Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA276018 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:DNA lesions can block a replication fork, leading to its collapse and gross chromosomal rearrangements. To circumvent such outcomes, DNA damage tolerance (DDT) pathways become engaged, allowing the replisome to bypass the lesion and complete S phase in the presence of unrepaired damage. Here we demonstrate a newly identified role for NuA4, including complex components Esa1 and Yng2, on the Translesion Synthesis (TLS) branch of DDT. Moreover, Our data suggest that NuA4 functionality within the tolerance pathway is likely direct as genome-wide transcriptional analysis with esa1-L254P mutants showed little changes in the expression of TLS factors compared to wild type during MMS treatment. When Yng2 expression is restricted to G2/M, cell viability and mutagenesis rates are restored to the levels measured when only the error-free branch of DDT is disrupted, indicating that the critical role of NuA4 in TLS functions in G2, after chromosomal replication is complete. Lastly, disruption of HTZ1, the Saccharomyces cerevisiae histone variant H2A.Z and target of NuA4, exhibits mutagenic rates of reversion that are comparable to the levels measured with NuA4 complex mutants, esa1-L254P and yng2M-NM-^T. The esa1-L254P strain was compared to wild type through a series of microarrays utilizing dye swaps with and without treatment of MMS. These included synchronized cells in G1 and S phase through alpha factor treatment. Four unique microarrays were performed each with dye swaps, comparing wild type to esa1-L254P in G1 and S phase with and without treatment with MMS. As a set of controls, four microarrays were performed comparing identical strains with and without MMS in G1 or S phase.
2015-02-21 | E-GEOD-66176 | biostudies-arrayexpress
Project description:DNA lesions can block a replication fork, leading to its collapse and gross chromosomal rearrangements. To circumvent such outcomes, DNA damage tolerance (DDT) pathways become engaged, allowing the replisome to bypass the lesion and complete S phase in the presence of unrepaired damage. Here we demonstrate a newly identified role for NuA4, including complex components Esa1 and Yng2, on the Translesion Synthesis (TLS) branch of DDT. Moreover, Our data suggest that NuA4 functionality within the tolerance pathway is likely direct as genome-wide transcriptional analysis with esa1-L254P mutants showed little changes in the expression of TLS factors compared to wild type during MMS treatment. When Yng2 expression is restricted to G2/M, cell viability and mutagenesis rates are restored to the levels measured when only the error-free branch of DDT is disrupted, indicating that the critical role of NuA4 in TLS functions in G2, after chromosomal replication is complete. Lastly, disruption of HTZ1, the Saccharomyces cerevisiae histone variant H2A.Z and target of NuA4, exhibits mutagenic rates of reversion that are comparable to the levels measured with NuA4 complex mutants, esa1-L254P and yng2Δ.
2015-02-21 | GSE66176 | GEO
Project description:Here we report our observations that have led us to propose that the transcription elongation factor NusA promotes a novel class of transcription-coupled repair (TCR) in addition to its previously proposed role in recruiting translesion synthesis (TLS) DNA polymerases to gaps encountered during transcription. Earlier we have reported that NusA physically and genetically interacts with the TLS DNA polymerase DinB (DNA pol IV). We find that Escherichia coli nusA11(ts) mutant strains, at the permissive temperature, are highly sensitive to nitrofurazone (NFZ) and 4-nitroquinolone-1-oxide but not to ultraviolet radiation. Gene expression profiling suggests this sensitivity is unlikely to be due to an indirect effect on gene expression affecting a known DNA repair or damage tolerance pathway. We demonstrate that an N2-furfuryl-dG (N2-f-dG) lesion, a structural analog of the principal lesion generated by NFZ, blocks transcription by E. coli RNA polymerase (RNAP) when present in the transcribed strand, but not when present in the non-transcribed strand. Our genetic analysis suggests that NusA participates in a nucleotide excision repair (NER)-dependent process to promote NFZ resistance. We provide evidence that transcription plays a role in the repair of NFZ-induced lesions through the isolation of RNAP mutants that display altered ability to survive NFZ exposure. We propose that NusA participates in a novel class of TCR involved in the identification and removal of a class of lesion, such as the N2-f-dG lesion, which are accurately and efficiently bypassed by DinB in addition to recruiting DinB for TLS at gaps encountered by RNAP. Wild-type and nusA11 samples were analyzed, with 3 replicates per sample.
