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.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“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]
Citations
Cites
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888
STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709
UCSF Chimera—A visualization system for exploratory research and analysis
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20084 · Cited by 46,047
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nature Protocols · doi:10.1038/nprot.2008.211 · Cited by 35,890
Comprehensive Integration of Single-Cell Data
Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck, W. M., Hao, Y., Stoeckius, M., Smibert, P., & Satija, R. (2019) · Cell · doi:10.1016/j.cell.2019.05.031 · Cited by 15,453
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn923 · Cited by 14,108
Trapnell, C., Cacchiarelli, D., Grimsby, J., Pokharel, P., Li, S., Morse, M., Lennon, N. J., Livak, K. J., Mikkelsen, T. S., & Rinn, J. L. (2014) · Nature Biotechnology · doi:10.1038/nbt.2859 · Cited by 7,314
Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets.
Macosko, E. Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas, A. R., Kamitaki, N., Martersteck, E. M., et al. (2015) · Cell · doi:10.1016/j.cell.2015.05.002 · Cited by 7,110
Spatial reconstruction of single-cell gene expression data
Satija, R., Farrell, J. A., Gennert, D., Schier, A. F., & Regev, A. (2015) · Nature Biotechnology · doi:10.1038/nbt.3192 · Cited by 7,055
Scenic: single-cell regulatory network inference and clustering.
Aibar, S., González-Blas, C. B., Moerman, T., Huynh-Thu, V. A., Imrichova, H., Hulselmans, G., Rambow, F., Marine, J.-C., Geurts, P., Aerts, J., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4463 · Cited by 6,520
Cited by
Sorted by citations
Items 101–200 of 326
Raptin, a sleep-induced hypothalamic hormone, suppresses appetite and obesity
Xie, L., Hu, B., Lu, R.-B., Cheng, Y., Chen, X., Wen, J., Xiao, Y., An, Y.-Z., Peng, N., Dai, Y., et al. (2025) · Cell Research · doi:10.1038/s41422-025-01078-8 · Cited by 18
Self-citationZhu, M., Peng, J., Wang, M., Lin, S., Zhang, H., Zhou, Y., Dai, X., Zhao, H., Yu, Y., Shen, L., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-57896-2 · Cited by 17
“Therefore, the same transcriptomic neuronal subtypes could establish different efferent projections during development 66 .”
Ness, N., Díaz-Clavero, S., Hoekstra, M. M., & Brancaccio, M. (2024) · The EMBO Journal · doi:10.1038/s44318-024-00324-w · Cited by 17
“Thus, analysis of the (Wen et al, 2020) dataset con fi rmed the cell-type speci fi c dichotomy of GABA biosynthesis in SCN astrocytes versus neurons, and ruled out any time-of-the-day-dependent “ ectopic ” upregulation of the respective GABA pathways, which may have not been captured by the larger…”
InfluentialKim, B., Kim, J., Chun, M., Park, I., Kwak, D., Choi, M., Kim, K., & Choe, H. K. (2021) · Scientific Reports · doi:10.1038/s41598-021-82287-0 · Cited by 17
Circadian Biology and the Neurovascular Unit
Li, W., Tiedt, S., Lawrence, J. H., Harrington, M. E., Musiek, E. S., & Lo, E. H. (2024) · Circulation Research · doi:10.1161/circresaha.124.323514 · Cited by 17
“26,27 Potentially to satisfy the need for highly contrasting activity within a 24-hour cycle, critical clock neurons show circadian structural plasticity: in Drosophila melanogaster , the small ventral lateral neurons, closely resembling VIP (vasoactive intestinal peptide)-positive neurons in the…”
BackgroundscLENS: data-driven signal detection for unbiased scRNA-seq data analysis
Kim, H., Chang, W., Chae, S. J., Park, J.-E., Seo, M., & Kim, J. K. (2024) · Nature Communications · doi:10.1038/s41467-024-47884-3 · Cited by 16
“…data have been widely employed in diverse downstreamanalyses, including clustering analysisfor identifying cell-type-speci fi c phenotypes 5 – 7 , trajectory analysis for exploring cell differentiation and development 8,9 , ligand-receptor network analysis for investigating cell-to-cell…”
Galichet, C., Clayton, R. W., & Lovell-Badge, R. H. (2021) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2021.673132 · Cited by 16
“Since then, two molecularly distinct OPC populations have been described in the adult suprachiasmatic nucleus, but no further characterization has yet been undertaken (Wen et al., 2020).”
