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ChIP-Seq analysis of Myc-tagged budding yeast Rif1

ABSTRACT: ChIP-Seq analysis of Myc-tagged budding yeast Rif1

PROVIDER: PRJEB67557 | ENA |

REPOSITORIES: ENA

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ChIP-Seq analysis of Myc-tagged budding yeast Rif1

Project description:Genomic locations of Myc-tagged budding yeast Rif1 (including wilt-type and designer mutants) were analysed by ChIP-Seq. Mutants tested were rif1-7A and rif1-7E, in which Ser/Thr residues in the cluster of SQ/TQ sites were mutated to Ala or Glu, respectively. The performance of RIF1-9V5 was also tested.

2023-11-19 | E-MTAB-13451 | biostudies-arrayexpress

ChIP-Seq analysis of V5-tagged budding yeast Rif1

Project description:Genomic locations of V5-tagged budding yeast Rif1 (including wilt-type and designer mutants) were analysed by ChIP-Seq. Mutants tested were rif1-7A and rif1-7E, in which Ser/Thr residues in the cluster of SQ/TQ sites were mutated to Ala or Glu, respectively. We also tested tested rif1-∆594, in which the C-terminal 594 amino acids were deleted.

2023-11-19 | E-MTAB-13452 | biostudies-arrayexpress

ChIP-Seq analysis of V5-tagged budding yeast Rif1

Project description:ChIP-Seq analysis of V5-tagged budding yeast Rif1

| PRJEB67558 | ENA

Genome-wide analysis reveals that budding yeast Rif1 binds to replication origins and at blocked replication forks to protect nascent DNA

Project description:This experiment details ChIP sequencing to decipher the binding sites of the Rif1 protein in budding yeast. Rif1 binds most strongly to telomeres where its binding is mediated by Rap1. To reduce telomere binding and help reveal Rap1-independent binding sites, a truncation mutant of Rif1 lacking the Rap1 interaction domain was constructed and analysed. Binding was examined at various cell-cycle stages to elucidate the role of Rif1 in DNA replication and other chromosome transactions.

2018-12-31 | E-MTAB-6736 | biostudies-arrayexpress

Rif1 acts through Protein Phosphatase 1 and independent of replication timing to suppresses telomere extension in budding yeast

Project description:The Rif1 protein negatively regulates telomeric TG repeat length in the budding yeast S. cerevisiae, but how it prevents telomere over-extension is unknown. Rif1 was recently shown to control DNA replication by acting as a Protein Phosphatase 1 (PP1)-targeting subunit. Therefore we investigated whether Rif1 controls telomere length by targeting PP1 activity. We find that a Rif1 mutant that cannot interact with PP1 causes a long-telomere phenotype, similar to that of rif1∆ cells. Compromised PP1 function also causes telomere extension. Tethering PP1 at a specific telomere partially substitutes for Rif1 in limiting TG repeat length, confirming the importance of PP1 in telomere length control. Ablating Rif1-PP1 interaction leads to precocious activation of telomere-proximal replication origins and aberrantly early telomere replication. However, we find that Rif1 still limits telomere length even if nearby replication origins are deleted, indicating that effects of Rif1 on telomere length are not mediated through replication timing. Instead we find that, even at a telomere created after DNA synthesis during a mitotic block, Rif1-PP1 interaction is required to suppress telomere lengthening and prevent inappropriate recruitment of Tel1 kinase. Overall, our results show that Rif1 controls telomere length by recruiting PP1 to directly suppress telomerase-mediated TG repeat lengthening.

2018-02-14 | GSE109241 | GEO

RNAi in budding yeast

Project description:RNAi in budding yeast

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DBP1 in budding yeast

Project description:DBP1 in budding yeast

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Small RNAs in budding yeast

Project description:Small RNAs in budding yeast

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Nucleosome exchange in budding yeast

Project description:Nucleosome exchange in budding yeast

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Rif1 Binding and Control of Chromosome-Internal DNA Replication Origins Is Limited by Telomere sequestration

Project description:The budding yeast telomere binding protein Rif1 (Rap1-interacting factor 1) plays an evolutionarily conserved role in the control of DNA replication timing, which operates through an interaction with the PP1 phosphatase. Rif1-PP1 has been proposed to inhibit origin firing by reversing the phosphorylation of key targets involved in replication initiation. However, it is not yet known if Rif1 binds directly to the replication origins that it controls. Here we show that in unperturbed yeast cells Rif1 primarily regulates late-replicating telomere-proximal origins. Using Chromatin Endogenous Cleavage (ChEC)-seq, we find that Rif1 is robustly detected at many late-replicating origins that we identify as targets of its inhibitory action. Abrogation of Rif1 telomere binding, through mutation of its Rap1 binding module, leads to increased Rif1 binding and late origin inhibition elsewhere in the genome. Our results support a model whereby Rif1 inhibits replication initiation by binding directly at origins, most of which are near telomeres, where Rif1 is concentrated through its interaction with telomere-bound Rap1 protein.

2018-04-24 | GSE97953 | GEO

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