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Gene networks under circadian control exhibit diurnal organization in primate organs

Jie Li, Pengxing Nie, Christoph W. Turck, Guang-Zhong Wang
doi: https://doi.org/10.1101/2021.09.17.460870
Jie Li
1CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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Pengxing Nie
1CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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Christoph W. Turck
2Max Planck Institute of Psychiatry, Proteomics and Biomarkers, Munich 80804, Germany
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Guang-Zhong Wang
1CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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  • For correspondence: guangzhong.wang@picb.ac.cn
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Abstract

Mammalian organs are individually controlled by autonomous circadian clocks. At the molecular level, this process is defined by the cyclical co-expression of both core transcription factors and off-target genes across time. While interactions between these molecular clocks are likely necessary for proper homeostasis, these features remain undefined. Here, we utilize integrative analysis of a baboon diurnal transcriptome atlas to characterize the properties of gene networks under circadian control. We found that 53.4% (8,120) of baboon genes are rhythmically expressed body-wide. In addition, >30% of gene-gene interactions exhibit periodic co-expression patterns, with core circadian genes more cyclically co-expressed than others. Moreover, two basic network modes were observed at the systems level: daytime and nighttime mode. Daytime networks were enriched for genes involved in metabolism, while nighttime networks were enriched for genes associated with growth and cellular signaling. A substantial number of diseases only form significant disease modules at either daytime or nighttime. In addition, we found that 216 of 313 genes encoding products that interact with SARS-CoV-2 are rhythmically expressed throughout the body. Importantly, more than 80% of SARS-CoV-2 related genes enriched modules are rhythmically expressed, and have significant network proximities with circadian regulators. Our data suggest that synchronization amongst circadian gene networks is necessary for proper homeostatic functions and circadian regulators have close interactions with SARS-CoV-2 infection.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 21, 2021.
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Gene networks under circadian control exhibit diurnal organization in primate organs
Jie Li, Pengxing Nie, Christoph W. Turck, Guang-Zhong Wang
bioRxiv 2021.09.17.460870; doi: https://doi.org/10.1101/2021.09.17.460870
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Gene networks under circadian control exhibit diurnal organization in primate organs
Jie Li, Pengxing Nie, Christoph W. Turck, Guang-Zhong Wang
bioRxiv 2021.09.17.460870; doi: https://doi.org/10.1101/2021.09.17.460870

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