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Non-human primate seasonal transcriptome atlas reveals seasonal changes in physiology and diseases

Author

Listed:
  • Junfeng Chen

    (Nagoya University
    Nagoya University
    Chinese Academy of Sciences)

  • Kousuke Okimura

    (Nagoya University
    Nagoya University)

  • Liang Ren

    (Nagoya University
    Nagoya University)

  • Yusuke Nakane

    (Nagoya University
    Nagoya University)

  • Tomoya Nakayama

    (Nagoya University
    Nagoya University)

  • Yang Chen

    (Nagoya University
    Yangzhou University)

  • Kai Fukawa

    (Nagoya University
    Nagoya University)

  • Soutarou Sugiyama

    (Kyoto University)

  • Takayoshi Natsume

    (Kyoto University)

  • Naoko Suda-Hashimoto

    (Kyoto University)

  • Mayumi Morimoto

    (Kyoto University)

  • Takako Miyabe-Nishiwaki

    (Kyoto University)

  • Takao Oishi

    (Kyoto University)

  • Yuma Katada

    (Nagoya University
    Nagoya University)

  • Manhui Zhang

    (Nagoya University
    Nagoya University)

  • Kohei Kobayashi

    (Nagoya University
    Nagoya University)

  • Shoko Matsumoto

    (Nagoya University
    Nagoya University)

  • Taiki Yamaguchi

    (Nagoya University
    Nagoya University)

  • Ying-Jey Guh

    (Nagoya University
    Nagoya University
    Academia Sinica)

  • Issey Takahashi

    (Nagoya University)

  • Taeko Nishiwaki-Ohkawa

    (Nagoya University
    Nagoya University)

  • Daiki X. Sato

    (Chiba University)

  • Yoshiharu Murata

    (Seien Clinic)

  • Kenta Sumiyama

    (Suita
    Nagoya University)

  • Atsushi J. Nagano

    (Ryukoku University
    Keio University)

  • Hiroo Imai

    (Kyoto University)

  • Takashi Yoshimura

    (Nagoya University
    Nagoya University
    Nagoya University)

Abstract

The metabolic, immune, and endocrine systems show profound seasonal changes in animals, including humans. In addition, morbidity from cardiovascular and psychiatric diseases is more severe and mortality rate is higher in winter. However, their molecular mechanisms remain unknown. Here we report the seasonal transcriptome of 80 tissues collected over 1 year from male and female rhesus macaques kept in a semi-natural outdoor environment. We find seasonal changes in plasma metabolites and hormones. Transcriptome analysis identifies sex differences in seasonally oscillating genes (SOGs) in all tissues studied, and we generate the web database ‘Non-Human Primate Seasonal Transcriptome Atlas (NHPSTA).’ Transcriptional regulatory network analysis, siRNA knockdown, and mutant mouse analyses reveal regulation of SOGs by GA-binding protein (GABP). We also demonstrate seasonal oscillations in the expression of disease risk factor genes and drug interacting genes. NHPSTA provides a molecular resource for seasonally regulated physiology and targets for therapeutic interventions for seasonally regulated diseases.

Suggested Citation

  • Junfeng Chen & Kousuke Okimura & Liang Ren & Yusuke Nakane & Tomoya Nakayama & Yang Chen & Kai Fukawa & Soutarou Sugiyama & Takayoshi Natsume & Naoko Suda-Hashimoto & Mayumi Morimoto & Takako Miyabe-N, 2025. "Non-human primate seasonal transcriptome atlas reveals seasonal changes in physiology and diseases," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-57994-1
    DOI: 10.1038/s41467-025-57994-1
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    References listed on IDEAS

    as
    1. Matthew B. Buechler & Rachana N. Pradhan & Akshay T. Krishnamurty & Christian Cox & Aslihan Karabacak Calviello & Amber W. Wang & Yeqing Angela Yang & Lucinda Tam & Roger Caothien & Merone Roose-Girma, 2021. "Cross-tissue organization of the fibroblast lineage," Nature, Nature, vol. 593(7860), pages 575-579, May.
    2. Yusuke Nakane & Keisuke Ikegami & Masayuki Iigo & Hiroko Ono & Korenori Takeda & Daisuke Takahashi & Maiko Uesaka & Meita Kimijima & Ramu Hashimoto & Natsumi Arai & Takuya Suga & Katsuya Kosuge & Tomo, 2013. "The saccus vasculosus of fish is a sensor of seasonal changes in day length," Nature Communications, Nature, vol. 4(1), pages 1-7, October.
    3. Yingyao Zhou & Bin Zhou & Lars Pache & Max Chang & Alireza Hadj Khodabakhshi & Olga Tanaseichuk & Christopher Benner & Sumit K. Chanda, 2019. "Metascape provides a biologist-oriented resource for the analysis of systems-level datasets," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    4. Senlin Yin & Keying Lu & Tao Tan & Jie Tang & Jingkuan Wei & Xu Liu & Xinlei Hu & Haisu Wan & Wei Huang & Yong Fan & Dan Xie & Yang Yu, 2020. "Transcriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
    5. Xaquin Castro Dopico & Marina Evangelou & Ricardo C. Ferreira & Hui Guo & Marcin L. Pekalski & Deborah J. Smyth & Nicholas Cooper & Oliver S. Burren & Anthony J. Fulford & Branwen J. Hennig & Andrew M, 2015. "Widespread seasonal gene expression reveals annual differences in human immunity and physiology," Nature Communications, Nature, vol. 6(1), pages 1-13, November.
    6. Nobuhiro Nakao & Hiroko Ono & Takashi Yamamura & Tsubasa Anraku & Tsuyoshi Takagi & Kumiko Higashi & Shinobu Yasuo & Yasuhiro Katou & Saburo Kageyama & Yumiko Uno & Takeya Kasukawa & Masayuki Iigo & P, 2008. "Thyrotrophin in the pars tuberalis triggers photoperiodic response," Nature, Nature, vol. 452(7185), pages 317-322, March.
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