A radial map of the budding yeast genome reveals novel organizational principles

Abstract The eukaryotic genome is non-randomly organized within the nucleus, with positioning linked to function. Still, genome-wide radial maps are missing for the majority of experimental model systems. We adapted Genomic loci Positioning by Sequencing (GPSeq) to Saccharomyces cerevisiae , enabling high-resolution mapping along the nuclear center–periphery axis. GPSeq confirms known spatial features and shows that peripheral telomeres and centromeres impose long-range constraints extending up to 200 kb, restricting short chromosome arms from the nuclear interior. Telomere repositioning to the nuclear center, either artificially or during quiescence, reorganizes much of the genome through inward movement of sub telomeric regions and compensatory shifts of mid-arm chromatin outward. In quiescence, reduced centromere peripheral localization further alters genome organization. While transcription has a modest impact on radial positioning in all studied conditions, we uncover that in the absence of centromere or telomere constraints, GC-content functionally organizes chromatin in the nucleus. Graphical abstract The budding yeast genome is spatially organized in a manner highly dependent on the positioning of centromeres ( CENs ) and telomeres ( TELs ). Anchoring of these chromosome landmarks constrains the positioning of adjacent chromatin up to 200 kb within the same radial zone. Beyond this range, genome organization is non-random, with processes like transcription and features such as GC- content associated with specific radial positions in the nucleus.