Repeated elements coordinate the spatial organization of the yeast genome

O’Sullivan, Justin M.; Sontam, Dharani M.; Grierson, R.; Jones, Beatrix

doi:10.1002/yea.1657

Cited by 34 publications

(34 citation statements)

References 55 publications

(72 reference statements)

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“…Yet, there are clearly nucleolar associated sequences. 2,26,41 Therefore, excluding rDNA interactions from the model 6 causes the nucleolus to become artificially disjoint from the rest of the genome. To address these conflicting issues, we incorporated only two rDNA repeats in our models and implemented interactions between the rDNA and other loci as attractive forces toward the nucleolusnucleoplasm boundary.…”

Section: Discussionmentioning

confidence: 99%

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Chromosome positioning and the clustering of functionally related loci in yeast is driven by chromosomal interactions

Gehlen

Gruenert

Jones

et al. 2012

Nucleus

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Section: Discussionmentioning

confidence: 99%

“…These data tend to reinforce the role of the nucleolus in chromosome organization. [22][23][24][25][26] based upon randomly chosen subsets of empirically defined interactions. We observe distinct chromosomal positioning and functional clustering in our conformations.…”

Section: Chromosome Positioning and The Clustering Of Functionally Rementioning

confidence: 99%

Chromosome positioning and the clustering of functionally related loci in yeast is driven by chromosomal interactions

Gehlen

Gruenert

Jones

et al. 2012

Nucleus

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“…This is further supported by the identification of specific interactions between repetitive and non-repetitive loci within the yeast genome including specific repeated elements that interact with rRNA genes. Therefore, it has been proposed that genomic architecture is organized by restricting the mobility of these repeat elements relative to the nucleolar interaction point (O'Sullivan et al, 2009). Similar results have been obtained using live cell imaging, with frequent interactions observed between the nucleolar and non-nucleolar chromatin (Berger et al, 2008).…”

Section: Alterations In Genome Organization In and Around The Nucleolmentioning

confidence: 99%

The Nucleolus and Ribosomal Genes in Aging and Senescence

Hein¹,

Sanij²,

Quin³

et al. 2012

Senescence

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“…Maintenance of copy number is achieved through the use of a dedicated rDNA maintenance system (reviewed in references 16 and 17) and involves the action of various nuclear factors, including the histone deacetylase Sir2 (18)(19)(20). Fluctuations in rDNA repeat copy number affect a variety of cellular processes and nuclear functions, including aging (21), telomere silencing (22), and cell sensitivity to DNA damage (16).The S. cerevisiae nucleolus is directly linked to other nuclear loci through a large number of chromosomal contacts (here called interactions) that involve the rDNA, both in cis (intrachromosomal) (23) and in trans (interchromosomal) (24,25). Functional roles for subsets of the connections between the rDNA and other genomic loci have been proposed (25) but have yet to be experimentally tested.…”

mentioning

confidence: 99%

“…The S. cerevisiae nucleolus is directly linked to other nuclear loci through a large number of chromosomal contacts (here called interactions) that involve the rDNA, both in cis (intrachromosomal) (23) and in trans (interchromosomal) (24,25). Functional roles for subsets of the connections between the rDNA and other genomic loci have been proposed (25) but have yet to be experimentally tested.…”

mentioning

confidence: 99%

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

Cahyani

Cridge

Engelke

et al. 2015

Molecular and Cellular Biology

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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. There are strong links between the spatial organization of a genome and its function (reviewed in references 1 to 3). This spatial organization is dynamic and specific for particular cell types and stages of the cell cycle (4-6). Genome spatial organization has been proposed to result from the physical properties of the chromosomes (e.g., volume and flexibility), the proteins (e.g., DNA binding and aggregation), and the nucleic acids (e.g., ability to form triplexes) that are present within the limited volume of the nucleus (7-10). While global genome structure contributes to cell identity (5) and differentiation and cycling (6), the contributions that individual contacts (i.e., interactions) between chromosomal loci make to genome function remain poorly understood. Here, we characterize a high-frequency interaction between the yeast rRNA genes (rDNA) and a locus encoding an RNA polymerase I subunit, RPA135 (Fig. 1A).In Saccharomyces cerevisiae, the rDNA is arranged as 150 to 200 tandem repeats on the long arm of chromosome XII (Chr XII) (11). Each of these tandemly arranged rDNA repeats consists of genes that encode the 35S and 5S rRNAs and two intergenic sequences, IGS1 and IGS2 (Fig. 1A). The rDNA is transcribed by two RNA polymerases: RNA polymerase I (RNAP I), which transcribes the 35S rRNA precursor, and RNAP III, which transcribes the 5S rRNA. Transcription of the rDNA by RNAP I is responsible for the majority of transcription in a cell (reviewed in reference 12).The high rate of transcription and the repetitive structure...

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Repeated elements coordinate the spatial organization of the yeast genome

Cited by 34 publications

References 55 publications

Chromosome positioning and the clustering of functionally related loci in yeast is driven by chromosomal interactions

Chromosome positioning and the clustering of functionally related loci in yeast is driven by chromosomal interactions

The Nucleolus and Ribosomal Genes in Aging and Senescence

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

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