A radial map of the budding yeast genome reveals novel organizational principles
The eukaryotic genome is organized non-randomly within the nucleus and associations with the nuclear periphery or center have functional consequences. Yet, genome-wide maps of the radial arrangement of chromatin in the nucleus are missing for most model systems. Here we adapted Genomic loci Positioning by Sequencing (GPSeq) to Saccharomyces cerevisiae, enabling high-resolution mapping of chromatin positioning along the nuclear center–periphery axis. GPSeq confirmed previous observations of genome spatial organization in cycling cells and revealed that peripheral telomeres and centromeres imposed long-range constraints in radial positioning that extended into neighbouring chromatin for up to 100-200 kb, thereby limiting access of short chromosome arms to the nuclear interior. We compared GPSeq scores between cycling cells with peripheral telomeres and cells with artificial or quiescence-induced telomere clustering at the nuclear center. Telomere internalizations reorganized large fractions of the genome. This reorganization arised from both direct inward movement of subtelomeric domains and a compensatory displacement of mid-arm chromatin toward the nuclear periphery. In quiescence, an additional loss of centromere peripheral localization further reshaped genome organization. Beyond effects of centromere and telomere positioning, we showed how transcription and associated features were modestly enriched toward the nuclear interior. Finally, we uncovered a context-dependent relationship between GC content and radial positioning, and demonstrated that insertion of GC-poor DNA nudged a locus toward the nuclear periphery, resulting in the silencing of a susceptible reporter. Together, we revealed novel principles of genome organization beyond centromeres and telomeres, with GC-content as a candidate to functionally organize chromatin in the nucleus.
The eukaryotic genome is organized non-randomly within the nucleus and associations with the nuclear periphery or center have functional consequences. Yet, genome-wide maps of the radial arrangement of chromatin in the nucleus are missing for most model systems. Here we adapted Genomic loci Positioning by Sequencing (GPSeq) to Saccharomyces cerevisiae, enabling high-resolution mapping of chromatin positioning along the nuclear center–periphery axis. GPSeq confirmed previous observations of genome spatial organization in cycling cells and revealed that peripheral telomeres and centromeres imposed long-range constraints in radial positioning that extended into neighbouring chromatin for up to 100-200 kb, thereby limiting access of short chromosome arms to the nuclear interior. We compared GPSeq scores between cycling cells with peripheral telomeres and cells with artificial or quiescence-induced telomere clustering at the nuclear center. Telomere internalizations reorganized large fractions of the genome. This reorganization arised from both direct inward movement of subtelomeric domains and a compensatory displacement of mid-arm chromatin toward the nuclear periphery. In quiescence, an additional loss of centromere peripheral localization further reshaped genome organization. Beyond effects of centromere and telomere positioning, we showed how transcription and associated features were modestly enriched toward the nuclear interior. Finally, we uncovered a context-dependent relationship between GC content and radial positioning, and demonstrated that insertion of GC-poor DNA nudged a locus toward the nuclear periphery, resulting in the silencing of a susceptible reporter. Together, we revealed novel principles of genome organization beyond centromeres and telomeres, with GC-content as a candidate to functionally organize chromatin in the nucleus.
Karolinska Institutet