Alcohol metabolism contributes to brain histone acetylation.

Emerging evidence suggests that epigenetic regulation is dependent on metabolic state, and implicates specific metabolic factors in neural functions that drive behaviour1. In neurons, acetylation of histones relies on the metabolite acetyl-CoA, which is produced from acetate by chromatin-bound acetyl-CoA synthetase 2 (ACSS2)2. Notably, the breakdown of alcohol in the liver leads to a rapid increase in levels of blood acetate3, and alcohol is therefore a major source of acetate in the body. Histone acetylation in neurons may thus be under the influence of acetate that is derived from alcohol4, with potential effects on alcohol-induced gene expression in the brain, and on behaviour5. Here, using in vivo stable-isotope labelling in mice, we show that the metabolism of alcohol contributes to rapid acetylation of histones in the brain, and that this occurs in part through the direct deposition of acetyl groups that are derived from alcohol onto histones in an ACSS2-dependent manner. A similar direct deposition was observed when mice were injected with heavy-labelled acetate in vivo. In a pregnant mouse, exposure to labelled alcohol resulted in the incorporation of labelled acetyl groups into gestating fetal brains. In isolated primary hippocampal neurons ex vivo, extracellular acetate induced transcriptional programs related to learning and memory, which were sensitive to ACSS2 inhibition. We show that alcohol-related associative learning requires ACSS2 in vivo. These findings suggest that there is a direct link between alcohol metabolism and gene regulation, through the ACSS2-dependent acetylation of histones in the brain.

Single sample sequencing (S3EQ) of epigenome and transcriptome in nucleus accumbens.

BACKGROUND: High-throughput sequencing has been widely applied to uncover the molecular mechanisms underlying neurological and psychiatric disorders. The large body of data support the role of epigenetic mechanisms in neurological function of both human and animals. Yet, the existing data is limited by the fact that epigenetic and transcriptomic changes have only been measured in separate cohorts. This has limited precise correlation of epigenetic changes in gene expression. NEW METHOD: Single Sample Sequencing (S3EQ) is an innovative approach to analyze both epigenetic and transcriptomic regulation within a single neuronal sample. Using this method, we analyzed chromatin immunoprecipitation (ChIP)- and RNA-sequencing data from the nucleus accumbens (NAc) of the same animal. RESULTS: ChIP-S3EQ of neuronal nuclei reliably identified hPTM enrichment in the adult mouse NAc with high precision. Comparing cellular compartments, we found that the spliceosome of whole cell RNA-seq was more closely recapitulated by cytosolic RNA-S3EQ than nuclear RNA-seq. Finally, S3EQ showed increased sensitivity for correlating chromatin modifications with gene expression, especially for lowly expressed transcripts. COMPARISON WITH EXISTING METHODS: S3EQ accurately generates both RNA- and ChIP-seq from a single sample, providing a clear advantage over existing methods which require two samples. ChIP-S3EQ performance was comparable to ChIP-seq, while RNA-S3EQ generated an almost identical expression profile to nuclear-enriched and whole cell RNA-seq. Finally, we directly compared RNA-seq by cellular compartments, addressing a limitation of RNA-seq studies limited to neuronal nuclei. CONCLUSION: The S3EQ method can be applied to improve the correlative power of transcriptomic and epigenomic studies in neuronal tissue.