Tse KM, Vandenbon A, Cui X, Mino T, Uehata T, Yasuda K, Sato A, Tsujimura T, Hia F, Yoshinaga M, Kinoshita M, Okuno T, Takeuchi O.
    Enhancement of Regnase-1 expression with stem loop-targeting antisense oligonucleotides alleviates inflammatory diseases.
    Sci Transl Med. 2022 May 11;14(644):eabo2137. doi: 10.1126/scitranslmed.abo2137. Epub 2022 May 11. PMID: 35544597.
  • Ito K, Nagata K, Ohta S, Matsuda Y, Ukai T, Yasuda I, Ota A, Kobayashi R, Kabata M, Sankoda N, Maeda T, Woltjen K, Yang L, Maruyama R, Katayama R, Yamamoto T, Yamada Y.
    The oncogene-dependent resistance to reprogramming unveils cancer therapeutic targets.
    Cell Rep. 2022 Apr 26;39(4):110721. doi: 10.1016/j.celrep.2022.110721. PMID: 35476996.
  • Oikawa M, Kobayashi H, Sanbo M, Mizuno N, Iwatsuki K, Takashima T, Yamauchi K, Yoshida F, Yamamoto T, Shinohara T, Nakauchi H, Kurimoto K, Hirabayashi M, Kobayashi T.
    Functional primordial germ cell-like cells from pluripotent stem cells in rats.
    Science. 2022 Apr 8;376(6589):176-179. doi: 10.1126/science.abl4412. Epub 2022 Apr 7. PMID: 35389778.
  • Hirano M, So Y, Tsunekawa S, Kabata M, Ohta S, Sagara H, Sankoda N, Taguchi J, Yamada Y, Ukai T, Kato M, Nakamura J, Ozawa M, Yamamoto T, Yamada Y.
    MYCL-mediated reprogramming expands pancreatic insulin-producing cells.
    Nat Metab. 2022 Feb;4(2):254-268. doi: 10.1038/s42255-022-00530-y. Epub 2022 Feb 10. PMID: 35145326.

2021

  • Okamoto I, Nakamura T, Sasaki K, Yabuta Y, Iwatani C, Tsuchiya H, Nakamura SI, Ema M, Yamamoto T, Saitou M.
    The X chromosome dosage compensation program during the development of cynomolgus monkeys.
    Science. 2021 Nov 19;374(6570):eabd8887. doi: 10.1126/science.abd8887. Epub 2021 Nov 19. PMID: 34793202.
  • Ishikura Y, Ohta H, Sato T, Murase Y, Yabuta Y, Kojima Y, Yamashiro C, Nakamura T, Yamamoto T, Ogawa T, Saitou M.
    In vitro reconstitution of the whole male germ-cell development from mouse pluripotent stem cells.
    Cell Stem Cell. 2021 Dec 2;28(12):2167-2179.e9. doi: 10.1016/j.stem.2021.08.005. Epub 2021 Sep 7. PMID: 34496297.

PREPRINTS

  • Kodai Yamaura, Naomichi Takemata, Masashi Kariya, Sonoko Ishino, Masataka Yamauchi, Shoji Takada,
    Yoshizumi Ishino, Haruyuki Atomi.
    Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA structure.
    bio Rxiv 2024.05.14.594075; doi: https://doi.org/10.1101/2024.05.14.594075