Associative learning supports learning about outcomes associated with contexts and cues. During learning, cellular ensembles that become active can be incorporated into memory engrams and later reactivated to support recall. Studies exploring engram formation and reactivation have primarily used contextual conditioning in mice and made little distinction between ensembles supporting contextual information versus cue-associated learning and recall. Furthermore, often missing in such analyses is exploration of sex differences in ensemble dynamics. Using auditory fear conditioning and activity-dependent tagging in mice, we set out to disaggregate context-associated ensembles from those associated with cue-related learning and recall while also profiling potential sex differences. Specifically, we quantified cellular activity during context exposure, fear recall, extinction training, and extinction recall in cortical and subthalamic brain regions supporting learning and memory. We found that male mice had denser ensembles of cells active in the infralimbic prefrontal cortex (IL-PFC) during context exposure, while female mice had a significantly greater proportion of newly active cells in the IL-PFC during fear recall. We also found a sexually dimorphic pattern of correlation between activity in the IL-PFC and in the zona incerta (ZI). Across sexes, we found denser overlapping cells and greater reactivation of extinction ensembles in the IL-PFC. These results emphasize that there is a distinction to be made between ensembles supporting contextual information from those encoding cue-associated memory and highlight important sex differences in ensemble dynamics.
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