オキラボ：京都大学大学院 医学研究科 創薬医学講座

沖ラボ：京都大学大学院 医学研究科 創薬医学講座

Oki Lab

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Publications

Peer-reviewed original research（*Corresponding author）

2024

    • Zou, Z., Ohta, T., Oki, S.* (2024). ChIP-Atlas 3.0: a data-mining suite to explore chromosome architecture together with large-scale regulome data. Nucleic Acids Res. gkae358. Link

2023

    • Cui, M., Yamano, K., Yamamoto, K., Yamamoto-Imoto, H., Minami, S., Yamamoto, T., Matsui, S., Kaminishi, T., Shima, T., Ogura, M., Tsuchiya, M., Nishino, K., Layden, B.T., Kato, H., Ogawa, H., Oki, S., Okada, Y., Isaka, Y., Kosako, H., Matsuda, N., Yoshimori, T., Nakamura, S. (2024). HKDC1, a target of TFEB, is essential to maintain both mitochondrial and lysosomal homeostasis, preventing cellular senescence. Proc Natl Acad Sci USA. 121(2), e2306454120. Link
    • Zou, Z., Yoshimura, Y., Yamanishi, Y., Oki, S.* (2023). Elucidating disease-associated mechanisms triggered by pollutants via the epigenetic landscape using large-scale ChIP-Seq data. Epigenetics Chromatin. 16(1), 34. Link
    • Miyazawa, K., Ito, K., Ito, M., Zou, Z., Kubota, M., Nomura, S., Matsunaga, H., Koyama, S., Ieki, H., Akiyama, M., Koike, Y., Kurosawa, R., Yoshida, H., Ozaki, K., Onouchi, Y., BioBank Japan Project, Takahashi, A., Matsuda, K., Murakami, Y., Aburatani, H., Kubo, M., Momozawa, Y., Terao, C., Oki, S., Akazawa, H., Kamatani, Y., Komuro, I (2023). Cross-ancestry genome-wide analysis of atrial fibrillation unveils disease biology and enables cardioembolic risk prediction. Nat Genet. 55(2), 187-197. Link

2022

    • Honda, M., Kimura, R., Harada, A., Maehara, K., Tanaka, K., Ohkawa, Y.*, Oki, S.* (2022). Photo-isolation chemistry for high-resolution and deep spatial transcriptome with mouse tissue sections. STAR Protoc. 3(2), 101346. Link
    • Zou, Z., Ohta, T., Miura, F., Oki, S.* (2022). ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data. Nucleic Acids Res. 50(W1), W175-W182. Link
    • Zou, Z., Iwata, M., Yamanishi, Y.*, Oki, S.* (2022). Epigenetic landscape of drug responses revealed through large-scale ChIP-seq data analyses. BMC Bioinform. 23(1), 51. Link
    • Iwata, M., Kosai, K., Ono, Y., Oki, S., Mimori, K., Yamanishi, Y. (2022). Regulome-based characterization of drug activity across the human diseasome. NPJ Syst Biol Appl. 8(1), 44. Link
    • Hino, Y., Nagaoka, K., Oki, S., Etoh, K., Hino, S., Nakao, M. (2022). Mitochondrial stress induces AREG expression and epigenomic remodeling through c-JUN and YAP-mediated enhancer activation. Nucleic Acids Res. 50(17), 9765-9779. Link
    • Hirata, H., Kamohara, A., Murayama, M., Nishioka, K., Honda, H., Urano, Y., Soejima, H., Oki, S., Kukita, T., Kawano, S., Mawatari, M., Kukita, A. (2022). A novel role of helix-loop-helix transcriptional factor Bhlhe40 in osteoclast activation. J Cell Physiol. 237(10), 3912-3926. Link
    • Eguchi, R., Hamano, M., Iwata, M., Nakamura, T., Oki, S., Yamanishi, Y. (2022). TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach. Bioinformatics. btac209. Link
    • Yamamoto-Imoto, H., Minami, S., Shioda, T., Yamashita, Y., Sakai, S., Maeda, S., Yamamoto, T., Oki, S., et al. (2022). Age-associated decline of MondoA drives cellular senescence through impaired autophagy and mitochondrial homeostasis. Cell Rep. 38(9), 110444. Link

