A Sequence-Specific Interaction between the Saccharomyces cerevisiae rRNA Gene Repeats and a Locus Encoding an RNA Polymerase I Subunit Affects Ribosomal DNA Stability

The spatial organization of eukaryotic genomes is linked to their functions. However, how individual features of the global spatial structure contribute to nuclear function remains largely unknown. We previously identified a high-frequency interchromosomal interaction within theSaccharomyces cerevisiae genome that occurs between the intergenic spacer of the ribosomal DNA (rDNA) repeats and the intergenic sequence between the locus encoding the second largest RNA polymerase I subunit and a lysine tRNA gene [i.e.,RPA135-tK (CUU )P ]. Here, we used quantitative chromosome conformation capture in combination with replacement mapping to identify a 75-bp sequence within theRPA135-tK (CUU )P intergenic region that is involved in the interaction. We demonstrate that theRPA135 -IGS1 interaction is dependent on the rDNA copy number and the Msn2 protein. Surprisingly, we found that the interaction does not governRPA135 transcription. Instead, replacement of a 605-bp region within theRPA135-tK (CUU )P intergenic region results in a reduction in theRPA135 -IGS1 interaction level and fluctuations in rDNA copy number. We conclude that the chromosomal interaction that occurs between theRPA135-tK (CUU )P and rDNA IGS1 loci stabilizes rDNA repeat number and contributes to the maintenance of nucleolar stability. Our results provide evidence that the DNA loci involved in chromosomal interactions are composite elements, sections of which function in stabilizing the interaction or mediating a functional outcome.