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The non-coding genome [electronic resource] : lncRNA and enhancer function in epidermal homeostasis and melanoma drug resistance

Information encoded within the ~3 billion base pairs of the human genome is processed to coordinate diverse biological functions. While ~2% of the human genome is well characterized as coding for canonical proteins, the function of the vast majority of non-coding DNA is unknown (discussed further in Chapter 1). The central aim of this thesis has been to identify functional non-coding regions of the genome and determine their role in human epidermal biology. The epidermis, or skin, maintains a tight balance between its regenerative capacity and its function as a protective tissue barrier. Progenitor cells located in the basal layer of the epidermis continually self-renew, while epidermal cells that divide and migrate outwards engage a terminal differentiation program to form a barrier. Transcriptome profiling of this differentiation process led to the identification of the long non-coding RNA (lncRNA) ANCR, which was then shown to regulate progenitor function of the epidermis (Chapter 2). A novel technology was developed to investigate the protein-binding partners of RNAs (Chapter 3), and this technique was used to uncover the functional significance of a second discovered lncRNA, TINCR, that regulates terminal differentiation of the epidermis in part by binding the protein STAU1 (Chapter 4). The most deadly cancer derived from the epidermis is malignant melanoma. While treatments targeting the mutated BRAF oncogene are initially effective against a subset of melanomas, drug resistance rapidly develops. A region of non-coding DNA was discovered that acts as a lineage-specific enhancer for the drug resistance gene, MET, and disruption of this enhancer by genome editing of < 7bp of DNA within an MITF motif can selectively block drug-induced MET expression and innate resistance to BRAF inhibition (Chapter 5). Taken together, this work demonstrates a framework for identifying functional non-coding RNA and DNA that regulate a diverse set of biological processes.