Spatial Specification of Replication Fork Integrity Pathways – Space-ForkIn

The 3D-organisation of eukaryotic genomes within compartmentalized nuclei is a critical layer of regulation of DNA-associated transactions such as transcription, DNA replication and repair, and thereby emerged as an important determinant of genetic stability. Yet, although the integrity of the genome is at its most vulnerable during DNA replication, our current knowledge about the regulatory function played by nuclear organization in the choice of fork repair pathways remains in its infancy. The Space-ForkIn proposal builds on pioneering works from the consortium showing that the nuclear periphery specifies a “fork-protective” environment to favor error-free fork restart pathways. Our integrated research program will thus expand the concept of “fork-protective” environment to several nuclear compartments and replication stress situations (WP1); decipher the molecular mechanisms at play by defining the atlas of factors acting at perturbed replication forks in distinct nuclear compartments (WP2); and determine how “fork-protective” environments are built in relation with spatially-segregated post-translational modifications (ubiquitin and SUMO modifications) and checkpoint activation (WP3). We will tackle such questions by combining genetics and molecular assays in yeast models, with innovative, spatially-resolved genomics and proteomics methodologies. The three partners of the consortium bring complementary expertise in the biology of DNA replication, telomeres and nuclear organization to expand our knowledge on the contribution of the nuclear architecture in handling replication-stress induced genome instability, which will be of general interest for a broad scientific community.