Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA292617 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3734670_1.fastq.gz | Fastqsanger.gz | |||
| SRR3734670_2.fastq.gz | Fastqsanger.gz | |||
| SRR3734680_1.fastq.gz | Fastqsanger.gz | |||
| SRR3734680_2.fastq.gz | Fastqsanger.gz | |||
| SRR3734690_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Saccharomyces cerevisiae encodes two distinct Pif1-family helicases – Pif1 and Rrm3 – which have been reported to play distinct roles in numerous nuclear processes. Here, we systematically characterize the roles of Pif1 helicases in replisome progression and lagging- strand synthesis in S. cerevisiae. We demonstrate that either Pif1 or Rrm3 redundantly stimulate strand-displacement by DNA polymerase δ during lagging-strand synthesis. By analyzing replisome mobility in pif1 and rrm3 mutants, we show that Rrm3, with a partially redundant contribution from Pif1, suppresses widespread terminal arrest of the replisome at tRNA genes. Although both head-on and codirectional collisions induce replication fork arrest at tRNA genes, head-on collisions arrest a higher proportion of replisomes; consistent with this observation, we find that head-on collisions between tRNA transcription and replisome progression are under-represented in the S. cerevisiae genome. Further, we demonstrate that tRNA-mediated arrest is R-loop independent, and propose that replisome arrest and DNA damage are mechanistically separable.
2016-10-17 | GSE71973 | GEO
Project description:Replication stress activates the Mec1ATR and Rad53 kinases. Rad53 phosphorylates nuclear pores to counteract gene gating, thus preventing aberrant transitions at forks approaching transcribed genes. Here, we show that Rrm3 and Pif1, DNA helicases assisting fork progression across pausing sites, are detrimental in rad53 mutants experiencing replication stress. Rrm3 and Pif1 ablations rescue cell lethality, chromosome fragmentation, replisome-fork dissociation, fork reversal, and processing in rad53 cells. Through phosphorylation, Rad53 regulates Rrm3 and Pif1; phospho-mimicking rrm3 mutants ameliorate rad53 phenotypes following replication stress without affecting replication across pausing elements under normal conditions. Hence, the Mec1-Rad53 axis protects fork stability by regulating nuclear pores and DNA helicases. We propose that following replication stress, forks stall in an asymmetric conformation by inhibiting Rrm3 and Pif1, thus impeding lagging strand extension and preventing fork reversal; conversely, under unperturbed conditions, the peculiar conformation of forks encountering pausing sites would depend on active Rrm3 and Pif1.
2015-09-24 | GSE68214 | GEO
Project description:Replication stress activates the Mec1ATR and Rad53 kinases. Rad53 phosphorylates nuclear pores to counteract gene gating, thus preventing aberrant transitions at forks approaching transcribed genes. Here, we show that Rrm3 and Pif1, DNA helicases assisting fork progression across pausing sites, are detrimental in rad53 mutants experiencing replication stress. Rrm3 and Pif1 ablations rescue cell lethality, chromosome fragmentation, replisome-fork dissociation, fork reversal, and processing in rad53 cells. Through phosphorylation, Rad53 regulates Rrm3 and Pif1; phospho-mimicking rrm3 mutants ameliorate rad53 phenotypes following replication stress without affecting replication across pausing elements under normal conditions. Hence, the Mec1-Rad53 axis protects fork stability by regulating nuclear pores and DNA helicases. We propose that following replication stress, forks stall in an asymmetric conformation by inhibiting Rrm3 and Pif1, thus impeding lagging strand extension and preventing fork reversal; conversely, under unperturbed conditions, the peculiar conformation of forks encountering pausing sites would depend on active Rrm3 and Pif1. BrdU incorporation profiles by ssDNA-BrdU IP on chip have been generated as described (Katou et al., 2003). Protein binding profiles by ChIP-chip analysis were generated as described (Bermejo et al., 2009). Labeled probes were hybridized to Affymetrix S.cerevisiae Tiling 1.0 (P/N 900645) arrays and processed with TAS software.
2015-09-24 | E-GEOD-68214 | biostudies-arrayexpress
Project description:Background G-quadruplexes (G4s) are stable non-canonical DNA secondary structures consisting of stacked arrays of four guanines, each held together by Hoogsteen hydrogen bonds. Sequences with the ability to form these structures in vitro, G4 motifs, are found throughout bacterial and eukaryotic genomes. The budding yeast Pif1 DNA helicase, as well as several bacterial Pif1 family helicases, unwind G4 structures robustly in vitro and suppress G4-induced DNA damage in S. cerevisiae in vivo. Results We determined the genomic distribution and evolutionary conservation of G4 motifs in four fission yeast species and investigated the relationship between G4 motifs and Pfh1, the sole S. pombe Pif1 family helicase. Using chromatin immunoprecipitation combined with deep sequencing, we found that many G4 motifs in the S. pombe genome were associated with Pfh1. Cells depleted of Pfh1 had increased fork pausing and DNA damage near G4 motifs, as indicated by high DNA polymerase occupancy and phosphorylated histone H2A, respectively. In general, G4 motifs were underrepresented in genes. However, Pfh1-associated G4 motifs were located on the transcribed strand of highly transcribed genes significantly more often than expected, suggesting that Pfh1 has a function in replication or transcription at these sites. Conclusions In the absence of functional Pfh1, unresolved G4 structures cause fork pausing and DNA damage of the sort associated with human tumors.
