Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1112421 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29084936_1.fastq.gz | Fastqsanger.gz | |||
| SRR29084936_2.fastq.gz | Fastqsanger.gz | |||
| SRR29084937_1.fastq.gz | Fastqsanger.gz | |||
| SRR29084937_2.fastq.gz | Fastqsanger.gz | |||
| SRR29084938_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:RAD51 paralogs interact with the replicative helicase to bypass DNA damage
| PRJNA1109738 | ENA
Project description:Accurate completion of replication relies on the ability of cells to activate error-free recombination-mediated DNA damage-bypass at sites of perturbed replication. However, as anti-recombinase activities are also recruited to replication forks, how recombination-mediated damage-bypass is enabled at replication stress sites remained puzzling. Here we uncovered that the conserved SUMO-like domains-containing Saccharomyces cerevisiae protein, Esc2, facilitates recombination-mediated DNA damage tolerance by allowing optimal recruitment of the Rad51 recombinase specifically at sites of perturbed replication. Mechanistically, Esc2 binds stalled replication forks and counteracts the anti-recombinase Srs2 helicase via a two-faceted mechanism involving chromatin recruitment and turnover of Srs2. Importantly, point mutations in the SUMO-like domains of Esc2 that reduce its interaction with Srs2 cause sub-optimal levels of Rad51 recruitment at damaged replication forks. In conclusion, our results reveal how recombination-mediated DNA damage tolerance is locally enabled at sites of replication stress, while globally prevented at undamaged replicating chromosomes.
2015-02-16 | GSE65701 | GEO
Project description:The proper maintenance of genetic material is essential for the survival of living organisms. One of the main safeguards of genome stability is homologous recombination involved in the faithful repair of DNA double-strand breaks, the restoration of collapsed replication forks, and the bypass of replication barriers. Homologous recombination relies on the formation of Rad51 nucleofilaments which are responsible for the homology-based interactions between DNA strands. Here we demonstrate that without the regulation of these filaments by Srs2 and Rad54, which are known to remove Rad51 from single-stranded and double-stranded DNA respectively, the filaments strongly inhibit damage-associated DNA synthesis during DNA repair. Furthermore, this regulation is essential for cell survival under normal growth conditions as in the srs2Δ rad54Δ mutants unregulated Rad51 nucleofilaments cause activation of the DNA damage checkpoint, formation of mitotic bridges and loss of genetic material. These genome instability features may stem from the problems at stalled replication forks as the lack of Srs2 and Rad54 in the presence of Rad51 nucleofilaments impedes cell recovery from replication stress. This study demonstrates that the timely and efficient disassembly of recombination machinery is essential for genome maintenance and cell survival.
2023-03-16 | GSE227383 | GEO
Project description:Homologous recombination (HR) plays an essential role in the maintenance of genome stability by promoting the repair of cytotoxic DNA double strand breaks (DSBs). More recently, the HR pathway has emerged as an integral component of the response to replication stress, in part by protecting stalled replication forks from nucleolytic degradation. In that regard, the mammalian RAD51 paralogs (RAD51B, RAD51C, RAD51D, XRCC2, and XRCC3) have been involved in both HR-mediated DNA repair and collapsed replication fork resolution. Still, it remains largely obscure how they participate in both processes, thereby maintaining genome stability and preventing cancer development. To gain better insight into their contribution in cellulo, we mapped the proximal interactome of the classical RAD51 paralogs using the BioID approach. Aside from identifying the well-established BCDX2 and CX3 sub-complexes, the spliceosome machinery emerged as an integral component of our proximal mapping, suggesting a crosstalk between this pathway and the RAD51 paralogs. Furthermore, we noticed that factors involved RNA metabolic pathways are significantly modulated within the BioID of the classical RAD51 paralogs upon exposure to hydroxyurea (HU), pointing towards a direct contribution of RNA processing during replication stress. Importantly, several members of these pathways have prognosis potential in breast cancer (BC), where their RNA expression correlates with poorer patient outcome. Collectively, this study uncovers novel functionally relevant partners of the different RAD51 paralogs in the maintenance of genome stability and could be used as biomarker for the prognosis of BC.
2022-05-20 | MSV000089507 | MassIVE
Project description:Plasma membrane damage-dependent senescence is a novel senescence subtype. Here, we compare the time-resolved proteomic profiles of plasma membrane damage-dependent senescence, DNA damage-dependent senescence, and replicative senescence to find the major differences between the senescence subtypes.
