DNA and RNA structures are involved in major biological processes, such as regulating gene expression, and can play an important role in cancer and neurodegenerative diseases. Huntington’s disease (HD) is the most common monogenic neurological disorder caused by the expanded and unstable CAG trinucleotide repeat in the first exon of the huntingtin gene (HTT). The pathology of HD has been traditionally associated with the mutant HTT protein, which confers toxic gain of function leading to dysfunction and death of neurons. However, recent evidence indicates that at least part of the gain of function may operate at the RNA level. In the first part of this thesis, the transcriptional and epigenetic regulation of the HTT gene in HD is investigated. It is shown that expanded CAG repeats of endogenous HTT transcript adopt double-stranded RNA structures that lead to RNA Polymerase II transcriptional repression and heterochromatin formation of the HTT gene in cis, providing a molecular link between dsRNA and the pathology of expansion diseases. Double-stranded RNA is a key player in numerous Biological activities in cells, however little is known about the proteins that bind to dsRNA. Therefore, a proteomics approach was established, employing the dsRNA pull-down to identify dsRNA-binding proteins in control and HD fibroblast cells. Analysis of the dsRNA interactome indicated that interaction with the top candidate ENO1 is enriched in HD and promotes dsRNA-mediated transcriptional repression of the HTT gene. This thesis work also elucidates on the importance of RNA/DNA hybrids in cancer as their accumulation is a major cause for genomic instability. The research demonstrated that cancer cells overexpressing oncogenes such as HRASV12, lead to increased RNA synthesis and RNA/DNA hybrid accumulation that can be correlated with replication stress. These events lead to DNA damage, revealing a strong link between R-loop-mediated genome instability and human disease. Overall, nucleic acid structures and their interactors could determine the ability of a single gene product to perform multiple functions, as potential disease modifiers and future targets to modulate diseases
