The proteomic landscape of the suprachiasmatic nucleus clock reveals large-scale coordination of key biological processes
Open accessAbstract
The suprachiasmatic nucleus (SCN) acts as the central clock to coordinate circadian oscillations in mammalian behavior, physiology and gene expression. Despite our knowledge of the circadian transcriptome of the SCN, how it impacts genome-wide protein expression is not well understood. Here, we interrogated the murine SCN proteome across the circadian cycle using SILAC-based quantitative mass spectrometry. Of the 2112 proteins that were accurately quantified, 20% (421 proteins) displayed a time-of-day-dependent expression profile. Within this time-of-day proteome, 11% (48 proteins) were further defined as circadian based on a sinusoidal expression pattern with a ∼24 h period. Nine circadianly expressed proteins exhibited 24 h rhythms at the transcript level, with an average time lag that exceeded 8 h. A substantial proportion of the time-of-day proteome exhibited abrupt fluctuations at the anticipated light-to-dark and dark-to-light transitions, and was enriched for proteins involved in several key biological pathways, most notably, mitochondrial oxidative phosphorylation. Additionally, predicted targets of miR-133ab were enriched in specific hierarchical clusters and were inversely correlated with miR133ab expression in the SCN. These insights into the proteomic landscape of the SCN will facilitate a more integrative understanding of cellular control within the SCN clock.
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It has been estimated that 6-20% of the murine proteome exhibits circadian rhythms in tissues such as the SCN and liver.
“Similar to the reported proportion of rhythmic transcripts, it has been estimated that 6-20% of the murine proteome exhibits circadian rhythms in tissues such as the SCN (33,34) and liver (35)(36)(37).”
From Circadian rhythms, metabolism, and chrononutrition in rodents and humans (2016) · cites this paper as [34]
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Design Principles and Analysis Guidelines for Understanding Time-of-Day Effects in the Brain
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Back-of-the-Envelope Guide (A Tutorial) to 10 Intracellular Landscapes
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Circadian proteomics reveal rampant tuning of post-transcriptional apparatus by Chlamydomonas clockPreprint
Jadhav, D. B., & Roy, S. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.28.550970
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Mapping Retinal Gene Expression to Cell Classes: Insights into Retinal Circadian Rhythms
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- Authors
- Chiang, C.-K., Mehta, N., Patel, A., Zhang, P., Ning, Z., Mayne, J., Sun, W. Y. L., Cheng, H.-Y. M., & Figeys, D.
- Affiliations
- University of Ottawa (CA)
- University of Toronto (CA)
- Corresponding author
- Cheng, Hai-Ying M.
- Figeys, Daniel
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2014-10-16
- Volume
- 10
- Issue
- 10
- Pages
- e1004695
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC4199512
- OpenAlex
- W2088651867
- Cited by
- 69
- References
- 33
- Citations by year
- 2026: 3 · 2025: 7 · 2024: 3 · 2023: 7 · 2022: 5 · 2021: 8 · 2020: 2 · 2019: 8 · 2018: 7 · 2017: 8 · 2016: 8 · 2015: 3
- FWCI
- 3.09
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Genetics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- Canadian Institutes of Health Research (MOP86549, MOP#126090)
- Natural Sciences and Engineering Research Council of Canada
- Ontario Ministry of Research and Innovation
- Topics
- Life Sciences › Neuroscience › Endocrine and Autonomic Systems › Circadian rhythm and melatonin
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Neuroscience › Cognitive Neuroscience › Sleep and Wakefulness Research
- Keywords
- suprachiasmatic nucleus, circadian clock, circadian rhythm, mitochondrial oxidative phosphorylation, circadian transcriptome, light-dark transition
- MeSH terms
- Animals, Circadian Rhythm, Gene Expression Regulation, Light, Male, Mice, Inbred C57BL, Oxidative Phosphorylation, Suprachiasmatic Nucleus, Proteome, Mitochondrial Proteins, MicroRNAs, Proteomics, Transcriptome, Protein Interaction Maps
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