2024-12-20 | PXD047976 | JPOST Repository
Project description:G-quadruplex (or G4) structures are non-canonical DNA structures that form in guanine-rich sequences and threaten genome stability when not properly resolved. G4 unwinding occurs during S phase via an unknown mechanism. Using Xenopus egg extracts, we define a three-step G4 unwinding mechanism that acts during DNA replication. First, the replicative helicase (CMG) stalls at a leading strand G4 structure. Second, the DHX36 helicase mediates the bypass of the CMG past the intact G4 structure, which allows approach of the leading strand to the G4. Third, G4 structure unwinding by the FANCJ helicase enables the DNA polymerase to synthesize past the G4 motif. A G4 on the lagging strand template does not stall CMG, but still requires active DNA replication for unwinding. DHX36 and FANCJ have partially redundant roles, conferring robustness to this pathway. Our data reveal a novel genome maintenance pathway that promotes faithful G4 replication thereby avoiding genome instability.
2022-02-17 | PXD027623 | Pride
Project description:Altered DNA methylation and associated destabilization of genome integrity and function is a hallmark of cancer. Replicative senescence imposes a limit on proliferative potential that all cancer cells must bypass. Compared to proliferating cells, senescent cells exhibit marked chromatin re-organization. Here we show by whole-genome single-nucleotide bisulfite sequencing that replicative senescent human cells exhibit widespread alterations in their DNA methylome. These changes are linked to mislocalization of the maintenance DNA methyltransferase (DNMT1) in cells approaching senescence, altered replication-coupled DNA methylation and de-repression of repetitive satellite sequences. Deficiency of DNMT1 triggers chromatin changes characteristic of senescence and expression of satellite sequences. Most importantly, but paradoxically, gains and losses of methylation in replicative senescence are similar to those in cancer, and this M-bM-^@M-^XreprogrammedM-bM-^@M-^Y methylation landscape is largely retained when cells escape or bypass senescence. In sum, altered regulation of DNMT1 in cells approaching replicative senescence contributes to changes in chromatin structure and function. Consequently, if senescent cells escape the proliferative barrier, they already harbor epigenetic changes likely to promote malignancy. Examination of methylation status in IMR90 cells
2013-11-25 | E-GEOD-48580 | biostudies-arrayexpress
Project description:Lesions on DNA can uncouple DNA synthesis from helicase unwinding, generating stretches of unreplicated single stranded DNA (ssDNA) behind the replication fork. These ssDNA gaps need to be filled in to complete DNA duplication and thereby avoid the generation of DNA double-stranded breaks (DSBs), a major source of genomic instability. Gap filling repair involves either translesion DNA synthesis (TLS) or template switching (TS) to bypass the lesion. At the heart of these processes, ubiquitylated PCNA recruits many proteins that dictate pathway choice, but the enzymes regulating PCNA ubiquitylation in vertebrates remain poorly defined. Here we report that the E3 ubiquitin ligase RFWD3 promotes non-specific ubiquitylation of proteins on ssDNA, to enhance protein accumulation and stimulate gap filling repair. The absence of RFWD3 leads to a profound defect in recruitment of key repair and signaling factors to damaged chromatin, including ubiquitin and proteins known to ubiquitylate and interact with ubiquitylated PCNA. As a result, PCNA ubiquitylation is severely inhibited without RFWD3, and TLS across different DNA lesions drastically impaired. We propose that RFWD3 is an essential coordinator of the response to ssDNA gaps, where it triggers non-specific ubiquitylation to drive recruitment of effectors of PCNA ubiquitylation and DNA damage bypass.
2020-12-15 | PXD021445 | Pride
Project description:Lesions on DNA can uncouple DNA synthesis from helicase unwinding, generating stretches of unreplicated single stranded DNA (ssDNA) behind the replication fork. These ssDNA gaps need to be filled in to complete DNA duplication and thereby avoid the generation of DNA double-stranded breaks (DSBs), a major source of genomic instability. Gap filling repair involves either translesion DNA synthesis (TLS) or template switching (TS) to bypass the lesion. At the heart of these processes, ubiquitylated PCNA recruits many proteins that dictate pathway choice, but the enzymes regulating PCNA ubiquitylation in vertebrates remain poorly defined. Here we report that the E3 ubiquitin ligase RFWD3 promotes non-specific ubiquitylation of proteins on ssDNA, to enhance protein accumulation and stimulate gap filling repair. The absence of RFWD3 leads to a profound defect in recruitment of key repair and signaling factors to damaged chromatin, including ubiquitin and proteins known to ubiquitylate and interact with ubiquitylated PCNA. As a result, PCNA ubiquitylation is severely inhibited without RFWD3, and TLS across different DNA lesions drastically impaired. We propose that RFWD3 is an essential coordinator of the response to ssDNA gaps, where it triggers wide spread ubiquitylation to drive recruitment of effectors of PCNA ubiquitylation and DNA damage bypass.
2020-12-15 | PXD018217 | Pride
Project description:In this study, we characterised the interactomes of PAXX and its paralogs, XLF and XRCC4, to show that these factors share the ability to interact with DNA polymerase lambda (Poll), stimulate its activityand are required for the recruitment of Poll to laser-induced DNA damage sites.
2018-09-24 | PXD010891 | Pride