The Pif1 helicase is actively inhibited during meiotic recombination to prevent excess length of gene conversions
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA690796 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13388785_1.fastq.gz | Fastqsanger.gz | |||
| SRR13388785_2.fastq.gz | Fastqsanger.gz | |||
| SRR13388786_1.fastq.gz | Fastqsanger.gz | |||
| SRR13388786_2.fastq.gz | Fastqsanger.gz | |||
| SRR13388787_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 8 |
Similar Datasets
Project description:Meiotic recombination ensures proper chromosome segregation to form viable gametes and results in gene conversion events between homologs. Conversion tracts are shorter in meiosis than in mitotically dividing cells. This results at least in part from the binding of a complex, formed of the Mer3 helicase and the MutL heterodimer, to meiotic recombination intermediates. The molecular actors inhibited by this complex are elusive. The Pif1 DNA helicase is known to stimulate DNA polymerase delta (Pol δ) -mediated DNA synthesis from D-loops in vitro, allowing long synthesis required for break-induced replication. We show that Pif1 is recruited genome wide to meiotic double-strand break (DSB) sites. We further show that Pif1, through its interaction with PCNA, is required for the long gene conversions observed in the absence of MutL recruitment to recombination sites. in vivo, Mer3 interacts with the PCNA clamp loader RFC, and in vitro, Mer3-MutL ensemble inhibits Pif1-stimulated D-loop extension by Pol δ and RFC-PCNA. Mechanistically, our results suggest that Mer3-MutL may compete with Pif1 for binding to RFC-PCNA. Taken together, our data show that Pif1’s activity to promote meiotic recombination-related DNA synthesis is restrained by the Mer3-MutL ensemble to prevent long gene conversion events and possibly associated mutagenesis.
2021-03-01 | GSE164467 | GEO
Project description:The Saccharomyces cerevisiae gene PIF1 encodes a conserved eukaryotic DNA helicase required for both mitochondrial and nuclear DNA integrity. Our previous work revealed that a pif1D strain is tolerant to zinc overload. We demonstrate here that this effect is independent of the Pif1 helicase activity and is only observed when the protein is absent from the mitochondria. pif1 cells accumulate abnormal amounts of mitochondrial zinc and iron. Transcriptional profiling reveals that pif1 cells under standard growth conditions overexpress aconitase-related genes. When exposed to zinc, pif1 cells show lower induction of genes encoding iron (siderophores) transporters and higher expression of genes related to oxidative stress responses than wild type cells. Coincidently, pif1 mutants are less prone to zinc-induced oxidative stress and display a higher reduced/oxidized glutathione ratio. Strikingly, although pif1 cells contain normal amounts of the Aco1 protein, they completely lack aconitase activity. Loss of Aco1 activity is also observed when the cell expresses a non-mitochondrially targeted form of Pif1. We postulate that lack of Pif1 forces aconitase to play its DNA protective role as nucleoid protein and that this would trigger a domino effect on iron homeostasis resulting in increased zinc tolerance. Four samples were analyzed: WT and pif1 mutant both, in the presence and in the absence of 5 mM ZnCl2 for 1 h. We compared the expression profile of: 1) WT+Zn vs WT-Zn, 2) pif1 mutant+Zn vs pif1 mutant-Zn, 3) pif1 mutant vs WT, and 4) pif1 mutant+Zn vs WT+Zn. A Dye-swap was carried out for each comparison of samples. Total number of chips analyzed: 8.
2010-05-31 | E-GEOD-18411 | biostudies-arrayexpress
Project description:Meiotic recombination ensures proper chromosome segregation to form viable gametes and results in gene conversions events between homologs. Conversion tracts are shorter in meiosis than in mitotically dividing cells. This results at least in part from the binding of a complex, containing the Mer3 helicase and the MutLβ heterodimer, to meiotic recombination intermediates. The molecular actors inhibited by this complex are elusive. The Pif1 DNA helicase is known to stimulate DNA polymerase delta (Pol δ) -mediated DNA synthesis from D-loops, allowing long synthesis required for break-induced replication. We show that Pif1 is also recruited genome wide to meiotic DNA double-strand break (DSB) sites. We further show that Pif1, through its interaction with PCNA, is required for the long gene conversions observed in the absence of MutLβ recruitment to recombination sites. In vivo, Mer3 interacts with the PCNA clamp loader RFC, and in vitro, Mer3-MutLβ ensemble inhibits Pif1-stimulated D-loop extension by Pol δ and RFC-PCNA. Mechanistically, our results suggest that Mer3-MutLβ may compete with Pif1 for binding to RFC-PCNA. Taken together, our data show that Pif1's activity that promotes meiotic DNA repair synthesis is restrained by the Mer3-MutLβ ensemble which in turn prevents long gene conversion tracts and possibly associated mutagenesis.
| S-EPMC8096244 | biostudies-literature
Project description:The Saccharomyces cerevisiae gene PIF1 encodes a conserved eukaryotic DNA helicase required for both mitochondrial and nuclear DNA integrity. Our previous work revealed that a pif1D strain is tolerant to zinc overload. We demonstrate here that this effect is independent of the Pif1 helicase activity and is only observed when the protein is absent from the mitochondria. pif1 cells accumulate abnormal amounts of mitochondrial zinc and iron. Transcriptional profiling reveals that pif1 cells under standard growth conditions overexpress aconitase-related genes. When exposed to zinc, pif1 cells show lower induction of genes encoding iron (siderophores) transporters and higher expression of genes related to oxidative stress responses than wild type cells. Coincidently, pif1 mutants are less prone to zinc-induced oxidative stress and display a higher reduced/oxidized glutathione ratio. Strikingly, although pif1 cells contain normal amounts of the Aco1 protein, they completely lack aconitase activity. Loss of Aco1 activity is also observed when the cell expresses a non-mitochondrially targeted form of Pif1. We postulate that lack of Pif1 forces aconitase to play its DNA protective role as nucleoid protein and that this would trigger a domino effect on iron homeostasis resulting in increased zinc tolerance.
2010-06-01 | GSE18411 | GEO
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:Actin associates with actively elongating genes
| PRJNA1000942 | ENA
Project description:Iron is an essential nutrient yet toxic in excess. Our understanding of mammalian mechanisms of dietary iron absorption exceeds our understanding of mechanisms of iron excretion. Here we demonstrate that biliary excretion of excess iron in mice requires the metal transporter SLC39A14 and that excess Fe is excreted into bile as ferritin and heme. The identification of a molecular determinant of iron excretion and the biochemical form of bile iron could lead to development of novel therapeutics for human diseases of iron excess
2021-02-10 | MSV000086836 | MassIVE
Project description:To further investigate the homeostatic response of E. faecalis to Fe exposure, we examine the whole-genome transcriptional response of wild-type (WT) exposed to non toxic Fe excess. This experiment correspond the work titled Transcriptomic response of Enterococcus faecalis to iron excess (work in preparation)
2012-03-01 | GSE34432 | GEO
Project description:Arabidopsis (Arabidopsis thaliana) leaf was exposed to excess light (1300 umol photons m-2 s-1) for 30 min and 2 hours. Expression levels relative to low light (LL - 65 umol photons m-2 s-1) were determined.
2010-12-31 | E-MTAB-392 | biostudies-arrayexpress
Project description:Transcription profiling of P. gingivalis W50 grown in continuous culture under conditions of heme-excess and heme-limitation. Reference design (using Cy5 labelled genomic DNA as the reference) to compare two conditions: heme-excess vs heme-limitation. Three samples for each condition, independently grown.
2010-05-16 | E-GEOD-13375 | biostudies-arrayexpress