UC Irvine

Development and differentiation are complex cellular processes that are regulated by a cohort of transcription factors (TFs) and signaling molecules that can be investigated at the levels of cells, tissues, and whole organisms. Regulation of these processes is, in part, controlled by changes in DNA accessibility surrounding protein-DNA binding sites around promoter and enhancer regions of downstream target genes. Differentiation of cell types that are homologous between species are controlled by conserved networks of regulatory elements driving gene expression. In order to identify conserved and species-specific aspects of gene expression and chromatin accessibility during cell differentiation, we conducted a time-course study of differentiation in two different species between two cell lineages. We are interested in investigating the extent of conservation of developmental gene expression between species and what we can learn from these similarities including their epigenetic basis. We hypothesize that the conservation of developmental expression is encoded at the epigenetic level in changes to open chromatin and DNA methylation. The environment of an organism also influences development, both on a whole organism level and during brain development. Epigenetic changes such as differences in DNA methylation, and accessibility of TFs can have lasting effects on the phenotype of the organism. Although some epigenetic changes, such as changes in the cellular transcriptome, are localized to the affected cell or tissue, other epigenetic changes such as changes in DNA methylation can occur on a systemic scale and affect more than one organ or developmental process. During sensitive periods of development, environmental factors may have serious consequences for an organism’s health. Immune disorders and psychiatric diseases have both been linked to disturbances in epigenetic regulation.In this thesis, I describe my studies of chromatin dynamics and TF expression as well as environmental impacts on the epigenetics of brain development in multiple mammalian species. In Chapter 2 I strive to determine conserved or species-specific candidate developmental regulatory elements in distantly-related species. I find that definitive endoderm (DE) differentiation from embryonic stem cells is more conserved than neural progenitor cell (NPC) differentiation, with 22% and 8% conservation of candidate cis-regulatory elements, between human and rat, respectively. In Chapter 3 I focus on investigating the developmental plasticity of epigenetic regulation in corticotropin-releasing hormone (CRH)-expressing hypothalamic paraventricular nucleus (PVN)-neurons during early life adversity. The differentially expressed genes between early life adversity (ELA) and control (CTL) suggest that ELA PVN neurons undergo more cellular stress and neuronal activity than control neurons. Glutamatergic PVN neurons of the ELA condition may have altered energy production or are not able to properly maintain excitability or synaptic transmission. In Chapter 4 I evaluate DNA methylation changes in a number of individuals between birth and one year of life to determine the correlation to a range of life experiences. Individuals from the high unpredictability group had striking increases in methylation, suggesting reduced expression, of genes involved in cell junction organization, actin filament-based processes and differentiation. They also had decreased methylation, suggesting overexpression, of genes associated with cell proliferation, growth factor signaling, and cell motility. From such data we may be able to predict genes involved in early life experiences and their possible long-term consequences.