Emotions play an adaptive role in shaping neural representations of strong aversive memories. Complex mood disorders like post-traumatic stress disorder (PTSD), depression and anxiety share common symptoms of memory impairment, though their link to mechanisms of memory consolidation is not well understood. The strength of ensemble formation in micro- and macro-circuits between the central nucleus of the amygdala (cea) and the hypothalamic paraventricular nucleus (pvn) facilitates associations between different internal states, innate behaviour and aversive experiences. Understanding how ensembles representing strong aversive experiences are consolidated at the circuit and molecular level, and identifying regulatory molecular mechanisms that can be used to control plasticity within this circuit might provide much needed future therapeutic opportunities for these conditions. In this study, we characterize transcriptomic changes in the cea and pvn over the course of fear memory consolidation. Thereby, we bioinformatically identify and experimentally validate activity-regulated miR-137-3p and miR-325-3p as regulators of transcripts associated with vesicles, neuropeptide hormones, immediate early genes, ion channels and synaptic genes in the cea. We are in the process of functionally validating the regulatory role of these microRNA candidates on engram connectivity and strength of innate behaviour linked to aversive memories. Shaping the recruitability of neurons into engrams by tuning the stage-specific abundance of dendritic transcripts within the cea using the identified microRNA candidates might enable functional remapping of representations of aversive experiences.