2021

    • Katada, S., Takouda, J., Nakagawa, T., Honda, M., Igarashi, K., Imamura, T., Ohkawa, Y., Sato, S., Kurumizaka, H., Nakashima K. (2021). Neural stem/precursor cells dynamically change their epigenetic landscape to differentially respond to BMP signaling for fate switching during brain development. Genes Dev. 35(21-22), 1431-1444. Link
    • Kimura, R., U Inoue, Y., Kikkawa, T., Tatehana, M., Morimoto, Y., Inada, H., Oki, S., Inoue, T., Osumi, N. (2022). Detection of REST expression in the testis using epitope-tag knock-in mice generated by genome editing. Dev Dyn. 251(3), 525-535. Link
    • Honda, M., Oki, S.*, Kimura R., Harada, R., Maehara, K., Tanaka, K., Meno C., Ohkawa, Y*. (2021). High-depth spatial transcriptome analysis by photo-isolation chemistry. Nat Commun. 12, 4416. Link
    • Pecori, F., Yokota, I., Hanamatsu, H., Miura, T., Ogura, C., Ota, H., Furukawa, J. ichi, Oki, S., Yamamoto, K., Yoshie, O., et al. (2021). A defined glycosylation regulatory network modulates total glycome dynamics during pluripotency state transition. Sci. Rep. 11, 1276. Link
    • Yoshizaki, K., Kimura, R., Kobayashi, H., Oki, S., Kikkawa, T., Mai, L., Koike, K., Mochizuki, K., Inada, H., Matsui, Y., et al. (2021). Paternal age affects offspring via an epigenetic mechanism involving REST/NRSF. EMBO Rep. 22, e51524. Link

2020

    • Hirayama, M., Wei, F.Y., Chujo, T., Oki, S., Yakita, M., Kobayashi, D., Araki, N., Takahashi, N., Yoshida, R., Nakayama, H., et al. (2020). FTO Demethylates Cyclin D1 mRNA and Controls Cell-Cycle Progression. Cell Rep. 31, 107464. Link
    • Miyamoto, Y., Sasaki, M., Miyata, H., Monobe, Y., Nagai, M., Otani, M., Whiley, P.A.F., Morohoshi, A., Oki, S., Matsuda, J., et al. (2020). Genetic loss of importin α4 causes abnormal sperm morphology and impacts on male fertility in mouse. FASEB J. 34, 16224–16242. Link
    • Suzuki, J., Inada, H., Han, C., Kim, M.-J., Kimura, R., Takata, Y., Honkura, Y., Owada, Y., Kawase, T., Katori, Y., Someya, S., Osumi, N. (2020). “Passenger gene” problem in transgenic C57BL/6 mice used in hearing research. Neurosci Res 158, 6–15. Link
    • Nakagawa, T., Hattori, S., Nobuta, R., Kimura, R., Nakagawa, M., Matsumoto, M., Nagasawa, Y., Funayama, R., Miyakawa, T., Inada, T., Osumi, N., Nakayama, K.I., Nakayama, K. (2020). The Autism-Related Protein SETD5 Controls Neural Cell Proliferation through Epigenetic Regulation of rDNA Expression. iScience 23, 101030. Link
    • Tatehana, M., Kimura, R., Mochizuki, K., Inada, H., Osumi, N. (2020). Comprehensive histochemical profiles of histone modification in male germline cells during meiosis and spermiogenesis: Comparison of young and aged testes in mice. PLoS ONE 15, e0230930. Link
    • Kaminuma, E., Baba, Y., Mochizuki, M., Matsumoto, H., Ozaki, H., Okayama, T., Kato, T., Oki, S., Fujisawa, T., Nakamura, Y., et al. (2020). DDBJ data analysis challenge: A machine learning competition to predict arabidopsis chromatin feature annotations from DNA sequences. Genes Genet. Syst. 95, 43–50. Link

