The integrity of a cell's genome is constantly challenged by DNA lesions such as base modifications and DNA strand breaks. A single double-strand break is lethal if unrepaired and may lead to loss-of-heterozygosity, mutations, deletions, genomic rearrangements and chromosome loss if repaired improperly. Such genetic alterations are the main cause of cancer and other genetic diseases. Homologous recombination is an error-free pathway for repairing DNA lesions such as single- and double-strand breaks, and for the restart of collapsed replication forks. This pathway is catalyzed by giga-Dalton protein complexes consisting of dozens of different proteins. These DNA repair factories are able to catalyze complex, multi-step biochemical processes, which have so far failed reconstitution in vitro. The aim of this project is to establish an understanding of how cells catalyze complex biochemical processes such as homologous recombination in vivo. To reach this goal, we will seek to define the complete set of RNA and protein components of DNA repair factories using a combination of genetic, cell biological and biochemical approaches in the yeast Saccharomyces cerevisiae. Further, we will characterize the molecular architecture of DNA repair factories using fluorescence resonance energy transfer (FRET) and by applying systematic hybrid loss-of-heterozygosity (LOH) to physical interactions among DNA repair proteins. Key findings will be extended to metazoans using the chicken DT40 model system. My aim is to determine the fundamental molecular principles that govern protein factories in living cells. As such, our results are likely to be directly relevant to other protein factories such as DNA replication factories, PML bodies, nuclear pore complexes and transcription clusters.