Neocortical Tet3-mediated accumulation of 5-hydroxymethylcytosine promotes rapid behavioral adaptation

Abstract

5-hydroxymethylcytosine (5-hmC) is a novel DNA modification that is highly enriched in the adult brain and dynamically regulated by neural activity. 5-hmC accumulates across the lifespan; however, the functional relevance of this change in 5-hmC and whether it is necessary for behavioral adaptation have not been fully elucidated. Moreover, although the ten-eleven translocation (Tet) family of enzymes is known to be essential for converting methylated DNA to 5-hmC, the role of individual Tet proteins in the adult cortex remains unclear. Using 5-hmC capture together with high-throughput DNA sequencing on individual mice, we show that fear extinction, an important form of reversal learning, leads to a dramatic genome-wide redistribution of 5-hmC within the infralimbic prefrontal cortex. Moreover, extinction learning-induced Tet3-mediated accumulation of 5-hmC is associated with the establishment of epigenetic states that promote gene expression and rapid behavioral adaptation.E pigenetic mechanisms are critically involved in the regulation of gene expression underlying learning and memory (1). Dynamic variation in the accumulation of a particular epigenetic mark, 5-methycytosine (5-mC), has emerged as a key factor in experience-dependent plasticity and the formation of fearrelated memory (2). However, 5-mC is not the only covalent modification of DNA in eukaryotes, as methylated cytosine guanine (CpG) dinucleotides can be successively oxidized and converted to 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC), and 5-carboxylcytosine by the Tet family of DNA dioxygenases (3, 4). Although little is known about the functional relevance of 5-fC and 5-carboxylcytosine (5, 6), an understanding of 5-hmC is starting to emerge. 5-hmC is highly enriched in the adult brain (7), dynamically regulated by neural activity (8), and accumulates across the lifespan (9). This epigenetic mark is critically involved in neuronal differentiation and in the reprogramming of pluripotent stem cells (10), and rather than being an intermediate state of active DNA demethylation, 5-hmC can be either dynamic or stable (8, 10). Unlike its repressive cousin, 5-mC, which is primarily found along CpG-rich gene promoters, 5-hmC is enriched within gene bodies and at intronexon boundaries of synaptic plasticity-related genes, as well as within distal cis-regulatory elements, which together point to an important role for 5-hmC in coordinating transcriptional activity (11-13). Thus, it is evident that the relationship between this particular covalent modification of DNA and gene expression is far more complex than currently realized.The inhibition of learned fear is an evolutionarily conserved behavioral adaptation that is essential for survival. This learning process, known as extinction, involves rapid reversal of previously learned contingencies, which depend on gene expression and protein synthesis. Impairments in the neural mechanisms that promote this beneficial response to threat can lead to the development of posttraumatic stress disorder ...

Regulation ofBDNFchromatin status and promoter accessibility in a neural correlate of associative learning

“…6,7 However, the function of Tet1 in learningdependent gene expression has recently come into question, as Tet3, but not Tet1, has been shown to be important in fear extinction learning. 24 Our co-IPs further indicate conditioningdependent interactions among regulatory proteins, given the caveat that they evaluate the global status of these protein-protein interactions across the genome. Specifically, MeCP2 strongly associates with Tet1 during conditioning suggesting the possibility that MeCP2 recruits Tet1 to CpG sites to be demethylated.…”

Reading the unique DNA methylation landscape of the brain: Non-CpG methylation, hydroxymethylation, and MeCP2

“…Such studies have implicated hmC regulation in aspects of learning and memory, hippocampal neurogenesis, and neuronal activity-regulated gene expression (35,41,42). Coupled with reports that a redistribution of genomic hmC accompanies some forms of neural plasticity (35,36), these findings suggest that hmC regulation may be intimately involved in CNS function. However, additional research will be required to distinguish more precisely the direct roles for hmC remodeling in neuronal plasticity from the secondary effects related to altered Tet function during neural development.…”

“…1). In addition, Tet1 and Tet3 mRNA levels have been found to respond to neuronal activity (35,36), raising the possibility that neuronal activity in newly formed circuits helps drive the increase in hmC in the brain and shapes the profile of hmC across the neuronal genome. It is notable that currently available evidence suggests that most hmC in the brain occurs in the CG context (>99% in mouse adult and fetal cortex) (8).…”

Driver or Passenger: Epigenomes in Alzheimer’s Disease

“…Specifically, the family of ten-eleven translocation enzymes has been shown to catalyze the conversion of mCG to 5hmC and further oxidation coupled with mechanisms such as DNA glycosylase-initiated base-excision can restore the final product into unmodified cytosine [61]. Functionally, recent findings suggest for DNA methylation a more dynamic role than originally thought and indicate that in mature neurons 5hmC could be a transient, intermediate state that is eliminated in a temporally and spatially highly constrained manner in small regions of the genome harboring regulatory function [62][63][64][65]. Independent from demethylation, neuronal 5hmC could also represent a stable mark associated with the loss of repressive chromatin structure characteristic of Polycomb-mediated repression [66].…”