| Although it is understood that intergenic regions of the genome are more than just "junk" DNA, there is still much to learn about its specialized function and powerful capabilities in affecting an entire cellular state. Herein, we shed light on higher order cis-regulatory mechanisms and enhancers that contribute to oncogene expression in a variety of cancer types.;The first step in comprehending distal regulatory elements is establishing an interaction between two distal genomic points. In Chapter 2, we explore the chromatin architecture surrounding multiple proto-oncogenes in mouse cancer cells and find that retroviruses hijack innate chromatin loops at these loci to deregulate gene expression and promote tumorigenesis. Through extensive mapping of the human Cyclin D1 locus, we characterize two large chromatin loops that link putative cis-regulatory elements to the proto-oncogene promoter. Finally, we classify a novel distal interaction in multiple myeloma cells harboring a pathogenic translocation event, and for the first time at this locus, provide mechanistic evidence for the abundant overexpression of Cyclin D1 occurring in this context. These studies further elucidate the aspects of epigenetic mechanisms that are crucial for distal cis-regulation.;It is well-established that environmental toxins such as exposure to arsenic are great risk factors in the development of urinary bladder cancer, yet recent genome-wide studies provide compelling evidence that there is a strong genetic component associated with disease predisposition. Through the use of genome-wide binding studies, focused functional assays and genome editing techniques, we have classified two novel regulatory elements within the bladder cancer genome that influence proto-oncogene expression, namely Cyclin E1 (CCNE1) and MYC. We characterize an intronic enhancer within CCNE1 that promotes transcription through binding of KLF5, a transcriptional activator implicated in bladder cancers. Notably, we also detect altered allelic binding of KLF5, with an enrichment of occupancy at the risk associated variant. Altogether our findings relate genetic variation within the vast non-coding genome to functional cis-regulatory mechanisms. A thorough grasp of the regulatory networks controlling important proto-oncogene expression allows for more targeted and personalized disease treatment options. |
