The role of chromosome conformation in DNA double-strand break repair

The integrity of eukaryotic genomes is constantly challenged by various endogenous and exogenous insults, whereby DNA double-strand breaks (DSBs) are particularly problematic.

DSBs can be repaired by multiple pathways, but only the homologous recombination (HR) pathway ensures error-free repair.

HR restores missing information around the lesion based on topological interactions with a homologous region on a distinct DNA molecule.

HR-directed repair can function across homologous chromosomes in diploid organisms, but is much more efficient between sister chromatids in replicated chromosomes, indicating an important role of chromosome conformation in repair.

Sister chromatids are organized by a dynamic interplay between cohesin-mediated loop extrusion, cohesin-mediated sister linkage, and chromatin-based affinity interactions. How these activities shape sister chromatids to support DNA repair is unclear.

The proposed project aims to reveal how sister chromatid conformation governs DSB repair efficiency and pathway choice in human cells and to identify and characterize the key molecular factors regulating chromosome conformation for efficient DSB repair.

Understanding how intra- and inter-molecular topological interactions contribute to DNA repair will become possible by using a new chromosome conformation capture technology developed in the hosting lab (sister-chromatid sensitive Hi-C).

This technology will be combined with a system for acute DSB induction, automated imaging and genomic profiling of DNA repair factors, and targeted protein degradation of cohesin and its regulators to elucidate topological interactions underlying DSB repair.

The proposed project will provide insights into how the core machinery shaping the three-dimensional organization of chromosomes contributes to the maintenance of genome integrity.