BackgroundSomatostatin regulates central clock function and circadian responses to light
Joye, D. A. M., Rohr, K. E., Suenkens, K., Wuorinen, A., Inda, T., Arzbecker, M., Mueller, E., Huber, A. T., Pancholi, H., Blackmore, M. G., et al. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2216820120 · Cited by 17
REST Targets JAK–STAT and HIF-1 Signaling Pathways in Human Down Syndrome Brain and Neural Cells
Huang, T., Fakurazi, S., Cheah, P.-S., & Ling, K. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24129980 · Cited by 15
“The last few decades have seen discoveries in gene expression analysis, which have not only elucidated disease mechanisms at different stages or phenotypes, but they have also enabled gene-targeted therapies and the development of targeted drugs [32,33].”
BackgroundLong-term high fructose intake promotes lacrimal gland dysfunction by inducing gut dysbiosis in mice
Qi, D., Zou, S., Lu, D., Pei, X., Huang, S., Huang, D., Liu, J., Si, H., & Li, Z. (2023) · Experimental Eye Research · doi:10.1016/j.exer.2023.109573 · Cited by 17
The Role of Circadian Rhythm in Neurological Diseases: A Translational Perspective
Huang, W., Zong, J., Zhang, Y. L., Zhou, Y., Zhang, L., Wang, Y., Shan, Z., Xie, Q., Li, M., Pan, S., et al. (2023) · Aging and Disease · doi:10.14336/ad.2023.0921 · Cited by 16
“The analysis of gene expression in the SCN showed that genes related to protein stabilization and folding are rhythmically expressed, such as heat shock proteins HSP70 and HSP90 [89].”
BackgroundHarding, C., Bechtold, D. A., & Brown, T. M. (2020) · BMC Biology · doi:10.1186/s12915-020-00871-8 · Cited by 15
Li, K., Shi, Y., Gonye, E. C., & Bayliss, D. A. (2021) · eNeuro · doi:10.1523/eneuro.0212-21.2021 · Cited by 14
“…of SCN neurons express either (or both) of the neuropeptides, vasoactive intestinal polypeptide (Vip) or arginine vasopressin (Avp), which are associated, respectively, with the core and shell regions of the SCN (Card et al., 1981; Abrahamson and Moore, 2001; Todd et al., 2020; Wen et al., 2020).”
BackgroundGene networks under circadian control exhibit diurnal organization in primate organs
Li, J., Nie, P., Turck, C. W., & Wang, G. (2022) · Communications Biology · doi:10.1038/s42003-022-03722-0 · Cited by 15
“Forthcoming research that applies single-cell sequencing technologies to the molecular architecture of the circadian clock could help validate our findings herein (Wen et al. 2020).”
BackgroundCircadian rhythm mechanism in the suprachiasmatic nucleus and its relation to the olfactory system
Tsuno, Y., & Mieda, M. (2024) · Frontiers in Neural Circuits · doi:10.3389/fncir.2024.1385908 · Cited by 14
“Recent single-cell transcriptomic analyses have shown that the SCN neurons can be classified into 5 (Park et al., 2016; Wen et al., 2020), 11 (Morris et al., 2021) or 12 subtypes (Xu et al., 2021).”
BackgroundHierarchy or Heterarchy of Mammalian Circadian Timekeepers?
Bechtel, W. (2024) · Journal of Biological Rhythms · doi:10.1177/07487304241286573 · Cited by 14
Genome-wide studies of time of day in the brain: Design and analysis
Wu, G., Ruben, M. D., Lee, Y., Li, J., Hughes, M. E., & Hogenesch, J. B. (2020) · Brain Science Advances · doi:10.26599/bsa.2020.9050005 · Cited by 12
“A lower sampling density may suffice when testing new and/or expensive technology or working with difficult to collect samples [35].”
BackgroundGenesis of the Master Circadian Pacemaker in Mice
Cheng, A. H., & Cheng, H. M. (2021) · Frontiers in Neuroscience · doi:10.3389/fnins.2021.659974 · Cited by 14
“This light-like response to GRP stimulation is accompanied by the upregulation of Per1 and c-Fos expression in the dorsal SCN (Aida et al., 2002).”
BackgroundInfluentialLuo, Y., Li, L., Chen, Z.-K., Dong, P., Xie, L., Farmer, W. T., Yu, Q.-S., Jiang, L.-X., Su, W.-K., Liu, H., et al. (2025) · Neuron · doi:10.1016/j.neuron.2025.09.006 · Cited by 14
Self-citationHitrec, T., Petit, C., Cryer, E., Muir, C., Tal, N., Fustin, J., Hughes, A. T. L., & Piggins, H. D. (2023) · iScience · doi:10.1016/j.isci.2023.106002 · Cited by 11
“In particular, Penk and Pdyn are mostly expressed in a different subpopulation of SCN neurons to those that synthesize Avp and Vip.(73) Therefore, our experimental design did not hinder us from making new observations on widespread genetic and exercise mediated changes in SCN transcriptome.”
