The hippocampus is a key brain region involved in both short-and long-term memory processes and may play critical roles in drugassociated learning and addiction. Using whole genome sequencing of mRNA transcripts (RNA-Seq) and immunoprecipitation-enriched genomic DNA (ChIP-Seq) coupled with histone H3 lysine 4 trimethylation (H3K4me3), we found extensive hippocampal gene expression changes common to both cocaine-addicted and alcoholic individuals that may reflect neuronal adaptations common to both addictions. However, we also observed functional changes that were related only to long-term cocaine exposure, particularly the inhibition of mitochondrial inner membrane functions related to oxidative phosphorylation and energy metabolism, which has also been observed previously in neurodegenerative diseases. Cocaineand alcohol-related histone H3K4me3 changes highly overlapped, but greater effects were detected under cocaine exposure. There was no direct correlation, however, between either cocaine-or alcohol-related histone H3k4me3 and gene expression changes at an individual gene level, indicating that transcriptional regulation as well as drug-related gene expression changes are outcomes of a complex gene-regulatory process that includes multifaceted histone modifications.drug addiction | histone methylation K nowledge of the cellular and molecular adaptations underlying addiction to cocaine and alcohol has primarily been gained from animal models of acute and chronic drug exposure, from which specific molecular pathways to addiction have been identified (1, 2). Studies on human postmortem brain (3) have yielded data that are complementary and tend to validate animal models of exposure. Addiction-associated molecular alterations observed in animal and human studies are diverse. Clearly, cellular and molecular responses to addictive drugs depend on the type and timing of exposure, the timing of observations within the progression to addiction, and the brain regions and cells in which observations are made. Specific changes in signal transduction pathways, including in the transcription factor ΔFosB and the cAMP-response element binding protein (CREB), are likely to be more prominent in early stages of drug-induced neuroadaptation (4). Longstanding adaptations may be marked by changes in expression of genes involved in the regulation of cellular functions including ion transport, chromosome remodeling, stress and immune response, cell adhesion, cell cycle, apoptosis, protein and lipid metabolism, and mitochondrial functions (3). Later changes may be more closely relevant to addictive behaviors and long-lasting vulnerability to relapse.The hippocampus is also a brain region critically involved in addiction. Most studies have focused on the mesolimbic system, in which medium-sized spiny neurons in the dorsal striatum and nucleus accumbens mediate dopaminergic, glutamatergic, and GABAergic neurotransmission (5) and are key in drug-reward and drug-seeking behavior. However, hippocampal functions related to short-and long...