title: A sequence-specific interaction between the Saccharomyces cerevisiae rRNA gene repeats and a locus encoding an RNA polymerase I subunit affects ribosomal DNA stability.
abstract: 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 the Saccharomyces 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 the RPA135-tK(CUU)P intergenic region that is involved in the interaction. We demonstrate that the RPA135-IGS1 interaction is dependent on the rDNA copy number and the Msn2 protein. Surprisingly, we found that the interaction does not govern RPA135 transcription. Instead, replacement of a 605-bp region within the RPA135-tK(CUU)P intergenic region results in a reduction in the RPA135-IGS1 interaction level and fluctuations in rDNA copy number. We conclude that the chromosomal interaction that occurs between the RPA135-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.
authors.affiliation: The Liggins Institute, The University of Auckland, Auckland, New Zealand.
authors.forename: Inswasti
authors.initials: I
authors.lastname: Cahyani
authors.affiliation: Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand.
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Cridge
authors.affiliation: Department of Biological Chemistry, The University of Michigan, Ann Arbor, Michigan, USA.
authors.forename: David R
authors.initials: DR
authors.lastname: Engelke
authors.affiliation: Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand.
authors.forename: Austen R D
authors.initials: AR
authors.lastname: Ganley
authors.affiliation: The Liggins Institute, The University of Auckland, Auckland, New Zealand justin.osullivan@auckland.ac.nz.
authors.forename: Justin M
authors.identifier: http://orcid.org/0000-0003-2927-450X
authors.initials: JM
authors.lastname: O'Sullivan
mesh_terms: D000818:Animals; D015825:Chromosomes, Fungal / Q000235:genetics; D004271:DNA, Fungal / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics*; D015966:Gene Expression Regulation, Fungal / Q000235:genetics*; D020459:Genes, rRNA / Q000235:genetics*; D056426:Genetic Loci; D012318:RNA Polymerase I / Q000235:genetics* / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D004271:DNA, Fungal; D004275:DNA, Ribosomal; D029701:Saccharomyces cerevisiae Proteins; D012318:RNA Polymerase I