〜2019

    • Wu, Z., Rao, Y., Zhang, S., Kim, E.J., Oki, S., Harada, H., Cheung, M., and Jung, H.S. (2019). Cis-control of Six1 expression in neural crest cells during craniofacial development. Dev. Dyn. 248, 1264–1272. Link
    • Lizio, M., Abugessaisa, I., Noguchi, S., Kondo, A., Hasegawa, A., Hon, C.C., De Hoon, M., Severin, J., Oki, S., Hayashizaki, Y., et al. (2019). Update of the FANTOM web resource: Expansion to provide additional transcriptome atlases. Nucleic Acids Res. 47, D752–D758. Link
    • Oki, S.*, Ohta, T., Shioi, G., Hatanaka, H., Ogasawara, O., Okuda, Y., Kawaji, H., Nakaki, R., Sese, J., and Meno, C. (2018). ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data. EMBO Rep. 19, e46255. Link
    • Mochizuki, K., Hayashi, Y., Sekinaka, T., Otsuka, K., Ito-Matsuoka, Y., Kobayashi, H., Oki, S., Takehara, A., Kono, T., Osumi, N., et al. (2018). Repression of Somatic Genes by Selective Recruitment of HDAC3 by BLIMP1 Is Essential for Mouse Primordial Germ Cell Fate Determination. Cell Rep. 24, 2682–2693.e6. Link
    • Anan, K., Hino, S., Shimizu, N., Sakamoto, A., Nagaoka, K., Takase, R., Kohrogi, K., Araki, H., Hino, Y., Usuki, S., Oki, S., et al. (2018). LSD1 mediates metabolic reprogramming by glucocorticoids during myogenic differentiation. Nucleic Acids Res. 46, 5441–5454. Link
    • Yoshizaki, K., Koike, K., Kimura, R., Osumi, N. (2017). Early postnatal vocalizations predict sociability and spatial memory in C57BL/6J mice: Individual differences in behavioral traits emerge early in development. PLoS ONE 12, e0186798. Link
    • Semba, Y., Harada, A., Maehara, K., Oki, S., Meno, C., Ueda, J., Yamagata, K., Suzuki, A., Onimaru, M., Nogami, J., et al. (2017). Chd2 regulates chromatin for proper gene expression toward differentiation in mouse embryonic stem cells. Nucleic Acids Res. 45, 8758–8772. Link
    • Ohshima, K., Nojima, S., Tahara, S., Kurashige, M., Hori, Y., Hagiwara, K., Okuzaki, D., Oki, S., Wada, N., Ikeda, J.I., et al. (2017). Argininosuccinate Synthase 1-Deficiency Enhances the Cell Sensitivity to Arginine through Decreased DEPTOR Expression in Endometrial Cancer. Sci. Rep. 7, 45504. Link
    • Matsuda, K., Mikami, T., Oki, S., Iida, H., Andrabi, M., Boss, J.M., Yamaguchi, K., Shigenobu, S., and Kondoh, H. (2017). ChIP-seq analysis of genomic binding regions of five major transcription factors highlights a central role for ZIC2 in the mouse epiblast stem cell gene regulatory network. Development. 144, 1948–1958. Link
    • Honda, M., Nakashima, K., Katada, S. (2017). PRMT1 regulates astrocytic differentiation of embryonic neural stem/precursor cells. J. Neurochem. 142, 901-907.
      Link
    • Yoshizaki, K., Furuse, T., Kimura, R., Tucci, V., Kaneda, H., Wakana, S., Osumi, N. (2016). Paternal Aging Affects Behavior in Pax6 Mutant Mice: A Gene/Environment Interaction in Understanding Neurodevelopmental Disorders. PLoS ONE 11, e0166665. Link
    • Hayashi, M., Maehara, K., Harada, A., Semba, Y., Kudo, K., Takahashi, H., Oki, S., Meno, C., Ichiyanagi, K., Akashi, K., et al. (2016). Chd5 Regulates MuERV-L/MERVL Expression in Mouse Embryonic Stem Cells Via H3K27me3 Modification and Histone H3.1/H3.2. J. Cell. Biochem. 117, 780–792. Link
    • Kimura, R., Yoshizaki, K., Osumi, N. (2015). Dynamic expression patterns of Pax6 during spermatogenesis in the mouse. J Anat 227, 1–9. Link