2010-07-14 | E-GEOD-22829 | biostudies-arrayexpress
Project description:Involvement of a chromatin remodeling complex in damage tolerance during DNA replication
| PRJNA120269 | ENA
Project description:DNA replication is sensitive to damage in the template. To bypass lesions and complete replication, cells activate recombination-mediated (error-free) and translesion synthesis-mediated (error-prone) DNA damage tolerance pathways. Crucial for error-free DNA damage tolerance is template switching, which depends on the formation and resolution of damage-bypass intermediates consisting of sister chromatid junctions. Here we show that a chromatin architectural pathway involving the high mobility group box protein Hmo1 channels replication-associated lesions into the error-free DNA damage tolerance pathway mediated by Rad5 and PCNA polyubiquitylation, while preventing mutagenic bypass and toxic recombination. In the process of template switching, Hmo1 also promotes sister chromatid junction formation predominantly during replication. Its C-terminal tail, implicated in chromatin bending, facilitates the formation of catenations/hemicatenations and mediates the roles of Hmo1 in DNA damage tolerance pathway choice and sister chromatid junction formation. Together, the results suggest that replication-associated topological changes involving the molecular DNA bender, Hmo1, set the stage for dedicated repair reactions that limit errors during replication and impact on genome stability. BrdU and proteins ChIP-chip analyses analysis were carried out as described (Bermejo et al., 2009). Labelled probes were hybridized to Affymetrix S.cerevisiae Tiling 1.0 (P/N 900645) arrays and processed with TAS software.
2014-01-28 | E-GEOD-46260 | biostudies-arrayexpress
Project description:TENT4A (PAPD7) is a non-canonical poly(A) polymerase, of which little is known. Here we show that TENT4A is involved in the regulation of multiple biological pathways, and focus on translesion DNA synthesis (TLS), a DNA-damage tolerance process in which unrepaired lesions are bypassed by error-prone DNA polymerases. We show that TENT4A regulates mRNA stability and/or translation of DNA polymerase η, and of the RAD18 E3 ligase that monoubiquitinates PCNA, the latter being a key step in TLS which enables recruitment of error-prone DNA polymerases to damaged DNA sites. Remarkably, in addition to the effect on RAD18 mRNA stability via controlling its poly(A) tail, TENT4A indirectly regulates RAD18 via the tumor suppressor CYLD, and via the long non-coding antisense RNA PAXIP1-AS2, which had no known function. Knocking down the expression of TENT4A or CYLD, or over-expression of PAXIP1-AS2 led each to a decrease in the amount of the RAD18 protein, but the effect on PCNA ubiquitination was variable. Still, TLS was reduced under these conditions, likely due a to a parallel decrease in DNA polymerase η. Bioinformatics analysis revealed that TLS error-prone DNA polymerase genes and their TENT4A-related regulators are frequently mutated in endometrial cancer genomes, suggesting that TLS is dysregulated in endometrial cancer.
