Validation of Predicted Transcription Factor Binding Sites in Alzheimer’s Disease

Validation of Predicted Transcription Factor Binding Sites in Alzheimer’s Disease

Jerry Falwell Library, Lower Esbenshade Atrium

Alzheimer’s Disease (AD) is a neurodegenerative disease characterized by accumulation of amyloid-beta plaques and hyper-phosphorylated tau in the brain. Research has investigated the role of epigenetics in the onset and progression of AD. Epigenetic changes alter gene expression by means other than mutation of the gene sequence, such as methylation of cytosine bases. When methylation occurs at transcription factor (TF) binding sites, gene expression can be increased or decreased. CpG methylation at promoter regions of TF binding sites inhibits TF recruitment, preventing polymerase from binding to the promoter, and resulting in subsequent suppression of the gene. Another project at Liberty University is working to predict enriched TF binding sites using bioinformatics programs such as FIMO, Matlab, Galaxy, and Excel. We plan to take the top predicted TF binding sites from a list of hypomethylated and hypermethylated genes. This list of genes was generated from previous expression comparison studies of wild type and AD genomes. An electrophoretic mobility shift assay (EMSA) is an effective assay for determining protein-DNA interactions and characterizing transcription factor-DNA complexes. This assay will be used to test whether or not the predicted DNA sequences are the actual TF binding sites in vitro. The accuracy of the TF binding sites can be quantified by migration distance through a agarose gel, as the greater affinity of the TF-DNA complex results in slower migration through the gel. This permits the validation of predicted transcription factor binding sites for differentially expressed genes in AD.