BackgroundLCoRL Regulates Growth and Metabolism
Wyler, S. C., Gahlot, S., Bideyan, L., Yip, C., Dushime, J., Chen, B., Lee, J. J., Tinajero, A., Limboy, C., Bordash, S., et al. (2024) · Endocrinology · doi:10.1210/endocr/bqae146 · Cited by 14
Nikhil, K. L., Singhal, B., Granados‐Fuentes, D., Li, J.-S., Kiss, I. Z., & Herzog, E. D. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2520674122 · Cited by 11
Astrocytes as essential time‐keepers of the central pacemaker
Astiz, M., Delgado‐García, L. M., & López‐Mascaraque, L. (2021) · Glia · doi:10.1002/glia.24121 · Cited by 12
Onodera, K., Tsuno, Y., Hiraoka, Y., Tanaka, K., Maejima, T., & Mieda, M. (2023) · Scientific Reports · doi:10.1038/s41598-023-44282-5 · Cited by 12
Loh, B. M. V., Yaw, A. M., Breuer, J. A., Jackson, B., Nguyen, D., Jang, K., Ramos, F., Ho, E. V., Cui, L. J., Gillette, D., et al. (2023) · Frontiers in Endocrinology · doi:10.3389/fendo.2023.1269672 · Cited by 13
Neuron-Astrocyte Interactions and Circadian Timekeeping in Mammals
Smyllie, N. J., Hastings, M. H., & Patton, A. P. (2024) · The Neuroscientist · doi:10.1177/10738584241245307 · Cited by 12
“…RNA sequencing has provided a more comprehensive view of the cellular complexity and network topology of the SCN (Morris and others 2021; Wen and others 2020), revealing additional cell clusters enriched in neuropeptides or neuropeptide receptor transcripts, including cholecystokinin,…”
Wang, Z., Yu, J., Zhai, M., Wang, Z., Sheng, K., Zhu, Y., Wang, T., Liu, M., Wang, L., Yan, M., et al. (2024) · Cell Research · doi:10.1038/s41422-024-00956-x · Cited by 13
“Wehaveuncovered a number of salient and rather distinctive features of SCN Ca 2 + signals.”
BackgroundQi, D., Huang, D., Ba, M., Xuan, S., Si, H., Lu, D., Pei, X., Zhang, W., Huang, S., & Li, Z. (2024) · Experimental Eye Research · doi:10.1016/j.exer.2024.110008 · Cited by 13
Cellular evolution of the hypothalamic preoptic area of behaviorally divergent deer mice
Chen, J., Richardson, P. R., Kirby, C., Eddy, S. R., & Hoekstra, H. E. (2025) · eLife · doi:10.1101/2024.08.22.608850 · Cited by 11
Imaging the Hypothalamo-Neurohypophysial System
Bárez‐López, S., Scanlon, L., Murphy, D., & Greenwood, M. P. (2021) · Neuroendocrinology · doi:10.1159/000519233 · Cited by 14
Circadian Rhythms and Sleep Are Dependent Upon Expression Levels of Key Ubiquitin Ligase Ube3a
Shi, S.-Q., Mahoney, C. E., Houdek, P., Zhao, W., Anderson, M. P., Zhuo, X., Beaudet, A. L., Sumová, A., Scammell, T. E., & Johnson, C. H. (2022) · Frontiers in Behavioral Neuroscience · doi:10.3389/fnbeh.2022.837523 · Cited by 14
Bussi, I. L., Neitz, A. F., Sanchez, R. E. A., Casiraghi, L. P., Moldavan, M. G., Kunda, D., Allen, C. N., Evans, J. A., & de la Iglesia, H. O. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2314857120 · Cited by 11
Kwon, J., Jang, M. W., & Lee, C. J. (2021) · Molecular Brain · doi:10.1186/s13041-021-00881-9 · Cited by 11
Characterization of mWake expression in the murine brain
Bell, B. J., Wang, A. A., Kim, D. W., Xiong, J., Blackshaw, S., & Wu, M. N. (2020) · The Journal of Comparative Neurology · doi:10.1002/cne.25066 · Cited by 12
Comparative transcriptomic rhythms in the mouse and human prefrontal cortex
Burns, J. N., Jenkins, A. K., Xue, X., Petersen, K. A., Ketchesin, K. D., Perez, M. S., Vadnie, C. A., Scott, M. R., Seney, M. L., Tseng, G. C., et al. (2025) · Frontiers in Neuroscience · doi:10.3389/fnins.2024.1524615 · Cited by 10
Krüppel-like factor 7 deficiency causes autistic-like behavior in mice via regulating Clock gene
Tian, H., Jiao, Y., Guo, M., Wang, Y., Wang, R. L., Wang, C., Chen, D., & Tian, W. (2022) · Cell & Bioscience · doi:10.1186/s13578-022-00903-6 · Cited by 10
“Klf7 is a rhythm transcription factor that can enrich rhythm genes in the suprachiasmatic nucleus (SCNs) and regulate the expression of rhythm genes with clock transcription factors [11, 12].”
