Epigenetic memory aids: Synaptic and molecular effects of HDAC inhibition that support memory formation

Learning and memory rely on synaptic communication in which intracellular signals are transported to the nucleus to stimulate transcriptional activation. Memory induced transcriptional increases are accompanied by alterations to the epigenetic landscape and can be pharmacologically mimicked to ameliorate memory in both healthy and cognitively impaired animals. Of particular interest in this regard is histone acetylation, as this epigenetic modification is enriched during memory formation and is readily amenable to pharmacological manipulation by means of histone deacetylase inhibitors (HDACis). Although multiple studies have shown that systemic HDACi administration can improve memory formation, their mode of action is not yet fully understood. In this study, we tested whether HDACis â given systemically â augment epigenetic, transcriptional and electrophysiological responses that are induced by learning, thus amplifying naturally occurring responses via cognitive epigenetic priming. To do this, we combined a system-wide HDACi treatment with a sub-threshold contextual fear conditioning (CFC) paradigm, a weakened Pavlovian modal that, alone, does not lead to long term memory formation. We found that, in combination, HDACi and CFC improve recent contextual memory that is accompanied by enhanced long-term potentiation in the hippocampus. Conversely, combined HDACi-CFC treatment induced no such synaptic strengthening in the striatum, a brain region that is not directly activated by fear conditioning. We then used bulk and single nuclear RNA-sequencing to show that HDACi activates unique transcriptional pathways, both between the two brain regions and between cell types within the hippocampus, indicating that HDACi does not act indiscriminatingly, but instead supports cellular processes that are already occurring in response to the conditioning. Finally, we show that HDACi treatment paired with contextual fear conditioning enriches H3K27ac at enhancers of known memory-related genes within the hippocampus but that not all these genes are necessarily more transcriptionally active at the same time point. These results indicate that systemic HDACi administration acts as a cognitive enhancer by amplifying brain-region specific processes that are naturally induced during memory formation but that these results may not be a direct effect of enhancer histone acetylation. These findings shed light on the mechanisms of HDACi-mediated cognitive epigenetic priming and help to pave the way for potential new therapies for memory-related disorders.

The HDAC inhibitor CI-994 acts as a molecular memory aid by facilitating synaptic and intracellular communication after learning

Allison Marie Burns, Johannes Gräff, Jose Vicente Sanchez Mut, Giulia Santoni

Long-term memory formation relies on synaptic plasticity, neuronal activity-dependent gene transcription, and epigenetic modifications. Multiple studies have shown that HDAC inhibitor (HDACi) treatments can enhance individual aspects of these processes and thereby act as putative cognitive enhancers. However, their mode of action is not fully understood. In particular, it is unclear how systemic application of HDACis, which are devoid of substrate specificity, can target pathways that promote memory formation. In this study, we explore the electrophysiological, transcriptional, and epigenetic responses that are induced by CI-994, a class I HDACi, combined with contextual fear conditioning (CFC) in mice. We show that CI-994–mediated improvement of memory formation is accompanied by enhanced long-term potentiation in the hippocampus, a brain region recruited by CFC, but not in the striatum, a brain region not primarily implicated in fear learning. Furthermore, using a combination of bulk and single-cell RNA-sequencing, we find that, when paired with CFC, HDACi treatment engages synaptic plasticity-promoting gene expression more strongly in the hippocampus, specifically in the dentate gyrus (DG). Finally, using chromatin immunoprecipitation-sequencing (ChIP-seq) of DG neurons, we show that the combined action of HDACi application and conditioning is required to elicit enhancer histone acetylation in pathways that underlie improved memory performance. Together, these results indicate that systemic HDACi administration amplifies brain region-specific processes that are naturally induced by learning.

2022

Nuclear protein phosphatase-1: an epigenetic regulator of fear memory and amygdala long-term potentiation

Johannes Gräff

Complex brain diseases and neurological disorders in human generally result from the disturbance of multiple genes and signaling pathways. These disturbances may derive from mutations, deletions, translocations or rearrangements of specific gene(s). However, over the past years, it has become clear that such disturbances may also derive from alterations in the epigenome affecting several genes simultaneously. Our work recently demonstrated that epigenetic mechanisms in the adult brain are in part regulated by protein phosphatase 1 (PP1), a protein Ser/Thr phosphatase that negatively regulates hippocampus-dependent long-term memory (LTM) and synaptic plasticity. PP1 is abundant in brain structures involved in emotional processing like the amygdala, it may therefore be involved in the regulation of fear memory, a form of memory related to post-traumatic stress disorder (PTSD) in human. Here, we demonstrate that PP1 is a molecular suppressor of fear memory and synaptic plasticity in the amygdala that can control chromatin remodeling in neurons. We show that the selective inhibition of the nuclear pool of PP1 in amygdala neurons significantly alters posttranslational modifications (PTMs) of histones and the expression of several memory-associated genes. These alterations correlate with enhanced fear memory, and with an increase in long-term potentiation (LTP) that is transcription-dependent. Our results underscore the importance of nuclear PP1 in the amygdala as an epigenetic regulator of emotional memory, and the relevance of protein phosphatases as potential targets for therapeutic treatment of brain disorders like PTSD.

2011

Protein phosphatase 1 regulates the histone code for long-term memory

Johannes Gräff

Chromatin remodeling through histone posttranslational modifications (PTMs) and DNA methylation has recently been implicated in cognitive functions, but the mechanisms involved in such epigenetic regulation remain poorly understood. Here, we show that protein phosphatase 1 (PP1) is a critical regulator of chromatin remodeling in the mammalian brain that controls histone PTMs and gene transcription associated with long-term memory. Our data show that PP1 is present at the chromatin in brain cells and interacts with enzymes of the epigenetic machinery including HDAC1 (histone deacetylase 1) and histone demethylase JMJD2A (jumonji domain-containing protein 2A). The selective inhibition of the nuclear pool of PP1 in forebrain neurons in transgenic mice is shown to induce several histone PTMs that include not only phosphorylation but also acetylation and methylation. These PTMs are residue-specific and occur at the promoter of genes important for memory formation like CREB (cAMP response element-binding protein) and NF-kappaB (nuclear factor-kappaB). These histone PTMs further co-occur with selective binding of RNA polymerase II and altered gene transcription, and are associated with improved long-term memory for objects and space. Together, these findings reveal a novel mechanism for the epigenetic control of gene transcription and long-term memory in the adult brain that depends on PP1.

Society for Neuroscience2009