Single-cell transcriptome depicts the molecular dynamics of synapse formation in mouse hippocampus

Synapses are asymmetric junctions between presynaptic and postsynaptic neurons that mediate information transfer in the brain. The proper formation of functional synapses is crucial for synaptic transmission and brain function. However, how neurons initially recognize each other to form synapses remain to be elucidated. Here, we performed single-cell RNA sequencing of the cultured hippocampal cells on the critical time points during synapse development. . We first built comprehensive single-cell transcriptomic atlas of hippocampus undergoing synapse formation. Furthermore, we focused on neurons, and systematically analyzed temporal dynamic functional transcription factors hubs.. We identified that transcription factors, such as EGR family genes, AP-1 family genes, NeuroD family genes, NF1 family genes, may act as key regulators of synapse formation. Besides, we provided the resources of increased membrane and secretory proteins associated with synapse formation, which including previously reported synapse formation genes, Nlgn3, Nectin1, Dag1, Snap25, and the newly identified potential genes, Tmem65, Grm5, Olfm1, Timp3. Finally, we analyzed the changes of cell communication signaling pathways in neurons before and after synapse formation, and identified several important signaling pathways, including NRXN, NCAM, BMP, NEGR, and so on. Collectively, our work provided a holistic view of the molecular dynamics of the hippocampal synapse formation. Single cells were sorted and used for 10x Genomics scRNA seq analyses across four key development time points days in vitro (DIV) 1,3,5,7.