Study design considerations in epigenetic studies of neuropsychiatric disease

Introduction In recent years, emerging evidencehas revealed the importance of epigenetic processes in neurodevelopment and disease. Neurodevelopmental disorders such as autism and schizophrenia are complex disorders that likely arise from the interaction of alleles at multiple loci with environmental factors. However, additional information that affects phenotype is encoded in the distribution of epigenetic marks, including DNA methylation and histone modifications. Traditionally, the term “epigenetics” refers to the ensemble of such alterations that are heritable through both mitosis and meiosis. This definition is limiting for epigenetic studies of the brain. A prevailing idea is that functional states of neurons, which can be stable for many years, involve epigenetic phenomena (Hong et al., 2005), but these states will not be transmitted to daughter cells because almost all neurons rarely divide. Such epigeneti phenomena have been reported in dynamic regulation of DNA methylation within differentiated neurons of human cerebral cortex throughout development, maturation, and aging. Striking DNA methylation changes have been observed in regulatory regions of a panel of 50 genes implicated in neurodevelopment (Siegmund et al., 2007). Therefore, for neuroepigenetic studies, a comprehensive definition can be adopted that is in line with the contemporary use of the term epigenetics that encompasses both DNA methylation and histone modification marks. A unifying definition of epigenetic events that has been proposed by Bird (2007) states: “the structural adaptation of chromosomal regions so as to register, signal or perpetuate altered activity states.” In the overview, we focus on DNA and histone methylation marks, because these marks are highly stable in postmortem brain. However, to simplify the subject matter in demonstrating relevant study design considerations in neuroepigenetic studies, we will in subsequent sections focus on DNA methylation. Epigenetic marks can function in concert through multiple feedforward and feedback mechanisms, facilitating enhanced chromatin condensation for transcriptional silencing or chromatin opening for transcriptional activity (Li et al., 2007; Ruthenburg et al., 2007). The repertoire of DNA and histone modifications is established by such enzymes as DNA methyltransferases (DNMTs), histone acetyltransferases (HATs), histone deacetylases (HDACs), histone methyltransferases (HMTs), and histone demethylases (HDMs) (Shiio and Eisenman, 2003; Levenson and Sweatt, 2005; Shilatifard, 2006). These enzymes operate both together and independently to establish epigenetic marks that are highly dynamic and flexible in determining the pattern of gene expression (Jenuwein and Allis, 2001; Turner, 2002). As such, epigenetic mechanisms play a fundamental role in neuronal function and in the nervous system.