Genome-wide alterations in hippocampal 5-hydroxymethylcytosine links plasticity genes to acute stress

Abstract

Environmental stress is among the most important contributors to increased susceptibility to develop psychiatric disorders, including anxiety and post-traumatic stress disorder. While even acute stress alters gene expression, the molecular mechanisms underlying these changes remain largely unknown. 5-hydroxymethylcytosine (5hmC) is a novel environmentally sensitive DNA modification that is highly enriched in post-mitotic neurons and is associated with active transcription of neuronal genes. Recently, we found a hippocampal increase of 5hmC in the glucocorticoid receptor gene (Nr3c1) following acute stress, warranting a deeper investigation of stress-related 5hmC levels. Here, we used an established chemical labeling and affinity purification method coupled with high-throughput sequencing technology to generate the first genome-wide profile of hippocampal 5hmC following exposure to acute restraint stress and a one-hour recovery. This approach found a genome-wide disruption in 5hmC associated with acute stress response, primarily in genic regions, and identified known and potentially novel stress-related targets that have a significant enrichment for neuronal ontological functions. Integration of these data with hippocampal gene expression data from these same mice found stress-related hydroxymethylation correlated to altered transcript levels and sequence motif predictions indicated that 5hmC may function by mediating transcription factor binding to these transcripts. Together, these data reveal an environmental impact on this newly discovered epigenetic mark in the brain and represent a critical step toward understanding stress-related epigenetic mechanisms that alter gene expression and can lead to the development of psychiatric disorders.

Discovery and replication of a peripheral tissue DNA methylation biosignature to augment a suicide prediction model

“…Sodium bisulfite modification cannot distinguish between 5-methyl cytosine (5-MC) and 5-hydroxy methyl cytosine (5-HMC) levels. Like 5-MC, 5-HMC can vary in the brain in response to stress [47, 48] and has been identified in various psychiatric disorders [49, 50]. Brain tissue analyses have the potential to be confounded by postmortem factors such as the method and timing of tissue preservation.…”

Sex-specific hippocampal 5-hydroxymethylcytosine is disrupted in response to acute stress

“…Related to disease, 5hmC functions independently from 5mC in neurological disorders ( e.g., Rett syndrome and Autism) (Mellen et al, 2012; Papale et al, 2015; Zhubi et al, 2014) and neurodegenerative diseases ( e.g., Huntington’s and Alzheimer’s) (Chouliaras et al, 2013; Condliffe et al, 2014; Wang et al, 2013). We recently reported a genome-wide disruption of 5hmC in the hippocampus of male mice exposed to acute stress followed by a one-hour recovery (Li et al, 2016). The differential 5hmC pattern significantly resided in known stress-related genes, which serves to validate a role for 5hmC in response to stress and also reveals potentially novel stress-related genes.…”

The potential of epigenetics in stress-enhanced fear learning models of PTSD

“…Furthermore, in the hippocampus of stressed animals, the 3 ′ -UTR of the glucocorticoid receptor gene Nr3c1 was hyper-hydroxymethylated, a modification associated with increased transcription (Li et al 2015). These parallel studies also identified a pattern of hydroxymethylation throughout the genome in stressed animals, with many sites of differential hydroxymethylation located on known stress-related genes that were concomitantly changed at the mRNA level (Li et al 2016). These large-scale data sets suggest that even brief stressors induce epigenetic patterns that are capable of changing the global transcriptional profile of the brain by creating an environment that is permissible for the up-regulation of stress response genes.…”