REVIEWS EPIGENETIC MECHANISMS IN MEMORY FORMATION Jonathan M. Levenson and J. David Sweatt Abstract | Discoveries concerning the molecular mechanisms of cell differentiation and development have dictated the definition of a new sub-discipline of genetics known as epigenetics. Epigenetics refers to a set of self-perpetuating, post-translational modifications of DNA and nuclear proteins that produce lasting alterations in chromatin structure as a direct consequence, and lasting alterations in patterns of gene expression as an indirect consequence. The area of epigenetics is a burgeoning subfield of genetics in which there is considerable enthusiasm driving new discoveries. Neurobiologists have only recently begun to investigate the possible roles of epigenetic mechanisms in behaviour, physiology and neuropathology. Strikingly, the relevant data from the few extant neurobiology-related studies have already indicated a theme — epigenetic mechanisms probably have an important role in synaptic plasticity and memory formation. Epigenetic mechanisms typically involve heritable alter- What is epigenetics? ations in chromatin structure, which, in turn, regulate Epigenetics and its associated terminology have several gene expression. Fundamental insights about epigenetic connotations, and specific terms need to be defined heritability have come from studies of cell division and before we can discuss them in detail. We define the development. However, there is increasing evidence that genome as a complete set of haploid DNA and the func- the regulation of chromatin structure through histone tional units that it encodes. In the nucleus, DNA exists as acetylation and DNA methylation might mediate long- a highly compressed structure that consists of DNA and lasting behavioural changes in the context of learning protein, known as chromatin. The epigenome is the and memory. This idea is fascinating because similar sum of both the chromatin structure and the pattern mechanisms are used for triggering and storing long- of DNA methylation, which is the result of an inter- term memories at the cellular level during, for example, action between the genome and the environment. Three cell differentiation. Another intriguing aspect of this definitions for the term ‘epigenetic’ are currently in use hypothesis is that the storage of lifelong behavioural in the literature. memory might involve lasting changes in the physical, The broadest definition includes the transmission three-dimensional structure of DNA itself. and perpetuation of information through meiosis or Epigenetics is unfamiliar to most neurobiologists. mitosis that is not based on the sequence of DNA. This Recently, cellular, molecular and behavioural approaches process is not restricted to DNA-based transmission and have led to several exciting developments in this area can also be protein-based. This definition is broadly Department of that specifically concern neurobiological systems. In this used in the yeast literature, wherein phenotypes that can Neuroscience, Baylor College of Medicine, One Baylor review, we first introduce the topic of epigenetics and be inherited by daughter cells are perpetuated past cell Plaza, S607, Houston, then discuss the idea that the conservation of epigenetic division using protein-based mechanisms1–3. Texas 77030, USA. mechanisms for information storage represents a uni- Developmental biologists and cancer researchers Correspondence to J.D.S. fying model in biology, with epigenetic mechanisms provide a second definition for epigenetic: meiotically e-mail: [email protected] being used for cellular memory at different levels that and mitotically heritable changes in gene expression doi:10.1038/nrn1604 range from cellular differentiation to development to that are not coded in the DNA sequence itself. The Published online 14 January 2005 behavioural memory. altered patterns of gene expression can occur through 108 | FEBRUARY 2005 | VOLUME 6 www.nature.com/reviews/neuro REVIEWS The genome is marked by, for example, DNA methyla- tion or histone acetylation (or lack thereof) at specific ES cell sites that are acquired as part of the differentiation process Determination but are self-perpetuating during DNA replication and cell division. Several hepatic nuclear factors have been shown to be involved in mediating liver-specific gene expression Liver stem Neural stem cell cell during development through the regulation of histone 6–8 Differentiation acetylation .Moreover, developmentally-induced changes in histone acetylation are stably propagated from mother to daughter cells in mammals9.So,a liver cell Liver cell 1 Liver cell 2 Neural cell 1 Neural cell 2 perpetuates its specific acquired pattern of gene expres- sion across cellular generations and over time through these heritable epigenetic marks — an example of lasting Preservation of Figure 1 | Memory at the cellular level. All embryonic stem epigenetic state (ES) cells begin with identical genotypes and phenotypes. memory at the cellular level. throughout future External signals trigger developmental events that lead to the The formation of epigenetic memory is not limited cell divisions differentiation of cells. Mature cells become phenotypically to mammalian cells. Plants are induced to flower by a distinct, but remain genotypically identical. The differences in process known as vernalization that also involves epige- gene expression persist in the face of numerous cell divisions, netic mechanisms (for a review, see REF.10). For example, which indicates that they are self-sustaining. These a biennial plant must experience a period of cold Liver cell developmentally induced changes in gene expression in mature cells are mediated by epigenetic regulation of gene expression. weather between its first and second years of existence for its flowering to be triggered. Exposure to cold in biennial plants results in the activation of epigenetic several mechanisms that are based on DNA, RNA or mechanisms that involve methylation of DNA-binding proteins (see below)4. proteins and acetylation of histones, and these processes A third definition posits that epigenetics is the trigger mitotically stable changes in the pattern of gene mechanism for the stable maintenance of gene expression. In this way, plant cells ‘remember’ their expression that involves physically ‘marking’ DNA or exposure to the winter cold and are prepared for the its associated proteins. This allows genotypically iden- plant to flower during the next spring. tical cells (such as all cells in an individual human) to Another example involves T cells of the mammalian be phenotypically distinct (for example, a neuron is immune system. The commitment of T-lymphocyte phenotypically distinct from a liver cell). The mole- precursors to a wide variety of differentiated states with cular and physical basis for this type of change in different patterns of gene expression is triggered by DNA or chromatin structure5 is the focus of this numerous epigenetic mechanisms that involve DNA review. By this definition, the regulation of chromatin methylation and histone modifications (for a review, see structure is equivalent to epigenetics. REF.11). These processes are important in the formation of long-lasting immunological memory in response to a Epigenetics for information storage transient signal from the environment. Several classic examples illustrate the importance of Are these epigenetic mechanisms also extant and epigenetic mechanisms in information storage at the operable in non-dividing, terminally differentiated cellular level. They indicate that epigenetic mechanisms neurons in the adult CNS? Adult neurons no longer are widely used for the formation and storage of cellular have the problem of heritability. However, are the basic information in response to transient environmental epigenetic mechanisms that are important for infor- signals. We present these examples to emphasize that the mation storage during development also important for storage of cellular information is in some ways analo- storing memories that manifest themselves behav- gous to memory storage in the adult nervous system. iourally in the adult? We predict that these mechanisms Moreover, the lasting cellular changes are triggered by a are conserved in the adult nervous system, where they transient signal in each case, which is also analogous to have been co-opted to serve the formation of behav- the formation of behavioural memory in the CNS. ioural memories. Epigenetic mechanisms subserve A prototype example is mammalian cellular differ- changes in neuronal function in the adult that are entiation. Once an embryonic precursor cell is triggered components of memory at the behavioural level. We to differentiate into a particular cell type (for example, a propose that epigenetic processes constitute a unified liver cell), that cell and its subsequent daughter cells set of molecular mechanisms that allow information might be required to undergo thousands of cell divi- storage in systems as diverse as yeast, plants, cellular sions over the lifetime of the animal. How does a liver differentiation and memory storage in the mammalian cell remember that it is a liver cell when, over the course CNS. To this end, we view chromatin as a dynamic of cell division, it must replicate de novo its entire structure that can integrate potentially hundreds of genome? The information clearly cannot be contained signals from the cell surface and effect a coordinated in the DNA sequence itself. As mentioned