Copy number of pericentromeric repeats impacts chromosome segregation in S. pombe
Centromeric sequences are among the most variable regions of the genome but paradoxically have highly conserved functions in chromosome segregation. Centromeric DNA sequences are frequently composed of repetitive elements which are highly variable in copy number. Although interindividual variation in copy number has been documented in many species, very little is known about its functional consequences. Here, we characterize pericentromere repeat variation and its functional consequences in the fission yeast Schizosaccharomyces pombe (S. pombe). S. pombe centromeres consist of a unique central core region flanked by arrays of repetitive pericentromeric elements which are packaged in heterochromatin. We characterize extensive natural copy number variation in the pericentromeric repetitive elements on chromosome 3. To confirm S. pombe isolate pericentromere size, we sequenced and assembled seven isolates with long-read technology. We generated and tested four isogenic S. pombe strains with a range of pericentromeric repeat copy numbers on chromosome 3 (2, 12, 36, and 50+ copies). We observed no growth differences under standard laboratory conditions. However, using RNA sequencing, we found that the transcriptional landscape reflected heterochromatin-dependent variation. Additionally, we observed that strains with more pericentric repeats are sensitive to spindle poisoning drugs. The isogenicity of these strains was confirmed with long-read sequencing and assembly, followed by polishing with short-read data. This work demonstrates that copy number variation at the pericentromere has functional consequences and offers a new set of tools to probe centromere function in a highly tractable system. Design: S. pombe natural isolates and laboratory generated strains were sequenced with Oxford Nanopore Technology. Hybrid (Oxford Nanopore Technology + Illumina) genome sequencing was performed by Plasmidsaurus and used in assembly and polishing steps. Transcriptome analysis was performed with AVITI 75bp RNA sequencing.