The serotonergic system in the brain plays important roles in alcohol consumption and abuse. Serotonergic neurotransmission is mainly mediated by serotonin receptors. Among the 7 known serotonin (5-HT) receptor subfamilies (5-HT1–7), only the 5-HT3 receptor directly gates an ion channel. Ethanol (EtOH) has been shown to directly interact with the 5-HT3 receptor and potentiate the action of 5-HT at the 5-HT3 receptor in a dose-dependent manner (Zhou et al., 1998). This effect can be blocked by administration of the specific 5-HT3 receptor antagonist troposetron (Lovinger and Zhou, 1998). Ondansetron, another 5-HT3 receptor antagonist, has been reported to be efficacious in reducing heavy drinking and increasing abstinence in alcoholics (Johnson et al., 2000, 2011). The 5-HT3 receptor is composed of 2 major subunits: 5-HT3A and 5-HT3B. 5-HT3A is the obligatory subunit; only 5-HT3A can form receptors independently, and it is required for the formation of functional receptors (Maricq et al., 1991). Importantly, the 5-HT3 receptor is expressed throughout the mesolimbic system, including the nucleus accumbens and the ventral tegmental area (VTA) that are known to be important for the formation of addictive behaviors (Mylecharane, 1996). Based on these data, it appears that abnormal transcription of the serotonin receptor 3A gene (HTR3A), resulting either from genetic polymorphisms or promoter DNA methylation alterations, could influence an individual’s vulnerability to alcohol dependence. There is a growing body of evidence demonstrates that epigenetic modifications (such as DNA methylation and histone modification that alter DNA accessibility and chromatin structure) are associated with alcohol dependence. Promoter DNA hypermethylation has been identified in a number of genes in peripheral blood of human alcoholics. These genes include the α-synuclein gene (SNCA) (Bonsch et al., 2005), the monoamine oxidase A gene (MAOA) (Philibert et al., 2008a), the serotonin transporter gene (SLC6A4) (Philibert et al., 2008b), the N-methyl-d-aspartate receptor subunit 2B gene (NR2B or GRIN2B) (Biermann et al., 2009), and the proopiomelanocortin gene (POMC) (Muschler et al., 2010). Our recent study also demonstrated increased DNA methylation in the promoter region of HTR3A in peripheral blood of human alcoholics (Zhang et al., in press). There is also evidence that epigenetic processes, including DNA methylation, could influence gene expression at the level of transcription (Gibney and Nolan, 2010). Therefore, altered methylation and subsequent expression of HTR3A may significantly influence vulnerability to AD by impacting serotonin signaling at the 5-HT3 receptor. Although the above-mentioned human studies are instrumental in examining the role of DNA methylation in alcohol dependence, the investigation of epigenetic changes in peripheral blood of human alcoholics has 2 major limitations. First, these experiments do not enable us to assess whether alcohol dependence-associated DNA methylation changes directly resulted from chronic alcohol consumption or whether these differences reflect preexisting changes that predispose individuals to alcoholism. It is already known that environmental factors such as early-life stress and malnutrition (that may be abnormal in alcoholic subjects) can also alter DNA methylation patterns (Alegria-Torres et al., 2011). Moreover, DNA methylation changes in alcoholic subjects may be caused by co-occurring drug use or comorbid psychiatric illness. Second, the above-cited studies used genomic DNA extracted from peripheral blood (or lymphoblastoid cell lines derived from peripheral blood lymphocytes) for determination of DNA methylation. It is as yet unclear whether DNA methylation patterns in peripheral blood are representative of brain DNA methylation and/or whether any effects of alcohol use impact peripheral blood and brain DNA methylation patterns in a homogeneous manner. Because these questions are not readily answerable using human studies, alternative models for addressing these issues are needed. To explore the causal role of EtOH exposure in DNA methylation and to assess whether EtOH-induced DNA methylation changes are consistent in peripheral blood and in the brain, we used a mouse model of subacute EtOH drinking. Specifically, we used a mouse drinking-in-the-dark (DID) paradigm (Rhodes et al., 2007), which has been shown to produce high levels of EtOH consumption while minimizing environmental stress to the animals, to investigate whether EtOH drinking directly produced hypermethylation of HTR3A promoter region, as recently seen in the peripheral blood of human alcoholics (Zhang et al., in press). DNA methylation was assessed in 9 different brain regions (dorsomedial prefrontal cortex [DMPFC], ventromedial prefrontal cortex [VMPFC], VTA, dorsolateral striatum [DLSTR], dorsomedial striatum [DMSTR], ventral striatum [VSTR], amygdala [AMY], hippocampus [HIPPO], and cerebellum [CBL]) that were selected based on their role in the reward pathway and their role in supporting the behavioral changes that are thought to underlie alcoholism (Everitt and Robbins, 2005; Oscar-Berman and Marinkovic, 2007). Additionally, expression levels of mouse Htr3a in specific brain regions were compared between alcohol- and water-drinking mice. This study made it possible to investigate (i) whether EtOH consumption led to altered DNA methylation in the promoter region of mouse Htr3a, (ii) whether EtOH drinking induced differential DNA methylation in mouse blood and different brain regions, and (iii) whether Htr3a promoter methylation changes are related to gene expression levels.