Master of Science in Bioinformatics (MSc)
Evolution of gene regulatory networks
Theses completed in 2010 or later are listed below. Please note that there is a 6-12 month delay to add the latest theses.
Transcription factors (TFs) are proteins that bind to deoxyribonucleic acid (DNA) in sequence-specific ways, activating or repressing gene expression of the genes in the vicinity of their binding ¹. Altering a gene’s expression can be an effective therapeutic strategy for many diseases. A possible strategy to regulate gene expression is manipulating the TFs by making use of the biochemistry they bind to DNA with. There are almost 1700 distinct TFs, many of which bind with a low-affinity to the intended regulatory DNA sequence in the genome ². As these TFs bind and release the DNA, transient pockets are formed at the interfaces of adjacently-binding TFs. If a chemical could neatly fit into one of these transient pockets, it would stabilize the binding of these two TFs with this particular DNA sequence and glue them in place. This approach is highly specific as it would only occur in cells that express both adjacently binding TFs, and only at locations in the genome where both TFs bind in a very precise arrangement. In order to establish this new class of therapeutics, two complimentary approaches have been employed. As the mutations in the promoter region of the human telomerase reverse transcriptase (hTERT) gene are permissive for different cancers, this regulatory region was studied. Reporter assays were first designed and optimized to measure the activity level of the hTERT promoter. Following making new cell lines with the integrated reporters in their genomes, High-throughput Screening (HTS) was used to identify allele specific modifiers of hTERT promoter; in other words, compounds that could change its expression level. Investigations show that among the tested compound libraries there were some hits that might have the desired effect. Also, as another approach, Interferon-beta (IFN-beta) enhanceosome and its enhancer were investigated for possible compounds that could change the expression level of IFN-beta in Plasmacytoid Dendritic cells (pDCs). Results show that more compounds need to be screened to find possible hits with the desired effects. Since most common diseases result, in part, from genetic changes to regulatory DNA that alter gene expression, this TF glue idea could prove to be broadly applicable.