Budding Yeast Rif1 Controls Genome Integrity by Inhibiting rDNA Replication

PLoS Genet. 2016 Nov 7;12(11):e1006414. doi: 10.1371/journal.pgen.1006414. eCollection 2016 Nov.


The Rif1 protein is a negative regulator of DNA replication initiation in eukaryotes. Here we show that budding yeast Rif1 inhibits DNA replication initiation at the rDNA locus. Absence of Rif1, or disruption of its interaction with PP1/Glc7 phosphatase, leads to more intensive rDNA replication. The effect of Rif1-Glc7 on rDNA replication is similar to that of the Sir2 deacetylase, and the two would appear to act in the same pathway, since the rif1Δ sir2Δ double mutant shows no further increase in rDNA replication. Loss of Rif1-Glc7 activity is also accompanied by an increase in rDNA repeat instability that again is not additive with the effect of sir2Δ. We find, in addition, that the viability of rif1Δ cells is severely compromised in combination with disruption of the MRX or Ctf4-Mms22 complexes, both of which are implicated in stabilization of stalled replication forks. Significantly, we show that removal of the rDNA replication fork barrier (RFB) protein Fob1, alleviation of replisome pausing by deletion of the Tof1/Csm3 complex, or a large deletion of the rDNA repeat array all rescue this synthetic growth defect of rif1Δ cells lacking in addition either MRX or Ctf4-Mms22 activity. These data suggest that the repression of origin activation by Rif1-Glc7 is important to avoid the deleterious accumulation of stalled replication forks at the rDNA RFB, which become lethal when fork stability is compromised. Finally, we show that Rif1-Glc7, unlike Sir2, has an important effect on origin firing outside of the rDNA locus that serves to prevent activation of the DNA replication checkpoint. Our results thus provide insights into a mechanism of replication control within a large repetitive chromosomal domain and its importance for the maintenance of genome stability. These findings may have important implications for metazoans, where large blocks of repetitive sequences are much more common.

MeSH terms

  • DNA Replication / genetics*
  • DNA, Ribosomal / genetics*
  • DNA-Binding Proteins / genetics
  • Genomic Instability
  • Protein Phosphatase 1 / genetics*
  • Replication Origin / genetics
  • Repressor Proteins / genetics*
  • Saccharomyces cerevisiae
  • Saccharomyces cerevisiae Proteins / genetics*
  • Silent Information Regulator Proteins, Saccharomyces cerevisiae / genetics
  • Sirtuin 2 / genetics
  • Telomere / genetics
  • Telomere-Binding Proteins / genetics*


  • CTF4 protein, S cerevisiae
  • DNA, Ribosomal
  • DNA-Binding Proteins
  • Mms22 protein, S cerevisiae
  • Repressor Proteins
  • Saccharomyces cerevisiae Proteins
  • Silent Information Regulator Proteins, Saccharomyces cerevisiae
  • Telomere-Binding Proteins
  • RIF1 protein, S cerevisiae
  • GLC7 protein, S cerevisiae
  • Protein Phosphatase 1
  • SIR2 protein, S cerevisiae
  • Sirtuin 2

Grant support

This work was supported by grants from the Swiss National Science Foundation to DS and funds provided by the Republic and Canton of Geneva. CB is supported by the Canadian Institutes of Health Research (FDN-143264). BA acknowledges support from an EMBO Long Term Fellowship (EMBO ALTF 842-2013). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.