BackgroundSingle-cell transcriptomics allows novel insights into aging and circadian processes
Costa, S. S. F., Robinson‐Rechavi, M., & Ripperger, J. A. (2020) · Briefings in Functional Genomics · doi:10.1093/bfgp/elaa014 · Cited by 11
“Recently, the organization of the SCN was reinvestigated by another group using scRNA-Seq [36].”
BackgroundMethodPhase Gradients and Anisotropy of the Suprachiasmatic Network: Discovery of Phaseoids
Yoshikawa, T., Pauls, S. D., Foley, N. C., Taub, A., LeSauter, J., Foley, D. K., Honma, K., Honma, S., & Silver, R. (2021) · eNeuro · doi:10.1523/eneuro.0078-21.2021 · Cited by 10
Hussein, L. E. C., Fontanaud, P., Mollard, P., & Bonnefont, X. (2022) · PNAS Nexus · doi:10.1093/pnasnexus/pgac112 · Cited by 10
“Since the SCN are composed of multiple neuronal subtypes, based on gene expression profiles or neuropeptide content (31-35), the question arises as to whether neurons exhibiting the same Cai code belong to the same subtype and/or eventually constitute functional units gating specific body”
BackgroundHunyara, J. L., Daly, K. M., Torres, K., Yurgel, M. E., Komal, R., Hattar, S. S., & Kolodkin, A. L. (2023) · PLoS Biology · doi:10.1371/journal.pbio.3002412 · Cited by 9
“It is comprised of multiple, spatially segregated, GABAergic neuron subtypes that are largely defined by differences in neuropeptide expression [7].”
BackgroundCox, O., Giannoni‐Guzmán, M. A., Cartailler, J., Cottam, M. A., & McMahon, D. G. (2024) · Journal of Biological Rhythms · doi:10.1177/07487304241265439 · Cited by 9
“In addition, similar high degrees of overlap were found in comparison to gene expression data from recent scRNA studies of SCN neurons (Morris et al., 2021; Wen et al., 2020).”
Patton, A. P., Krogager, T. P., Maywood, E. S., Smyllie, N. J., Morris, E. L., Skehel, M. J., & Hastings, M. H. (2025) · Glia · doi:10.1002/glia.70018 · Cited by 9
“The cellular SCN network is heterogeneous, including neurons and astrocytes (Morris et al. 2021; Wen et al. 2020; Xu et al. 2021).”
Evolving perspectives on the molecular and neural foundations of mammalian circadian rhythms
Liu, Y., Huo, R., & Zhang, E. E. (2025) · Trends in Neurosciences · doi:10.1016/j.tins.2025.09.009 · Cited by 9
Coomans, C. P., Saaltink, D., Deboer, T., Tersteeg, M. M. H., Lanooij, S. D., Schneider, A.-F. E., Mulder, A. A., van Minnen, J., Jost, C. R., Koster, A. J., et al. (2021) · Glia · doi:10.1002/glia.24069 · Cited by 9
“(Abrahamson & Moore, 2001; Park et al., 2016; Wen et al., 2020).”
BackgroundCircadian regulation of endoplasmic reticulum calcium response in cultured mouse astrocytesPreprint
Ryu, J. E., Shim, K.-W., Roh, H. W., Park, M., Lee, J., & Kim, E. Y. (2024) · eLife · doi:10.7554/elife.96357 · Cited by 10
Cellular evolution of the hypothalamic preoptic area of behaviorally divergent deer micePreprint
Chen, J., Richardson, P. R., Kirby, C., Eddy, S. R., & Hoekstra, H. E. (2024) · eLife · doi:10.7554/elife.103109 · Cited by 11
“For example, cluster 2 forms a clear “island” on our UMAP and is transcriptionally specified by high expression of Pvalb , Gad1 , and Gad2 (Fig 1D, Supp Figs 6-7).”
