Harmful R-loops: from molecular mechanisms to human disease

R-loops are three-stranded RNA-DNA hybrids, formed during transcription across all organisms, and regulate cellular processes including gene expression and DNA repair. Disrupted R-loop homeostasis is implicated in neurodegeneration, autoimmunity, and cancer, yet the mechanistic links between R-loop dysfunction and disease remain unclear. I recently uncovered a pathway that connects harmful R-loops to genome instability and activation of innate immune responses. Harmful R-loops are excised from the genome by nucleases, releasing RNA-DNA hybrid fragments that accumulate in the cytoplasm and activate innate immune signalling, potentially leading to cell death. I hypothesise that R-loop excision shifts R-loops from physiological regulators to pathological agents by inducing genome instability and immune activation. We aim to dissect how harmful R-loops form, are processed, and contribute to disease. Leveraging my first-in-class biochemical, imaging, and genomic approaches to characterise excised RNA-DNA hybrids, we will address three key questions: 1. What mechanisms drive harmful R-loop formation and excision? 2. How do cytoplasmic RNA-DNA hybrids activate innate immune signalling? 3. How are hybrids released extracellularly, and do they mediate intercellular signalling and aberrant immune activation? This proposal will transform our understanding of genome biology and its interplay with immunity, potentially uncovering new therapeutic strategies for a range of diseases.