2014-12-03 | GSE59178 | GEO
Project description:tRNA genes (tDNAs) are widely studied sites of replication-fork arrest and genome instability in the budding yeast Saccharomyces cerevisiae. tDNAs are extremely highly transcribed, and serve as constitutive condensin binding sites. Although tRNA transcription by RNA polymerase III (RNAPIII) has previously been identified as stimulating replication-fork arrest at these loci, the nature of the block to replication has not been incontrovertibly demonstrated. Here, we describe a systematic, genome-wide analysis of the contributions of transcription factor binding, transcription, topoisomerase activity, and condensin-mediated clustering to replication-fork arrest at tDNAs in yeast. We show that a polar block to replication is maintained at tDNAs even when tRNA transcription is abolished by depletion of one or more subunits of RNAPIII. By contrast, analogous depletion of the essential transcription factor TFIIIB removes the obstacle to replication in the same background. Therefore, our data suggest that the RNA polymerase III transcription complex itself represents an asymmetric obstacle to replication even in the absence of RNA synthesis. We additionally demonstrate that replication-fork mobility past tDNAs is unaffected by the global depletion of condensin from the nucleus, but can be stimulated by the removal of topoisomerases or Rad18-dependent DNA repair pathways.
2019-11-02 | GSE139860 | GEO
Project description:Rad53-mediated regulation of Rrm3 and Pif1 DNA helicases contributes to prevention of aberrant fork transitions under replication stress.
| PRJNA282034 | ENA
Project description:Schlafen family member 11 (SLFN11) expression sensitizes cells to a spectrum of DNA-damaging chemotherapies. Previous studies have shown that SLFN11 is recruited to stalled replication forks in response to replication stress; however, the role of SLFN11 at stressed replication forks remains unclear. Using single-molecule DNA fiber analysis and super-resolution microscopy to interrogate the dynamics of individual replication forks, we show that SLFN11 acts upon stalled replication forks to suppress efficient fork restart. In the absence of SLFN11 expression, fork restart proceeds through a pathway involving the ubiquitin ligase RFWD3 and the DNA primase-polymerase PRIMPOL to facilitate gapped DNA synthesis. In the absence of SLFN11 expression, this pathway ensures that cells do not accumulate replication-associated DNA damage in response to stalled forks. Collectively, our results provide a mechanistic basis for how SLFN11 can counteract DNA damage tolerance by suppressing the RFWD3-PRIMPOL axis.
The deposit includes the mass spectrometry data files generated from this study.
2025-07-16 | MSV000098536 | MassIVE
Project description:Zika virus (ZIKV) infection in human neural progenitors triggers DNA damage and activates DNA damage response, leading to cell cycle arrest that can retard brain development. Here we link the ZIKV- induced S phase arrest to replication fork stalling and R-loop induction. DRIP-seq reveals that ZIKV infection induces R-loops at specific loci strongly enriched in the interferon-stimulated genes (ISGs). Bru-seq results further indicate that nascent ISGs transcripts are prone to R-loop induction upon infection. Knockout of interferon receptor eliminated the R-loops on ISGs and partially rescued S phase arrest in infected cells. And overexpression of RNaseH1 reduced ZIKV-mediated DNA damage and cell cycle arrest. We conclude that unscheduled expression of ISGs induced by ZIKV alters R-loop homeostasis and perturbs replication fork progression, leading to fork stalling and eventually DNA damage. IFN- dependent R-loop induction represents a previously unknown, nucleic acid-based mechanism for cell cycle arrest.
2025-05-29 | GSE274207 | GEO
Project description:Zika virus (ZIKV) infection in human neural progenitors triggers DNA damage and activates DNA damage response, leading to cell cycle arrest that can retard brain development. Here we link the ZIKV- induced S phase arrest to replication fork stalling and R-loop induction. DRIP-seq reveals that ZIKV infection induces R-loops at specific loci strongly enriched in the interferon-stimulated genes (ISGs). Bru-seq results further indicate that nascent ISGs transcripts are prone to R-loop induction upon infection. Knockout of interferon receptor eliminated the R-loops on ISGs and partially rescued S phase arrest in infected cells. And overexpression of RNaseH1 reduced ZIKV-mediated DNA damage and cell cycle arrest. We conclude that unscheduled expression of ISGs induced by ZIKV alters R-loop homeostasis and perturbs replication fork progression, leading to fork stalling and eventually DNA damage. IFN- dependent R-loop induction represents a previously unknown, nucleic acid-based mechanism for cell cycle arrest.
2025-05-29 | GSE274208 | GEO
Project description:Zika virus (ZIKV) infection in human neural progenitors triggers DNA damage and activates DNA damage response, leading to cell cycle arrest that can retard brain development. Here we link the ZIKV- induced S phase arrest to replication fork stalling and R-loop induction. DRIP-seq reveals that ZIKV infection induces R-loops at specific loci strongly enriched in the interferon-stimulated genes (ISGs). Bru-seq results further indicate that nascent ISGs transcripts are prone to R-loop induction upon infection. Knockout of interferon receptor eliminated the R-loops on ISGs and partially rescued S phase arrest in infected cells. And overexpression of RNaseH1 reduced ZIKV-mediated DNA damage and cell cycle arrest. We conclude that unscheduled expression of ISGs induced by ZIKV alters R-loop homeostasis and perturbs replication fork progression, leading to fork stalling and eventually DNA damage. IFN- dependent R-loop induction represents a previously unknown, nucleic acid-based mechanism for cell cycle arrest.
2025-05-29 | GSE274206 | GEO