This application is dedicated to understanding of primary molecular cause(s) of major depressive disorder (MDD). Unlike the majority of etiological studies that concentrate on genetic and/or environmental factors, the emphasis of this project is shifted to the inter-individual variation of epigenetic modifications of DMA. The epigenetic theory can provide a cohesive interpretation for numerous epidemiological, clinical, and molecular findings in MDD. Such include the non-Mendelian mode of inheritance of MDD, molecular effects of adverse life events, discordance of monozygotic twins, sex differences in susceptibility to the disease, major fluctuations in the disease course, and inconsistent findings of molecular genetic studies. In this project, two null hypotheses will be tested: i) there is no association between epigenetic changes and MDD, and ii) if such association exists, it is non-causal. Epigenetic profiles will be investigated in 850 DNA samples from: a) monozygotic twins discordant for MDD, b) unrelated MDD patients and matched controls (peripheral blood samples, post-mortem brain tissues, and sperm samples), and c) MD0D patients during remission vs. relapse. DNA methylation profiles will be identified through the microarray-based mapping of unmethylated and hypermethylated fractions of genomic DNA. Two types of microarrays will be used: i) 12,192- element CpG island microarray that interrogates gene promoter regions, and ii) 2,000-element microarray that investigates the genes of proteins that are of primary interest in MDD, such as serotonin transporter and glucocorticoid receptor. Bioinformatics tools will be used to process over 12 M microarray data points in order to identify disease specific DNA methylation changes in the affected individuals vs. controls in both within and between all the listed comparisons. If the null hypotheses cannot be rejected, the study will provide a new perspective on the fundamental issues in MDD and other complex diseases.