DNA is the long-term storage unit for genetic information and the encoder of instructions for cellular function. However, access to this information is regulated in part by surface chemical changes to DNA, termed epigenetic modifications. In mammals, methylation of cytosine DNA bases is a prevalent epigenetic modification found in normal cells that is required for genomic stability and control of gene expression. When these DNA methylation patterns are misregulated, they can lead to inappropriate gene silencing and the onset of many diseases, including cancer. The ZBTB family consists of three members and represents a set of specialized transcription factors, termed methyl-CpG binding proteins (MBPs), that specifically recognize methylated DNA sites and mediate gene silencing. Of particular interest, prostate cancer cells produce these proteins at higher levels in a manner that correlates with increasing tumorigenicity, allowing for regulation of gene expression that promotes the disease state. While there is a clear link for the biological activities of these proteins in cancer, we have only begun to understand the underlying complexities by which they mediate gene expression. Thus, we utilize a multidisciplinary approach consisting of parallel in vitro biophysical and in cell genomic methodologies to delineate the mechanisms by which these MBPs recognize their specific DNA targets and regulate gene expression in cancer. Specifically, we aim to identify and characterize the biological activities of these MBPs in prostate cancer, with the goals of developing innovative methodologies for identifying cancer-specific genes and advancing our understanding of their molecular basis for DNA recognition.