Epigenetic mechanisms in cognition

Abstract

Although the critical role for epigenetic mechanisms in development and cell differentiation has long been appreciated, recent evidence reveals that these mechanisms are also employed in postmitotic neurons as a means of consolidating and stabilizing cognitive-behavioral memories. In this review, we discuss evidence for an "epigenetic code" in the central nervous system that mediates synaptic plasticity, learning, and memory. We consider how specific epigenetic changes are regulated and may interact with each other during memory formation and how these changes manifest functionally at the cellular and circuit levels. We also describe a central role for mitogen-activated protein kinases in controlling chromatin signaling in plasticity and memory. Finally, we consider how aberrant epigenetic modifications may lead to cognitive disorders that affect learning and memory, and we review the therapeutic potential of epigenetic treatments for the amelioration of these conditions.

Figure 1. Dynamic regulation of histone modifications directs transcriptional activity

A, Individual residues on histone tails undergo of a number of unique modifications, including acetylation, phosphorylation, and mono-, di-, and tri-methylation surround the transcription start site (TSS) for a given gene. These modifications in turn correlate with transcriptional repression (top), in which DNA is tightly condensed on the nucleosome and therefore inaccessible, or transcriptional activation (bottom), in which transcription factors (TF) or RNA polymerase II (RNAP II) can access the underlying DNA to promote gene expression. The specific epigenetic marks listed correlate with transcriptional activation or repression, although this list is by no means exhaustive. B, Expanded view of individual modifications on the tail of histone H3. See text for details and acronyms. The concept of a histone “code” suggests that individual marks interact with each other to form a combinatorial outcome. In this case, methylation at lysine 9 on H3 (a mark of transcriptional repression) and phosphorylation at serine 10 on H3 repress each other, whereas phosphorylation at serine 10 enhances acetylation on lysine 14 (a mark of transcriptional activation.

Figure 2. DNA methylation status affects gene transcription

A number of plasticity-related genes in the brain possess large CpG islands within the gene promoter region. Each CpG dinucleotide in the DNA sequence can undergo methylation by DNA methyltransferases (DNMTs), resulting in hemimethylation and/or double-stranded DNA methylation. Proteins with methyl binding domains, bind to methylated DNA and associate with other co-factors, such as HDACs or transcription factors like CREB, to alter gene expression. It is presently unclear is the specific combination of CpG methylation marks constitutes a “code” for unique outcomes, or if the overall or average density of methylation is a larger determinant of transcriptional efficacy.

Figure 3. The ERK/MAP kinase cascade in the hippocampus

The ERK/MAPK cascade can integrate a wide variety of signals and result in a final common output. The ERK cascade is initiated by the activation of Raf kinase via the small GTP-binding protein, ras, or the ras-related protein, rap-1. Activated Raf then phosphorylates MEK, a dual specific kinase. MEK phosphorylates ERK 1 and 2 on a tyrosine and threonine residue. Once activated, ERK exerts many downstream effects, including the regulation of cellular excitability and the activation of transcription factors leading to altered gene expression. Each MAP kinase cascade (ERK, JNK, and p38 MAPK) is composed of three distinct kinases activated in sequence, and despite the fact that many separate MAP kinase families exist, there is limited crosstalk between these highly homologous cascades. While many of the steps of the ERK cascade have been elucidated, the mechanisms by which the components of the MAP kinase cascade come into physical contact have not been investigated. In this context it is interesting to note that there are multiple upstream regulators of ERK in the hippocampus: NE, DA, nicotinic ACh, muscarinic ACh, histamine, estrogen, serotonin, BDNF, NMDA receptors, metabotropic glutamate receptors, AMPA receptors, voltage-gated calcium channels, reactive oxygen species, various PKC isoforms, PKA, NO, NF1, and multiple ras isoforms and homologs.

Figure 4. Model for ERK-mediated regulation of histone acetylation and gene transcription

Activation of the NMDA subtype of glutamate receptors (NMDARs) and voltage-gated Ca++ channels leads to influx of Ca++ and activation of the ras-MEK-ERK signaling cascade in adult neurons. This leads to activation of CREB-mediated transcription via intermediary actions of RSK2 or the Mitogen Stimulated Kinase, MSK. A downstream target of these kinases, CREB, is postulated to facilitate transcription through interaction with CREB-binding protein (CBP) and acetylation of histones. Additional pathways for regulating chromatin structure in memory include metabotropic glutamate receptor (mGluR) and NMDAR activation of Protein Kinase M zeta (PKMzeta) and downstream targeting of NFkappaB signaling in the nucleus. ERK MAPK signaling can also activate this pathway as an ancillary mechanism for chromatin regulation. Targets of this pathway include the transcription factors c-rel and Elk-1, which can regulate the expression of the MAPK Phosphatase MKP-3, which represents a likely site of negative feedback control of the pathway. See text and (Lubin and Sweatt, 2007) for additional discussion.