| Summary: | <p>Huntington’s Disease (HD) is a repeat expansion disease where a CAG-triplet expansion in the first exon 1 of the huntingtin (<em>HTT</em>) gene leads to the production of a mutant HTT (mHTT) protein. mHTT forms toxic aggregates that alter mitochondrial function, impair protein degradation and lead to neuronal cell death, causing degeneration of medium spiny neurons (MSNs) in the brains of HD patients. Despite the well-defined genetic cause, the molecular mechanisms underlying HD pathology are still not fully understood.</p>
<p>Little is known about the transcriptional regulation of the <em>HTT</em> gene itself. To address this, I carried out transcriptional and chromatin analysis in cells from Control and HD patients. I observed transcriptional down-regulation of the <em>HTT</em> gene which correlates with its epigenetic signature in HD. The evidence from multiple repeat expansion diseases suggests that unusual nucleic acid structures are involved in their pathogenesis. Non-canonical RNA/DNA structures can interfere with transcription and have been implicated in repeat instability; therefore, I investigated their formation in HD cells. Interestingly, I observed an enrichment of double-stranded RNAs over expanded CAG repeat <em>HTT</em> transcripts, implicating them in HD pathogenesis.</p>
<p>The current understanding of the role of HTT protein in transcription and genome maintenance is still limited. Here I show that the HTT protein binds to active forms of RNA Polymerase II and several factors important for transcription and R-loop resolution. R-loops are non-canonical structures composed of an RNA/DNA hybrid and a single strand of DNA formed during transcription. Recently, R-loops have emerged as key regulators of important biological processes including transcription, DNA replication, generation of antibody diversity and epigenetics. However, if not properly regulated, R-loops can become pathogenic and accumulate in neurodegenerative disorders and cancer. Until now, the contribution of R-loops to HD pathology has not been investigated but here I show that the HTT protein is in complex with R-loop structures and may be important for their resolution during transcription. Consistent with this role of HTT protein, I detected an accumulation of pathological R-loops in several HD cellular models, including MSNs, the most affected cells in HD. In line with this, global transcription down-regulation was observed in HD cells. R-loops can be a source of DNA damage and inflammation, hallmarks of HD. Therefore, an investigation of the mechanistic link relating these phenotypes was also addressed.</p>
<p>This work provides novel insight into the role of unusual RNA/DNA structures in HD and their contribution to early neurotoxicity in HD, potentially uncovering new targets for therapeutic interventions.</p>
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