Thirouin, Z. S., Gizowski, C., Murtaz, A., & Bourque, C. W. (2023) · Journal of Neuroendocrinology · doi:10.1111/jne.13273 · Cited by 8
“Indeed, there is good reason to believe that several subsets of VP neurons exist within the SCN based on the fact that small groups of SCN VP neurons can be found to project to distinct anatomical sites, 19 on the identification of distinct transcriptomic clusters of SCN neurons that express VP, 41 and on the existenc…”
BackgroundCircadian Clocks, Daily Stress, and Neurodegenerative Disease
Nyamugenda, E., Rosensweig, C., & Allada, R. (2024) · Annual Review of Pathology Mechanisms of Disease · doi:10.1146/annurev-pathmechdis-031521-033828 · Cited by 9
Transcriptomic DN3 clock neuron subtypes regulate Drosophila sleep
Ma, D., Le, J. Q., Dai, X., Díaz, M. M., Abruzzi, K. C., & Rosbash, M. (2025) · Science Advances · doi:10.1126/sciadv.adr4580 · Cited by 8
Self-citationMa, D., Ojha, P., Yu, A. D., Araújo, M. D. S., Luo, W., Keefer, E., Díaz, M. M., Wu, M., Joiner, W. J., Abruzzi, K. C., et al. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2321338121 · Cited by 6
Self-citationKahan, A., Mahe, K., Dutta, S., Kassraian, P., Wang, A. Z., & Gradinaru, V. (2023) · iScience · doi:10.1016/j.isci.2023.107865 · Cited by 9
“Based on singlecell mRNA sequencing data, SCN neurons can be genetically separated further into two major neuropeptidergic subpopulations, Vip+/ Grp+ and Vip+/Nms+, with a relatively low percentage of rhythmic genes in the Vip+/Grp+ subgroup compared to the Vip+/Nms+ subgroup.(6,7) Functionally, it was shown that SCN…”
BackgroundBafna, A., Banks, G. T., Hastings, M. H., & Nolan, P. M. (2023) · Genome Research · doi:10.1101/gr.277581.122 · Cited by 13
“Consequently, the SCN-enriched enhancers were also seen adjacent to the genes defining SCN cell types such as neurons, astrocytes, and ependyma (Wen et al. 2020; Xu et al. 2021) and hold potential to further delimit the sub-types based on the regulatory elements.”
Liao, M., Gao, X., Chen, C., Li, Q., Guo, Q., Huang, H., Zhang, E. E., & Ju, D. (2023) · Science China Life Sciences · doi:10.1007/s11427-023-2420-7 · Cited by 7
“…2020) and single-cell RNA sequencing techniques are widely used to characterize the transcriptomic features of neuronal subtypes (Morris et al., 2021; Wen et al., 2020; Xu et al., 2021), methods that simultaneously reflect both projection and gene expression patterns have not been well applied.”
Pierre-Ferrer, S., Collins, B. H., Lukacsovich, D., Wen, S., Cai, Y., Winterer, J., Yan, J., Pedersen, L., Földy, C., & Brown, S. A. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114220 · Cited by 7
Self-citationNarain, P., Petković, A., Šušić, M., Haniffa, S., Anwar, M., Arnoux, M., Drou, N., Saldi, G.-A., & Chaudhury, D. (2024) · Translational Psychiatry · doi:10.1038/s41398-024-03100-w · Cited by 7
Detecting Rhythmic Gene Expression in Single-cell Transcriptomics
Xu, B., Ma, D., Abruzzi, K. C., & Braun, R. (2024) · Journal of Biological Rhythms · doi:10.1177/07487304241273182 · Cited by 7
“Our choice of methods is motivated both by their popularity (Ray et al., 2020; Wolff et al., 2022; Ma et al., 2021; Wen et al., 2020) and their ability to handle replicates and run efficiently when sample size is low (Mei et al., 2021).”
Self-citationHung, C. J., Tsai, C.-T., Rahaman, S. M., Yamanaka, A., Seo, W., Yokoyama, T., Sakamoto, M., & Ono, D. (2024) · Journal of Neuroscience · doi:10.1523/jneurosci.0351-24.2024 · Cited by 9
Role of circadian clock in female embryo implantation
Zhou, Y., He, X., Chen, Z., Gou, Y., Zhou, K., Huang, J., Chen, M., Hong, J., & Gao, L. (2025) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2025.1607491 · Cited by 8
A Journey in the Brain’s Clock: In Vivo Veritas?
Davidson, A., Beckner, D., & Bonnefont, X. (2023) · Biology · doi:10.3390/biology12081136 · Cited by 7
Zhu, Y., Yan, A., Shu, B., Chen, X., Chen, Y., Duan, G., & Huang, H. (2022) · Frontiers in Neuroscience · doi:10.3389/fnins.2022.810166 · Cited by 7
Developmental patterning of peptide transcription in the central circadian clock in both sexes
Carmona‐Alcocer, V., Brown, L. S., Anchan, A., Rohr, K. E., & Evans, J. A. (2023) · Frontiers in Neuroscience · doi:10.3389/fnins.2023.1177458 · Cited by 7
Vasculature of the Suprachiasmatic Nucleus: Pathways for Diffusible Output Signals
Yao, Y., Green, I. K., Taub, A., Tazebay, R., LeSauter, J., & Silver, R. (2023) · Journal of Biological Rhythms · doi:10.1177/07487304231189537 · Cited by 8
“The SCN is a heterogeneous nucleus in terms of neuronal phenotypes in its core and shell subregions (Abrahamson and Moore, 2001; Varadarajan et al., 2018; Wen et al., 2020).”
