Epigenetics Core

University Of Illinois At Chicago, Chicago IL

Investigators

Linked publications, trials & patents

Abstract

Project Summary/Abstract The goal of the Epigenetics core is to provide a robust platform for the identification of genes and their epigenetic regulation that are altered in distinct brain regions of male and female rats during withdrawal after chronic ethanol exposure. During the current award period, the Epigenetics Core identified a large number of genes altered in multiple brain regions during withdrawal and obtained information relevant to local changes in chromatin architecture. These studies were carried out on bulk tissue dissected from the amygdala, hippocampus, ventral tegmental area, and medial prefrontal cortex of male and female rats. Moreover, similar, translational studies were carried out defining the differentially expressed genes and the chromatin domains present in the prefrontal cortex (BA10) of alcohol use disorder (AUD) subjects as compared with age- and sex-matched control PFC. While the studies performed in bulk tissues were informative regarding key genes and pathways associated with ethanol withdrawal, little information was obtained regarding changes occurring in individual cell types in these specific brain regions. In the current submission, the proposed aims will complement the studies outlined above by analyzing the RNA- and ATAC-seq profiles obtained from single nuclei from the central amygdala, dorsal hippocampus, ventral tegmental area, and medial prefrontal cortex using 10x Genomics (Aim 1). The proposed single nuclei sequencing strategy will provide information relevant to changes in gene expression and chromatin accessibility in identified cell types in each brain region. We will prepare and sequence libraries from both male and female control rats and rats exposed to chronic ethanol followed by a 24 h withdrawal (6 replicates per sex per group per brain region). These data will also provide novel information regarding which cell types in each brain region are most responsive to the consequences of withdrawal from chronic ethanol administration. All sequences will be mapped to the genome and differential expression as well as differential chromatin accessibility will be determined. All information will be reported to Project PIs as it becomes available. The Core will use a spatial transcriptomics approach to validate cellular localization of key genes of interest in each brain region (Aim 2). We will provide epigenetic editing tools to Project PIs to allow for sequence-specific alterations in epigenetic marks which will be designed to manipulate the expression of specific genes and behavioral phenotypes (Aim 3). In addition, the Core will perform scanning electron microscopy (Aim 4) to image various synaptic features including dendritic spines, synaptic vesicles, excitatory synapses, etc.to analyze changes in these features in response to withdrawal from chronic ethanol. Collectively, these data will provide each CARE project with novel information regarding changes in gene expression and chromatin accessibility in response to withdrawal from chronic ethanol and the requisite tools to further explore these changes mechanistically.