Lysine crotonylation acts as an epigenetic switch for glutamate neurotransmission and spatial memory

Histone posttranslational modifications, particularly lysine acetylation (Kac), are critical epigenetic regulators of transcriptional programs underlying long-term memory consolidation. Beyond Kac, several other non-acetyl acylations have been identified with the ability to regulate transcription; however, their role in memory consolidation remains unknown. Here, we identify histone lysine crotonylation (Kcr) as a molecular switch for long-term memory and glutamatergic neurotransmission. We find that spatial learning induces distinct spatiotemporal patterns of Kcr across hippocampal subregions. Through genetic manipulations, we show that reducing hippocampal Kcr levels impairs memory, while increasing Kcr levels by means of crotonate administration enhances long-term memory. Single-nuclei transcriptome and chromatin accessibility analyses reveal that crotonate facilitates activation of genes regulating glutamate signaling. Cell–cell communication analysis further suggests a strengthening of glutamatergic signaling within hippocampal excitatory neurons following crotonate administration. Real-time fluorescence imaging with genetically encoded sensors functionally validates our multiomics and computational findings—demonstrating the role of Kcr in regulating presynaptic glutamate release and neuronal activity. In summary, our findings elucidate a key mechanism underlying long-term memory consolidation and excitatory neurotransmission, linking epigenetic events to synaptic function and behavior.