    • Hachisuga, M., Oki, S., Kitajima, K., Ikuta, S., Sumi, T., Kato, K., Wake, N., and Meno, C. (2015). Hyperglycemia impairs left-right axis formation and thereby disturbs heart morphogenesis in mouse embryos. Proc. Natl. Acad. Sci. U. S. A. 112, E5300–E5307. Link
    • Shiratori, H., Yashiro, K., Iwai, N., Oki, S., Minegishi, K., Ikawa, Y., Kanata, K., and Hamada, H. (2014). Self-regulated left-right asymmetric expression of Pitx2c in the developing mouse limb. Dev. Biol. 395, 331–341. Link
    • Suzuki, J., Oshima, T., Yoshida, N., Kimura, R., Takata, Y., Owada, Y., Kobayashi, T., Katori, Y., Osumi, N. (2014). Preservation of cochlear function in Fabp3 (H-Fabp) knockout mice. Neurosci Res 81-82, 64–68. Link
    • Oki, S.*, Maehara, K., Ohkawa, Y., and Meno, C. (2014). SraTailor: Graphical user interface software for processing and visualizing ChIP-seq data. Genes to Cells 19, 919–926. Link
    • Kitajima, K., Oki, S., Ohkawa, Y., Sumi, T., and Meno, C. (2013). Wnt signaling regulates left-right axis formation in the node of mouse embryos. Dev. Biol. 380, 222–232. Link
    • Guo, N., Yoshizaki, K., Kimura, R., Suto, F., Yanagawa, Y., Osumi, N. (2013). A sensitive period for GABAergic interneurons in the dentate gyrus in modulating sensorimotor gating. J. Neurosci. 33, 6691–6704. Link
    • Sumi, T., Oki, S., Kitajima, K., and Meno, C. (2013). Epiblast Ground State Is Controlled by Canonical Wnt/β-Catenin Signaling in the Postimplantation Mouse Embryo and Epiblast Stem Cells. PLoS One 8, e63378. Link
    • Miki, R., Yoshida, T., Murata, K., Oki, S., Kume, K., and Kume, S. (2012). Fate maps of ventral and dorsal pancreatic progenitor cells in early somite stage mouse embryos. Mech. Dev. 128, 597–609. Link
    • Noda, T., Oki, S., Kitajima, K., Harada, T., Komune, S., and Meno, C. (2012). Restriction of Wnt signaling in the dorsal otocyst determines semicircular canal formation in the mouse embryo. Dev. Biol. 362, 83–93. Link
    • Oki, S., Kitajima, K., and Meno, C. (2010). Dissecting the role of Fgf signaling during gastrulation and left-right axis formation in mouse embryos using chemical inhibitors. Dev. Dyn. 239, 1768–1778. Link
    • Oki, S., Kitajima, K., Marques, S., Belo, J.A., Yokoyama, T., Hamada, H., and Meno, C. (2009). Reversal of left-right asymmetry induced by aberrant Nodal signaling in the node of mouse embryos. Development 136, 3917–3925. Link
    • Oki, S., Hashimoto, R., Okui, Y., Shen, M.M., Mekada, E., Otani, H., Saijoh, Y., and Hamada, H. (2007). Sulfated glycosaminoglycans are necessary for Nodal signal transmission from the node to the left lateral plate in the mouse embryo. Development 134, 3893–3904. Link
    • Saijoh, Y., Oki, S., Tanaka, C., Nakamura, T., Adachi, H., Yan, Y.T., Shen, M.M., and Hamada, H. (2005). Two nodal-responsive enhancers control left-right asymmetric expression of Nodal. Dev. Dyn. 232, 1031–1036. Link
    • Saijoh, Y., Oki, S., Ohishi, S., and Hamada, H. (2003). Left-right patterning of the mouse lateral plate requires Nodal produced in the node. Dev. Biol. 256, 161–173. Link
    • Todoriki, M., Oki, S., Matsuyama, S.I., Ko-Mitamura, E.P., Urabe, I., and Yomo, T. (2002). An observation of the initial stage towards a symbiotic relationship. BioSystems 65, 105–112. Link

