The DOI matches its Crossref record; 57 of the 58 references it cites were found in a registry or an index.
Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus
Abstract
Mammalian circadian behaviors are orchestrated by the suprachiasmatic nucleus (SCN) in the ventral hypothalamus, but the number of SCN cell types and their functional roles remain unclear. We have used single-cell RNA-sequencing to identify the basic cell types in the mouse SCN and to characterize their circadian and light-induced gene expression patterns. We identified eight major cell types, with each type displaying a specific pattern of circadian gene expression. Five SCN neuronal subtypes, each with specific combinations of markers, differ in their spatial distribution, circadian rhythmicity and light responsiveness. Through a complete three-dimensional reconstruction of the mouse SCN at single-cell resolution, we obtained a standardized SCN atlas containing the spatial distribution of these subtypes and gene expression. Furthermore, we observed heterogeneous circadian gene expression between SCN neuron subtypes. Such a spatiotemporal pattern of gene regulation within the SCN may have an important function in the circadian pacemaker.
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“suggesting that the pacemaker cells are at a different phase of the circadian cycle of gene expression from the rest of the brain, consistent with previous findings117”
From A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain (2023) · cites this paper as [117]
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“…and spatial transcriptomic profiling of the adult human SCN identified seven neuronal subtypes with distinct transcriptomic signatures and spatial distributions, while a cross-species comparison revealed both conserved and reorganized neuropeptide architectures in human and mouse SCN [ 50, 66 ].”
Melanopsin regulates axonal translation underlying retinohypothalamic circuit assemblyPreprint
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Jandot, A., Calligaro, H., Dianak-Shoori, A., Tartour, K., Sandu, C., Haddjeri, N., Ribelayga, C., Ananthasubramaniam, B., Padmanabhan, K., Felder‐Schmittbuhl, M., et al. (2026) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-026-06298-8
“The absence of significant Per1 upregulation by light at 30 min likely reflects early sampling, stringent statistical criteria, and SCN cellular heterogeneity [30, 66].”
MAGED1 stabilizes NEUROD1 to promote Per3 expression in the pineal gland
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Synaptic output from suprachiasmatic nucleus cholecystokinin neurons regulates locomotor rhythmicity
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“Previous SCN single-cell data show that Pde10a RNA levels are rhythmic in Avp ⁺ /Nms ⁺ neurons in constant darkness (DD) 26 .”
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“10,17,18 For example, clustering algorithms paired with neural networks 10 and other representation learning methods for time series 11,19,20 have been employed to identify distinct SCN cell types and functional subgroups.”
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“Although SCN neurons outside the core region also receive direct retinal inputs 39,40 , their light responses are weaker than those of core neurons 41,42 .”
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Metadata
- Authors
- Wen, S., Ma, D., Zhao, M., Xie, L., Wu, Q., Gou, L., Zhu, C., Fan, Y., Wang, H., & Yan, J.
- Affiliations
- Chinese Academy of Sciences (CN)
- Corresponding author
- Yan, Jun
- Venue
- Nature Neuroscience
- Published
- 2020-02-17
- Volume
- 23
- Issue
- 3
- Pages
- 456-467
- ISSN
- 1097-6256 (ISSN-L)
- 1546-1726
- OpenAlex
- W3005834749
- Cited by
- 328
- References
- 58
- Citations by year
- 2026: 35 · 2025: 50 · 2024: 75 · 2023: 54 · 2022: 37 · 2021: 45 · 2020: 32
- FWCI
- 21.56
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Nature Neuroscience (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Natural Science Foundation of Shanghai (16ZR1448800)
- National Natural Science Foundation of China (31571209)
- Science and Technology Commission of Shanghai Municipality (No. 2018SHZDZX05)
- Topics
- Life Sciences › Neuroscience › Endocrine and Autonomic Systems › Circadian rhythm and melatonin
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Circular RNAs in diseases
- Keywords
- suprachiasmatic nucleus, circadian rhythm, circadian pacemaker, neuronal cell types, circadian gene expression, light-induced gene expression, single-cell RNA sequencing, 3D reconstruction, mice, ventral hypothalamus
- MeSH terms
- Animals, Atlases as Topic, Circadian Rhythm, Gene Expression Regulation, Light, Male, Mice, Inbred C57BL, Neurons, Photic Stimulation, Suprachiasmatic Nucleus, Gene Expression, Genomics, Mice, Circadian Rhythm Signaling Peptides and Proteins, Single-Cell Analysis
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