Immediate-early genes Arc and c-Fos show divergent brain-wide expression following contextual fear conditioning

Encoding or retrieving a fear memory induces activity across the entire brain. Neurons involved in these processes are often identified by the expression of immediate-early genes (IEGs), but the extent to which the patterns of this expression correspond between IEGs has not been well characterized. Here, male mice were administered either context exposure (no shock) or 3-shock contextual fear conditioning and euthanized 1 h after encoding, retrieval 1 day later, or retrieval 5 days later. Brain tissue was immunostained for Arc and c-Fos protein, and expression was quantified across several brain regions. We find that expression of the two IEGs substantially diverges, with fewer than 50% of total labeled cells expressing both markers across memory states. Furthermore, memory state broadly influences Arc⁺ but not c-Fos⁺ cell density in select regions. These results suggest that the ensembles identified by each gene may be more anatomically and functionally distinct than commonly thought.