BackgroundCell-type and sex-specific rhythmic gene expression in the nucleus accumbens
DePoy, L. M., Petersen, K. A., Zong, W., Ketchesin, K. D., Matthaei, R. C., Yin, R., Perez, M. S., Vadnie, C. A., Becker‐Krail, D. D., Scott, M. R., et al. (2024) · Molecular Psychiatry · doi:10.1038/s41380-024-02569-7 · Cited by 8
Arginine vasopressin: Critical regulator of circadian homeostasis
Yamaguchi, Y. (2024) · Peptides · doi:10.1016/j.peptides.2024.171229 · Cited by 5
Suprachiasmatic nucleus VIPergic fibers show a circadian rhythm of expansion and retraction
Neitz, A. F., Carter, B. M., Ceriani, M. F., Ellisman, M. H., & de la Iglesia, H. O. (2024) · Current Biology · doi:10.1016/j.cub.2024.07.051 · Cited by 6
The role of BMAL1 in glial cells: Implications for cognitive function in neurodegenerative diseases
Ding, Z., Zhuang, Y., Jian, J., Jiang, T., Huang, J., Yang, M., Yang, L., & Liu, W. (2025) · Brain Research Bulletin · doi:10.1016/j.brainresbull.2025.111463 · Cited by 6
“Single-cell RNA sequencing showed that rhythmic expression of BMAL1 was largely absent in oligodendrocytes and microglia in the SCN (Wen et al., 2020).”
InfluentialNeuronal feedback loop of the suprachiasmatic nucleus generates robust circadian rhythms
Wang, M., Tsuno, Y., Peng, Y., Islam, M. T., Matsui, A., Maejima, T., & Mieda, M. (2026) · Nature Communications · doi:10.1038/s41467-025-68218-x · Cited by 6
“In addition, each population still contains molecularly heterogeneous subpopulations 25,26,34 .”
Time matters: circadian genetics and the molecular logic of human health and disease
Kuo, T. T., Wang, J., & Kay, S. A. (2026) · Nature Reviews Genetics · doi:10.1038/s41576-026-00962-2 · Cited by 8
Yang, N.-D., Mellor, R. L., Hermanstyne, T. O., & Nerbonne, J. M. (2023) · Journal of Neuroscience · doi:10.1523/jneurosci.0182-23.2023 · Cited by 6
Saurabh, S., Meier, R. J., Pireva, L. M., Mirza, R. A., & Cavanaugh, D. J. (2024) · Journal of Biological Rhythms · doi:10.1177/07487304241263734 · Cited by 5
“…suprachiasmatic nucleus, the mammalian equivalent of the Drosophila clock neurons, suggest a similar organization with multiple, molecularly distinct populations of interconnected neurons that together generate rhythmic behavioral outputs (Hastings et al., 2018; Wen et al., 2020; Xu et al., 2021).”
Helfrich‐Förster, C. (2024) · Journal of Biological Rhythms · doi:10.1177/07487304241290861 · Cited by 6
“These are neurons containing the neuropeptide cholecystokinin (CKK) (Xie et al., 2023), some of which also appear to express AVP and prokineticin, as revealed by RNA sequencing analyses (Wen et al., 2020; Xu et al., 2021; summarized in Mieda, 2023).”
Loss of Bmal1 impairs the glutamatergic light input to the SCN in mice
Korkmaz, H., Anstötz, M., Wellinghof, T., Fazari, B., Hallenberger, A., Bergmann, A. K., Niggetiedt, E., Güven, F. D., Tundo‐Lavalle, F., Purath, F. F. A., et al. (2025) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2025.1538985 · Cited by 6
“Almost all SCN neurons are GABAergic (Reghunandanan and Reghunandanan, 2006; Varadarajan et al., 2018; Wen et al., 2020).”
Yeh, P., Jhan, K.-C., Chua, E.-P., Chen, W.-C., Chu, S., Wu, S., & Chen, S. (2025) · Nature Communications · doi:10.1038/s41467-025-58661-1 · Cited by 6
“Also, the methods mention 6 trials per time point but the results mention 9 trials per time point.”
