Role of the histone variant H2A.Z.1 in memory, transcription, and alternative splicing is mediated by lysine modification

Creating long-lasting memories relies on learning-induced changes in gene expression, which are regulated by epigenetic modifications of DNA and associated histone proteins. Post-translational modifications (PTMs) of histone proteins are key regulators of transcription, with different PTMs producing unique effects on gene activity and behavior. Although recent studies began to investigate histone variants as key regulators of memory formation, PTMs are rarely considered in relation to their function. Here, we analyze the role of acetylation of histone variant H2A.Z.1 in memory and gene expression. To this end, we developed AAV constructs to overexpress mutated H2A.Z.1 isoforms that either mimic acetylation (acetyl-mimetic) by replacing lysines 4, 7 and 11 with glutamine (KQ), or that have impaired acetylation (acetyl-defective) by replacing the same lysine with alanine (KA). We found that overexpression of the acetyl-mimetic (H2A.Z.1KQ) or the acetyl-defective (H2A.Z.1KA) isoforms of H2A.Z.1 in the hippocampus produces different effects on memory depending on strength of the task and sex, with H2A.Z.1KQ generally having a beneficial effect on memory, while H2A.Z.1KA results in impaired memory. We further analyzed gene expression data and found that H2A.Z.1KQ and H2A.Z.1KA uniquely impact the expression of different classes of genes in females and males. However, different genes are regulated by different isoforms in the 2 sexes. Finally, we describe, for the first time, that H2A.Z is involved in the alternative splicing of neuronal genes. Notably, H2A.Z depletion and its replacement with different isoforms influence transcription and splicing of different genes, suggesting that H2A.Z.1 can regulate genes through splicing and expression levels. This is the first study demonstrating that direct manipulation of the levels of AcH2A.Z regulates memory, gene expression and splicing. Overall, this study adds another layer of complexity to the contribution of histone variants to higher brain functions, consolidating H2A.Z as a key regulator of memory. Overall design: To investigate the effect of knocking down, and of acetylation on the histone variant H2A.Z, we injected AAVs expressing Cre into the hippocampus of H2A.Z.1/H2A.Z.2 floxed mice to konck down endogenous H2A.Z.1/H2A.Z.2 and expressing our H2A.Z.1 mutants, acetyl mimic, acetyl block or a wildtype overexpression, or overexpressing Myc as the control.