Isaac P. Vingan ^1* Shwetha Phatarpekar ² Victoria Sook Keng Tung ³ Alejandro Iván Hernández ^1,4,5 Oleg Evgrafov ^2,3,6,7 Juan M. Alarcon ^1,4,5*

• ¹ School of Graduates Studies, Program in Neural and Behavioral Sciences, State University of New York, Downstate Health Sciences University, Brooklyn, NY, United States
• ² Institute of Genomics in Health, State University of New York, Downstate Health Sciences University, Brooklyn, NY, United States
• ³ School of Graduates Studies, Program in Molecular and Cell Biology, State University of New York, Downstate Health Sciences University, Brooklyn, NY, United States
• ⁴ Department of Pathology, Downstate Health Sciences University, Brooklyn, New York, United States
• ⁵ The Robert F. Furchgott Center for Neural & Behavioral Science, State University of New York, Downstate Health Sciences University, Brooklyn, NY, United States
• ⁶ Department of Cell Biology, Downstate Health Sciences University, Brooklyn, New York, United States
• ⁷ Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States

The rodent hippocampus is a spatially organized neuronal network that supports the formation of spatial and episodic memories. We conducted bulk RNA sequencing and spatial transcriptomics experiments to measure gene expression changes in the dorsal hippocampus following the recall of active place avoidance (APA) memory. Through bulk RNA sequencing, we examined the gene expression changes following memory recall across the functionally distinct subregions of the dorsal hippocampus. We found that recall induced differentially expressed genes (DEGs) in the CA1 and CA3 hippocampal subregions were enriched with genes involved in synaptic transmission and synaptic plasticity, while DEGs in the dentate gyrus (DG) were enriched with genes involved in energy balance and ribosomal function. Through spatial transcriptomics, we examined gene expression changes following memory recall across an array of spots encompassing putative memory-associated neuronal ensembles marked by the expression of the IEGs Arc, Egr1, and c-Jun. Within samples from both trained and untrained mice, the subpopulations of spatial transcriptomic spots marked by these IEGs were transcriptomically and spatially distinct from one another. DEGs detected between Arc+ and Arc-spots exclusively in the trained mouse were enriched in several memory-related gene ontology terms, including "regulation of synaptic plasticity" and "memory." Our results suggest that APA memory recall is supported by regionalized transcriptomic profiles separating the CA1 and CA3 from the DG, transcriptionally and spatially distinct IEG expressing spatial transcriptomic spots, and biological processes related to synaptic plasticity as a defining the difference between Arc+ and Arc-spatial transcriptomic spots.