The Making and Breaking of RNAs: Dynamics of Rhythmic RNA Expression in Mammals
Unruh, B. A., & Kojima, S. (2020) · Journal of Biological Rhythms · doi:10.1177/0748730420957498 · Cited by 6
“Tissue-specific rhythmic RNA expression may be derived from the unique rhythmic RNA profile at the single-cell level from various cell types and interindividual variability (Chakrabarti et al., 2018; Wen et al., 2020).”
BackgroundPhenotyping of light-activated neurons in the mouse SCN based on the expression of FOS and EGR1
Riedel, C. S., Georg, B., & Hannibal, J. (2024) · Frontiers in Physiology · doi:10.3389/fphys.2023.1321007 · Cited by 6
“In the rat SCN, a subpopulation of Ngb neurons, some of which co-stored GRP, was found to express FOS after light stimulation at night.”
BackgroundResultInfluentialExtensive soma‐soma plate‐like contact sites (ephapses) connect suprachiasmatic nucleus neurons
Czeisler, M. É., Shan, Y., Schalek, R. L., Berger, D. R., Suissa‐Peleg, A., Takahashi, J. S., & Lichtman, J. W. (2024) · The Journal of Comparative Neurology · doi:10.1002/cne.25624 · Cited by 6
“Third, recent studies have discovered distinctive roles of different SCN cell types in the structural (Wen et al., 2020) and functional (Shan et al., 2020) connectome.”
BackgroundCorrêa‐da‐Silva, F., Berkhout, J. B., Schouten, P., Sinnema, M., Schrander-Stumpel, C. T. R. M., Curfs, L., Höybye, C., Mahfouz, A. E., Meijer, O. C., Pereira, A. M., et al. (2025) · Journal of Neuroendocrinology · doi:10.1111/jne.70015 · Cited by 5
“AVP-and VIP-containing neurons are the most abundant neuronal populations in the SCN of rodents 31 and humans, 52 with AVP-expressing neurons being the pivotal pacesetter cells.”
Kim, H., Park, I., Park, J.-E., Kim, J. K., Seo, M., & Kim, J. K. (2025) · Nature Communications · doi:10.1038/s41467-025-60702-8 · Cited by 9
Molecular and cellular rhythms in excitatory and inhibitory neurons in the mouse prefrontal cortex
Burns, J. N., Jenkins, A. K., Yin, R., Zong, W., DePoy, L. M., Petersen, K. A., Kaminsky, M., Vadnie, C. A., Scott, M. R., Tseng, G. C., et al. (2025) · Cerebral Cortex · doi:10.1093/cercor/bhaf188 · Cited by 4
Cells and Circuits of the Suprachiasmatic Nucleus and the Control of Circadian Behaviour and Sleep
Patton, A. P., Hastings, M. H., & Smyllie, N. J. (2023) · Healthy ageing and longevity · doi:10.1007/978-3-031-22468-3_2 · Cited by 6
The isolation strategy and chemical analysis of oil cells from Asari Radix et Rhizoma
Hu, H., Liu, G., & Li, Y. (2024) · Plant Methods · doi:10.1186/s13007-024-01184-5 · Cited by 5
SOX2 Regulates Neuronal Differentiation of the Suprachiasmatic Nucleus
Cheng, A. H., Fung, S. W., Hegazi, S., Abdalla, O. H. M. H., & Cheng, H. M. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms23010229 · Cited by 5
Author response: OpenNucleome for high resolution nuclear structural and dynamical modeling
Lao, Z., Kamat, K., Jiang, Z., & Zhang, B. (2024) · eLife · doi:10.7554/elife.93223.2.sa4 · Cited by 4
Paul, J. R., Rhoads, M. K., Elam, A., Pollock, D. M., & Gamble, K. L. (2025) · Function · doi:10.1093/function/zqaf014 · Cited by 4
“28 However, less is known about the impact of the ET system in the centr al re gulation of acclimation to an HSD despite evidence for endothelial cell expression of Edn3 in the SCN ( Supplemental Figure S1 ; Wen et al. 12 ), as well as expression of ET B receptors in multiple hypothalamic regions, including the SCN. 9…”
InfluentialPanda, M., Fakitsa, M., Markaki, M., & Tavernarakis, N. (2025) · Advanced Drug Delivery Reviews · doi:10.1016/j.addr.2025.115655 · Cited by 4
Izumo, M., Cox, K. H., & Takahashi, J. S. (2026) · Neurobiology of Sleep and Circadian Rhythms · doi:10.1016/j.nbscr.2026.100143 · Cited by 5
“So far, the analysis has been performed for dissociated SCN neurons (Park et al., 2016; Wen et al., 2020; Xu et al., 2021).”
