Browsing by Subject "Epigenome"

The genomic DNA is bound by a myriad of proteins to form the chromatin inside the nucleus of the cell. The proteins can bind to the genome in different combinations leading to a combinatorial explosion in the number of possible chromatin configurations. The differences in the chromatin configurations for the same genome sequence give rise to distinct cell types. Likewise, cells of the same type also undergo changes in chromatin configurations under different environmental conditions. Key changes to the occupancy profile of the chromatin may dictate changes in gene regulation or vice versa. Therefore, it is important to decipher the chromatin occupancy profiles of the genome and understand how these configurations are related to the transcription of genes.

In this dissertation, we analyze chromatin using chromatin accessibility data sets, particularly MNase-seq and ATAC-seq, that describe the protein-bound and unbound regions of the genome. We first describe a state-space model that uses chromatin accessibility data to jointly infer the occupancy profile of hundreds of proteins binding to the genome. We apply our model to the yeast genome to study the occupancy profile of transcription factors and nucleosomes. We further extend our model to study chromatin dynamics of yeast cells subjected to cadmium stress. In doing so, we identify genomic regions exhibiting changes in the occupancy profile of transcription factors and nucleosomes. Upon comparing with available gene expression data we find that key changes in chromatin configuration occur around gene bodies that are differentially regulated during cadmium stress. Our analyses highlight how specific changes to the occupancy profiles relate to gene expression.

Building upon the interrelatedness of chromatin and transcription, we describe a regression-based approach that predicts transcription from chromatin accessibility data sets. We find that the chromatin accessibility in specific parts of the genome is highly correlated to gene expression. These genomic regions are potential regulatory regions that can lie far away from the gene body and interact with the genes due to the looping of the DNA. Our model identifies these regulatory regions in a gene-specific manner that helps us further understand the connections between chromatin and transcription.

Low-dose ionizing radiation (LDIR) exposure (under 10.0 centigray (cGy)) from man-made sources, such as diagnostic imaging, predominates in the US population and comprises nearly 50% of an average individual's yearly radiation exposure (Ullrich, Brooks et al. 2009). The increase in such exposures has led to public and government alarm about the impact of LDIR on human health (Ullrich, Brooks et al. 2009). Besides the mutational effects of radiation exposure, there is concern it might also result in modifications of the epigenome. Such aberrations can disrupt normal development and are involved in the progression of numerous diseases, including cancer (Gasser and Li 2011). High doses of radiation (>100.0 cGy) have been shown to cause epigenetic disruption (Kaup, Grandjean et al. 2006; Tamminga, Koturbash et al. 2008; Ilnytskyy, Koturbash et al. 2009), which is necessary for the persistence of radiation-induced genomic instability (Rugo, Mutamba et al. 2011); however, it is presently unclear to what extent LDIR in vivo alters the epigenome.

The viable yellow agouti (Avy) mouse was used here to characterize the dose-dependent epigenetic response to LDIR. The Avy mouse is a unique biological model that functions as a biosensor for environmentally induced epigenetic changes and disease susceptibility due to the presence of a metastable epiallele that modulates coat color (Waterland and Jirtle 2003). Pregnant dams were whole-body exposed to one of five doses of X-ray radiation ranging from 0-10.0 cGy on gestational day 4.5. Using a phantom mouse model, the intrauterine doses were estimated to be 0.0 cGy, 0.4 cGy, 0.7 cGy, 1.4 cGy, 3.0 cGy, and 7.6 cGy, respectively. At weaning, offspring coat colors were assessed and tissues were collected for methylation analysis. First, methylation changes at CpG sites in the Avy and Cdk activator binding protein (CabpIAP) metastable epialleles and at intracisternal a particle (IAP) elements across the genome were quantified using Sequenom technology. Second, three imprinted genes, Peg3, Nnat, and H19, were assessed for methylation changes in differentially methylated regions (DMRs) that regulate their parent-of-origin monoallelic expression using Sequenom technology. Lastly, it was postulated that the epigenetic changes at the Avy locus could be counteracted with dietary alterations. To test this hypothesis, female mice were placed on an antioxidant-supplemented diet prior to pregnancy and throughout gestation and lactation. Pregnant dams were irradiated with 3.0 cGy of whole-body X-rays. Offspring coat colors were assessed and methylation changes at the Avy allele were measured with the Sequenom platform.

Herein, I demonstrate that in utero LDIR exposure induced epigenetic changes in the Avy mouse in a dose-dependent and sex-specific manner. Acute, whole-body exposure to 0.7 cGy, 1.4 cGy, 3.0 cGy or 7.6 cGy X-rays significantly shifted offspring coat color distribution toward pseudoagouti. Acute exposure to 1.4 cGy, 3.0 cGy, and 7.6 cGy significantly increased methylation at multiple CpG sites in the Avy metastable epiallele in male offspring, but not female offspring. Methylation changes at DMRs in Nnat, Peg3, and H19 also occurred in a dose-dependent manner. Furthermore, inhibition of the phenotypic and Avy methylation changes with an antioxidant-supplemented diet suggests that the mechanisms to induce epigenetic changes are mediated by oxidative stress. These results demonstrate that relevant, low doses of radiation can elicit epigenetic changes that lead to a persistent phenotype, but can be mitigated with dietary supplementation. The successful completion of this project has resulted in the first in vivo epigenetic characterization of LDIR exposure and will contribute to the development of more relevant risk assessment strategies for protecting human populations.

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