Heterochromatin Repair Mechanisms: a Chromatin Perspective

SUMMARY About 10-30% of human and fly genomes comprises pericentromeric heterochromatin, a poorly characterized component of the genome where defective repair of double-strand breaks (DSB) can trigger widespread aberrant recombination and genome instability. Previous studies identified specialized mechanisms for “safe” homologous recombination (HR) repair of heterochromatin, including a poorly understood role for “silent” chromatin marks. The chromatin state is also deeply reorganized in response to damage in heterochromatin, but little is known about the nature of these changes and their roles in repair. This lack of knowledge is a major barrier to understanding how misregulation of this pathway contributes to cancer initiation and progression, and how epigenetic therapies contribute to cancer recurrence. This proposal will fill this knowledge gap by illuminating the role of chromatin composition and regulation in heterochromatin repair. We will test the hypothesis that specific chromatin modifications and non-coding RNA synthesis coordinate HR progression in space and time to enable faithful repair of heterochromatin. Specifically, this study will: 1) establish the role of ‘silent’ chromatin marks in promoting early steps of heterochromatin repair; 2) identify chromatin changes and chromatin modifiers responsible for repair progression in heterochromatin; and 3) define how damage-induced long non-coding RNAs (dilncRNAs) contribute to heterochromatin repair. We are particularly well-positioned to conduct this research. We pioneered the development of innovative approaches and tools that will be used for this study and we generated robust preliminary results at the foundation of this proposal. A particularly creative and original aspect of this research is the combination of unique strengths of the Drosophila system for the 3D analysis of heterochromatin repair dynamics, with transformative tools for site-specific DSB induction and next-generation sequencing, and with innovative in vitro assays. This unique combination of approaches will enable the first systematic characterization of chromatin responses contributing to heterochromatic repair, significantly advancing the understanding of genome stability mechanisms in multi-cellular eukaryotes. By establishing the role of chromatin composition and regulation in heterochromatin repair, this study will contribute to understanding essential mechanisms preventing cancer formation. This study will also help predict the consequences of epigenetic treatments on genome destabilization and cancer recurrences. Misregulation of heterochromatin repair is likely one of the most underestimated and powerful sources of tumorigenesis, and understanding heterochromatin repair mechanisms is a necessary step for understanding cancer etiology and for developing more effective approaches for cancer prevention, detection, and treatment.