MISC

    • 鄒 兆南, 沖 真弥. (2023). ChIP-Atlas 〜転写制御ランドスケープの歩き方〜. JSBi Bioinformatics Review. 4(1). 1-9. PDF
    • 鄒 兆南, 沖 真弥. (2022). ChIP-Atlas 2.0 ─ 転写制御機構＆エピゲノムランドスケープを可視化する. 実験医学増刊：バイオDBとウェブツール ラボで使える最新70選. 40(17). 2848-2851. PDF
    • 本田瑞季, 沖 真弥. (2022). 空間トランスクリプトミクス. 生物工学会誌. 100(6). 295-297. PDF
    • 本田瑞季, 沖 真弥. (2021). Photo-Isolation Chemistry：光照射による高解像度かつ高感度なトランスクリプトーム技術. 実験医学 9月号. 39(14). PDF
    • 沖 真弥, 大川恭行. (2021). 概論―空間トランスクリプトーム技術の最前線. 実験医学 9月号. 39(14). PDF
    • Oki, S. and Ohta, T. (2021). ChIP-Atlas. Practical Guide to Life Science Databases.
    • 沖 真弥, 本田瑞季. (2020). 局所的かつ高深度の空間トランスクリプトーム技術：Photo-Isolation Chemistry. 実験医学別冊クロマチン解析実験プロトコール. 247–250.
    • 木村龍一, 吉崎嘉一, 大隅典子. (2020). エピゲノムの経世代影響. 遺伝子医学 10(1) 68–73.
    • 舘花美沙子, 木村龍一, 大隅典子. (2020). 老化による精子の変化と発達障害発症リスク. 実験医学 38(6) 932–936.
    • 沖 真弥, 大田達郎. (2019). ChIP-Atlas：公共ChIP-seqデータを統合的に活用するためのウェブサービス. The Lung. 27 243–249.
    • 沖 真弥, 大田達郎. (2019). ChIP-Atlas：既報のChIP-seqデータをフル活用するためのウェブサービス. 実験医学. 37 2760–2763. PDF
    • 木村龍一, 稲田仁, 大隅典子. (2019). 自閉スペクトラム症発症リスクとエピジェネティクス. 医学のあゆみ 268(3) 180–183.
    • Honda, M., Nakashima, K., Katada, S. (2018). Epigenetic Regulation of Human Neural Stem Cell Differentiation. Publisher: Springer Verlag, Results Probl Cell Differ. 125–136.
    • Kimura, R., Yoshizaki, K., Osumi, N. (2018). Risk of Neurodevelopmental Disease by Paternal Aging: A Possible Influence of Epigenetic Alteration in Sperm. Adv Exp Med Biol 1012, 75–81.
    • 大隅典子, 木村龍一. (2017). 父加齢・エピゲノム・精神疾患. Medical Science Digest 43(12) 612–615.
    • 大隅典子, 木村龍一. (2016). 精子形成過程におけるエピゲノム修飾と次世代への影響. BIO Clinica 31(5) 470–474.
    • 沖 真弥. (2014). SraTailor: 誰でも使えるChIP-seqデータの可視化ツール. 実験医学 32(19), 3101-3106.
    • 本田瑞季, 堅田明子,中島欽一 (2014). エピジェネティクスの基礎（エピジェネティクスを制御する分子機構） アレルギー・免疫 12, 13-19.
    • Sakayori, N., Kimura, R., Osumi, N. (2013). Impact of Lipid Nutrition on Neural Stem/Progenitor Cells. Stem Cells International 2013.
    • 沖 真弥, 目野主税. (2010). マウス初期発生における硫酸化グリコサミノグリカンの役割. 福岡医学雑誌 101(8), 157-164.
    • 沖 真弥, 目野主税, 濱田博司. (2008). 左右決定におけるNodalシグナル. 細胞工学 27 (6).
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