Condensin and Hmo1 Mediate a Starvation-Induced Transcriptional Position Effect within the Ribosomal DNA Array

• Published in: Cell reports (Cambridge) Vol. 14; no. 5; pp. 1010 - 1017
• Main Authors: Wang, Danni, Mansisidor, Andres, Prabhakar, Gayathri, Hochwagen, Andreas
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 09-02-2016; Elsevier
• Subjects: Adenosine Triphosphatases - metabolism; Cell Nucleolus - metabolism; DNA, Ribosomal - genetics; DNA-Binding Proteins - metabolism; Genes, Reporter; High Mobility Group Proteins - metabolism; Multiprotein Complexes - metabolism; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - metabolism; Transcription, Genetic
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2016.01.005

Repetitive DNA arrays are important structural features of eukaryotic genomes that are often heterochromatinized to suppress repeat instability. It is unclear, however, whether all repeats within an array are equally subject to heterochromatin formation and gene silencing. Here, we show that in starving Saccharomyces cerevisiae, silencing of reporter genes within the ribosomal DNA (rDNA) array is less pronounced in outer repeats compared with inner repeats. This position effect is linked to the starvation-induced contraction of the nucleolus. We show that the chromatin regulators condensin and Hmo1 redistribute within the rDNA upon starvation; that Hmo1, like condensin, is required for nucleolar contraction; and that the position effect partially depends on both proteins. Starvation-induced nucleolar contraction and differential desilencing of the outer rDNA repeats may provide a mechanism to activate rDNA-encoded RNAPII transcription units without causing general rDNA instability.
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•Starvation induces a transcriptional position effect in the yeast rDNA•The position effect arises during condensin-dependent nucleolar contraction•Nucleolar contraction also requires the HMG-protein Hmo1•The position effect is reduced upon disruption of condensin or Hmo1
The regulation of individual repeats within a tandem DNA array remains poorly understood. Wang et al. use repeat-specific reporters in the highly repetitive rDNA of Saccharomyces cerevisiae to show that RNAPII activity in starved cells depends on relative repeat position. They also identify two nucleolar factors controlling this position effect.