2021-06-29 | GSE141870 | GEO
Project description:Essential Roles of the Smc5/6 complex in Replication through Pausing Sites and Endogenous DNA Damage Tolerance
| PRJNA293458 | ENA
Project description:DNA replication is sensitive to damage in the template. To bypass lesions and complete replication, cells activate recombination-mediated (error-free) and translesion synthesis-mediated (error-prone) DNA damage tolerance pathways. Crucial for error-free DNA damage tolerance is template switching, which depends on the formation and resolution of damage-bypass intermediates consisting of sister chromatid junctions. Here we show that a chromatin architectural pathway involving the high mobility group box protein Hmo1 channels replication-associated lesions into the error-free DNA damage tolerance pathway mediated by Rad5 and PCNA polyubiquitylation, while preventing mutagenic bypass and toxic recombination. In the process of template switching, Hmo1 also promotes sister chromatid junction formation predominantly during replication. Its C-terminal tail, implicated in chromatin bending, facilitates the formation of catenations/hemicatenations and mediates the roles of Hmo1 in DNA damage tolerance pathway choice and sister chromatid junction formation. Together, the results suggest that replication-associated topological changes involving the molecular DNA bender, Hmo1, set the stage for dedicated repair reactions that limit errors during replication and impact on genome stability.
2014-01-28 | GSE46260 | GEO
Project description:Many DNA tumor viruses inhibit or repurpose host DNA repair pathways to evade viral defense mechanisms or promote their own replication. High risk genus α human papillomaviruses (α-HPVs) express two versatile oncogenes (α-HPV E6 and E7) that use both approaches simultaneously. To identify new interactions with DNA repair pathways, we conducted a computational analysis of gene expression in cervical cancer (CaCx) transcriptomic datasets and identified a frequent upregulation of translesion synthesis (TLS) genes. TLS polymerase genes, particularly the gene for POLη (POLH), did not follow this pattern. Characterization of α-HPV oncogene expressing cell lines and premalignant cervical tissue confirm these data. They also show that the increased TLS protein abundance come in response to nucleoside depletion. Primary and transformed cell lines to demonstrate that α-HPV E6 blocks POLη induction by degrading p53. Lack of POLη dooms the pathway, preventing it from facilitating tolerance of replication stress. Failed TLS results in replication fork stalling and collapse into deleterious double strand breaks in the DNA (DSBs). Consequently, cellular genome fidelity decreases in a manner consistent with the mutations that accumulate during CaCx progression. Alterations in TLS are determinants for the efficacy of the chemotherapeutics most often used to treat CaCx (cisplatin and carboplatin). Exogenous expression of POLη protected CaCx cells from cisplatin-associated toxicity/damage, effectively stabilizing their genome. TLS polymerase expression is also a prognostic factor in CaCx. Analysis of the cancer genome atlas database (TCGA) shows increased expression of these genes correlated with over a decade shorter median survival.
2020-05-01 | GSE145976 | GEO
Project description:Here we report our observations that have led us to propose that the transcription elongation factor NusA promotes a novel class of transcription-coupled repair (TCR) in addition to its previously proposed role in recruiting translesion synthesis (TLS) DNA polymerases to gaps encountered during transcription. Earlier we have reported that NusA physically and genetically interacts with the TLS DNA polymerase DinB (DNA pol IV). We find that Escherichia coli nusA11(ts) mutant strains, at the permissive temperature, are highly sensitive to nitrofurazone (NFZ) and 4-nitroquinolone-1-oxide but not to ultraviolet radiation. Gene expression profiling suggests this sensitivity is unlikely to be due to an indirect effect on gene expression affecting a known DNA repair or damage tolerance pathway. We demonstrate that an N2-furfuryl-dG (N2-f-dG) lesion, a structural analog of the principal lesion generated by NFZ, blocks transcription by E. coli RNA polymerase (RNAP) when present in the transcribed strand, but not when present in the non-transcribed strand. Our genetic analysis suggests that NusA participates in a nucleotide excision repair (NER)-dependent process to promote NFZ resistance. We provide evidence that transcription plays a role in the repair of NFZ-induced lesions through the isolation of RNAP mutants that display altered ability to survive NFZ exposure. We propose that NusA participates in a novel class of TCR involved in the identification and removal of a class of lesion, such as the N2-f-dG lesion, which are accurately and efficiently bypassed by DinB in addition to recruiting DinB for TLS at gaps encountered by RNAP.
2010-07-14 | GSE22829 | GEO