InfluentialSpatial and single-cell transcriptomic atlas of human suprachiasmatic nucleus
Yang, Q., Wang, H., Gao, L., Ma, D., Xiong, Y., Tian, Y., Liu, Y., Shen, Z., Zhang, X., Li, W., et al. (2026) · Neuron · doi:10.1016/j.neuron.2025.12.032 · Cited by 4
Self-citationNikhat, A., Mandal, T., Veerasubramanian, N., & Chakrabarti, S. (2026) · iScience · doi:10.1016/j.isci.2026.115394 · Cited by 4
“38,39 In this study, we systematically probe the limits of single-cell circadian phase decoding from RNA measurements of core-clock genes.”
Hypothalamic clock governs circadian pain
Wei, H.-R., Lou, Q., Li, L.-X., Tang, L., Wu, R.-J., Li, H.-Y., Jiang, A., Yang, X., Gao, W., Zhao, X., et al. (2026) · Science · doi:10.1126/science.ady6455 · Cited by 5
Reghunandanan, V. (2024) · Exploration of neuroscience · doi:10.37349/en.2024.00059 · Cited by 4
Zeman, M., Štefánik, P., Rumanova, V. S., & Okuliarová, M. (2025) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2025.112559 · Cited by 5
Vasopressin Neurons: Master Integrators of Time and Homeostasis
Bussi, I. L., Sanchez, R. E. A., & de la Iglesia, H. O. (2020) · Trends in Neurosciences · doi:10.1016/j.tins.2020.08.007 · Cited by 4
Olejniczak, I., Campbell, B. F. N., Tsai, Y., Tyagarajan, S. K., Albrecht, U., & Ripperger, J. A. (2022) · Frontiers in Physiology · doi:10.3389/fphys.2022.909795 · Cited by 4
“Detailed single-cell analysis of the SCN region revealed at least five different subregions based on their neuronal composition (Wen et al., 2020; Morris et al., 2021).”
BackgroundRegulation of CRE-Dependent Transcriptional Activity in a Mouse Suprachiasmatic Nucleus Cell Line
Langiu, M., Bechstein, P., Neumann, S., Spohn, G., & Maronde, E. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms232012226 · Cited by 4
“The suprachiasmatic nucleus (SCN) of the mouse consists of a number of different cell types [7].”
BackgroundOpenNucleome for high-resolution nuclear structural and dynamical modeling
Lao, Z., Kamat, K., Jiang, Z., & Zhang, B. (2024) · eLife · doi:10.7554/elife.93223 · Cited by 12
“However, it is worth noting that these sequencing methods often offer averaged contacts, which can mask the heterogeneity present across populations, although single-cell techniques are also emerging ( Wen et al., 2020 ; Ramani et al., 2017 ; Nagano et al., 2013 ).”
BackgroundWang, J., Gu, C., Xu, Y., & Zou, W. (2024) · Chaos An Interdisciplinary Journal of Nonlinear Science · doi:10.1063/5.0189672 · Cited by 5
Daily electrical activity in the master circadian clock of a diurnal mammalPreprint
Baño‐Otálora, B., Moye, M. J., Brown, T. M., Lucas, R. J., Diekman, C. O., & Belle, M. D. C. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.12.23.424225 · Cited by 4
“The transcripts for these auxiliary proteins are expressed brain-wide across different mammals, including in the SCN of nocturnal rodents (Wen et al., 2020) and the diurnal baboon (Mure et al.”
BackgroundNguyen, H. P., Chan, C. S. Y., Cintrón, D. L., Sheng, R. R., Harshman, L., Nobuhara, M., Ushiki, A., Biellak, C., An, K., Gordon, G., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.11.06.515311 · Cited by 5
Molecularly stratified hypothalamic astrocytes are cellular foci for obesityPreprint
Harkany, T., Tretiakov, E. O., Varela, L., Jarc, J., Rebernik, P., Newbold, S. A., Keimpema, E., Verkhratsky, A., Horváth, T. L., & Romanov, R. A. (2024) · Research Square · doi:10.21203/rs.3.rs-3748581/v1 · Cited by 4
“…and integrated from the paraventricular nucleus (PVN) 47 , arcuate nucleus/median eminence (ARC/ME) 37,40,62,64 , suprachiasmatic nucleus (SCN) 48,49 , ventromedial hypothalamus (VMH) 42,65 , ventroposterior hypothalamus (VPH) 50 , lateral hypothalamus (LH) 51,66 , preoptic area (POA) 52 , and…”
BackgroundMethodInfluentialBafna, A., Banks, G. T., Vasilyev, V., Dallmann, R., Hastings, M. H., & Nolan, P. M. (2025) · eLife · doi:10.7554/elife.102019 · Cited by 4
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
