High plasticity of ribosomal DNA organization in budding yeast

Ribosomal DNA (rDNA), which encodes genes for structural RNA components of the ribosome, is highly repetitive and dynamic in eukaryotic genomes, making it difficult to study the plasticity of its organization. Here, a short synthetic rDNA array, in which each rDNA repeat contained a loxPsym site, was generated on the right arm of chromosome III (chrIIIR) in budding yeast as the sole source of rDNA. With the induction of rDNA rearrangement mediated by loxPsym sites, the rDNA copy number was reduced to only about eight copies. In addition, to mimic the multiple-array organization in higher organisms, haploid yeast strains with two or three rDNA arrays were constructed. Interestingly, all these strains form a single nucleolus like the ones with a single array. Although alteration of the genomic position and the number of rDNA arrays did affect 3-D genome structure, the existence of additional rDNA arrays showed no negative influence on cell growth and transcriptomes. Together, this study reveals insights into the high plasticity of rDNA organization, laying a foundation for rDNA engineering during the construction of minimal yeast genomes.