The spatial organization of eukaryotic genomes is linked to its functions. However, how individual features of the global spatial structure contribute to nuclear function remains largely unknown. We previously identified a high frequency inter-chromosomal interaction within the @entity375 genome that occurs between the intergenic spacer of the ribosomal DNA repeats (rDNA) and the intergenic sequence between the locus encoding the second largest RNA Polymerase I subunit and a lysine tRNA gene (i.e. @entity59578 -tK(CUU)P). Here we used quantitative Chromosome Conformation Capture in combination with replacement mapping to identify a 75 bp sequence within the @entity59578 -tK(CUU)P intergenic region that is involved in the interaction. We demonstrate that the @entity59578 -IGS1 interaction is dependent on the rDNA copy number and the @entity23763 protein. Surprisingly, we found that the interaction does not govern @entity59578 transcription. Instead, replacement of a 605bp region within the @entity59578 -tK(CUU)P intergenic region results in a reduction in the @entity59578 -IGS1 interaction level and fluctuations in rDNA copy number. We conclude that the chromosomal interaction that occurs between the @entity59578 -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 to stabilizing the interaction or mediating a functional outcome.

A sequence-specific interaction between the XXXX ribosomal RNA gene repeats and a locus encoding an RNA polymerase I subunit affects rDNA stability.

@entity23763 :: ('855053(Tax:4932)', 'Gene') :: ['Msn2'] @entity375 :: ('4932', 'Species') :: ['Saccharomyces cerevisiae'] @entity59578 :: ('856119(Tax:4932)', 'Gene') :: ['RPA135']
@entity375 :: (4932,Species) :: ['Saccharomyces cerevisiae']
