PMID- 32066983 OWN - NLM STAT- MEDLINE VI - 23 IP - 3 TI - Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus. PG - 456-467 LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Nat Neurosci JT - Nature neuroscience JID - 9809671 IS - 1546-1726 (Electronic) LID - 10.1038/s41593-020-0586-x [doi] FAU - Wen, Shao'ang AU - Wen S AUID- ORCID: http://orcid.org/0000-0002-8927-9938 AD - Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China. AD - University of Chinese Academy of Sciences, Shanghai, China. FAU - Ma, Danyi AU - Ma D AUID- ORCID: http://orcid.org/0000-0001-5701-3089 AD - Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China. AD - University of Chinese Academy of Sciences, Shanghai, China. FAU - Zhao, Meng AU - Zhao M AD - Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China. FAU - Xie, Lucheng AU - Xie L AD - Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China. AD - University of Chinese Academy of Sciences, Shanghai, China. FAU - Wu, Qingqin AU - Wu Q AD - Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China. FAU - Gou, Lingfeng AU - Gou L AD - Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China. FAU - Zhu, Chuanzhen AU - Zhu C AUID- ORCID: http://orcid.org/0000-0002-8361-490X AD - Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China. AD - University of Chinese Academy of Sciences, Shanghai, China. FAU - Fan, Yuqi AU - Fan Y AD - Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China. FAU - Wang, Haifang AU - Wang H AD - Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China. FAU - Yan, Jun AU - Yan J AUID- ORCID: http://orcid.org/0000-0002-0405-0502 AD - Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China. junyan@ion.ac.cn. AD - Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China. junyan@ion.ac.cn. AD - School of Future Technology, University of Chinese Academy of Sciences, Beijing, China. junyan@ion.ac.cn. IS - 1097-6256 (Linking) RN - 0 (Circadian Rhythm Signaling Peptides and Proteins) SB - IM MH - Animals MH - Atlases as Topic MH - Circadian Rhythm/physiology MH - Circadian Rhythm Signaling Peptides and Proteins/genetics MH - Gene Expression/*physiology/radiation effects MH - Gene Expression Regulation/physiology MH - Genomics MH - Light MH - Male MH - Mice MH - Mice, Inbred C57BL MH - Neurons/classification/*physiology MH - Photic Stimulation MH - *Single-Cell Analysis MH - Suprachiasmatic Nucleus/anatomy & histology/cytology/*physiology DCOM- 20200413 LR - 20210406 DP - 202003 DEP - 20200217 AB - 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.