Quantitative sensing and signalling of single-stranded DNA during the DNA damage response
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA514440 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8433460.fastq.gz | Fastqsanger.gz | |||
| SRR8433461.fastq.gz | Fastqsanger.gz | |||
| SRR8433452.fastq.gz | Fastqsanger.gz | |||
| SRR8433462.fastq.gz | Fastqsanger.gz | |||
| SRR8433453.fastq.gz | Fastqsanger.gz |
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Project description:The DNA damage checkpoint senses the presence of DNA lesions and controls the cellular response thereto. A crucial DNA damage signal is single-stranded DNA (ssDNA), which is frequently found at sites of DNA damage and recruits the sensor checkpoint kinase Mec1-Ddc2. However, how this signal – and therefore the cells’ DNA damage load – is quantified, is poorly understood. Here, we use genetic manipulation of DNA end resection at a site-specific DNA double-strand break (DSB) in budding yeast to generate quantitatively different DNA damage (ssDNA) signals. Interestingly, two major targets of the Mec1-Ddc2 kinase – Rad53 and γH2A – differ in their response to the ssDNA signal, indicating distinct signalling circuits within the checkpoint. The local checkpoint signalling circuit leading to γH2A phosphorylation is non-quantitative and unresponsive to increased amounts of damage-associated Mec1-Ddc2 kinase. In contrast, the global checkpoint signalling circuit, which triggers Rad53 activation, integrates the ssDNA signal quantitatively. We find that not only Mec1-Ddc2 association, but also loading of the 9-1-1 co-sensor complex is enhanced during ongoing resection. Moreover, we can uncouple global checkpoint activation from the amount of Mec1-Ddc2 kinase at the lesion by using mutant conditions that hyper-activate the 9-1-1 signalling axis and at the same time show reduced amounts of damage-associated Mec1-Ddc2 kinase. We therefore propose that a key function of the 9-1-1 complex and the downstream checkpoint mediators is to generate a checkpoint response, which is quantitative and proportional to the cellular DNA damage load. The DNA damage checkpoint senses the presence of DNA lesions and controls the cellular response thereto. A crucial DNA damage signal is single-stranded DNA (ssDNA), which is frequently found at sites of DNA damage and recruits the sensor checkpoint kinase Mec1-Ddc2. However, how this signal – and therefore the cells’ DNA damage load – is quantified, is poorly understood. Here, we use genetic manipulation of DNA end resection at a site-specific DNA double-strand break (DSB) in budding yeast to generate quantitatively different DNA damage (ssDNA) signals. Interestingly, two major targets of the Mec1-Ddc2 kinase – Rad53 and γH2A – differ in their response to the ssDNA signal, indicating distinct signalling circuits within the checkpoint. The local checkpoint signalling circuit leading to γH2A phosphorylation is non-quantitative and unresponsive to increased amounts of damage-associated Mec1-Ddc2 kinase. In contrast, the global checkpoint signalling circuit, which triggers Rad53 activation, integrates the ssDNA signal quantitatively. We find that not only Mec1-Ddc2 association, but also loading of the 9-1-1 co-sensor complex is enhanced during ongoing resection. Moreover, we can uncouple global checkpoint activation from the amount of Mec1-Ddc2 kinase at the lesion by using mutant conditions that hyper-activate the 9-1-1 signalling axis and at the same time show reduced amounts of damage-associated Mec1-Ddc2 kinase. We therefore propose that a key function of the 9-1-1 complex and the downstream checkpoint mediators is to generate a checkpoint response, which is quantitative and proportional to the cellular DNA damage load.
2019-01-12 | GSE124948 | GEO
Project description:The DNA damage checkpoint senses the presence of DNA lesions and controls the cellular response thereto. A crucial DNA damage signal is single-stranded DNA (ssDNA), which is frequently found at sites of DNA damage and recruits the sensor checkpoint kinase Mec1-Ddc2. However, how this signal - and therefore the cell's DNA damage load - is quantified, is poorly understood. Here, we use genetic manipulation of DNA end resection to induce quantitatively different ssDNA signals at a site-specific double strand break in budding yeast and identify two distinct signalling circuits within the checkpoint. The local checkpoint signalling circuit leading to γH2A phosphorylation is unresponsive to increased amounts of ssDNA, while the global checkpoint signalling circuit, which triggers Rad53 activation, integrates the ssDNA signal quantitatively. The global checkpoint signal critically depends on the 9-1-1 and its downstream acting signalling axis, suggesting that ssDNA quantification depends on at least two sensor complexes.
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Project description:DNA damage activates diverse cellular responses – either protective or deleterious –that ultimately promote or inhibit proliferation. How the distinct responses conferring crucial cell fate decisions are chosen is unclear. Using a systems approach, we demonstrate that the dynamic features of Atm dependent DNA double-strand break (DSB) signalling response dictate cellular outcome. Combining temporal phosphoproteome and nascent transcriptome analyses after low or high DNA-damage-load, we discovered that some responses, such as Tp53 activation, have an activation threshold and others arise independently of DNA-damage-load. Using DSB repair deficient cells, we show that persistent DSBs alter the kinetics – but not the amplitude – of Atm signalling. Thus, we demonstrate that pathway choices are dictated by the signalling dynamics and hence cell fate decisions are responsive to DNA-damage-load and repair capacity of the cells.
2023-01-18 | PXD013620 | Pride
Project description:In order to identify protein involved in sensing DNA double strand breaks and recruiting the repair machinry, we performed in vitro assembly of chromatin on small circular and linear DNA templates, respectively. Proteins involved in chromatin assembly and sensing of free DNA ends were isolated and subjected to proteomics analysis.
2019-10-14 | PXD012990 | Pride
Project description:DNMT3A R882 mutations promote anthacyline resistance through impaired DNA-damage sensing
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Project description:Cornelia de Lange Syndrome is a multisystem developmental disorder typically caused by mutations in the gene encoding the cohesin loader NIPBL. The associated phenotype is generally assumed to be the consequence of aberrant transcriptional regulation. Recently, we identified a residue substitution in BRD4 associated with a Cornelia de Lange-like Syndrome, that reduces BRD4 binding to acetylated histones. Here we show that, although this mutation reduces BRD4-enhancer interaction in mouse embryonic stem cells, it does not affect transcription. Rather it delays the cell cycle, increased DNA damage signalling, and perturbs regulation of DNA repair in mutant cells. This uncovers a new role for BRD4 in DNA repair pathway choice. Furthermore, we find evidence of a similar increase in DNA damage signalling in cells derived from NIPBL-deficient individuals, suggesting that defective DNA damage signalling and repair is also a feature of typical Cornelia de Lange Syndrome.
2021-03-09 | GSE130659 | GEO
Project description:Cellular innate immune sensors of DNA are essential for host defense against invading pathogens. However, the presence of self-derived DNA inside cells poses a biological risk of triggering an inappropriate immune response. The mechanisms limiting induction of inflammation by self nucleic acids are poorly understood. BLM RecQ like helicase is essential for the maintenance of genome integrity and deficient in Bloom syndrome, a rare genetic disease characterized by genome instability, susceptibility to cancer and immunodeficiency. Here, we show that BLM-deficient cells exhibit a constitutively upregulated inflammatory interferon-stimulated gene (ISG) signature. Restoring BLM expression reverts ISG expression to baseline. ISG expression in BLM-deficient fibroblasts is mediated by the cGAS-STING-IRF3 cytosolic DNA sensing pathway. Increased DNA damage or downregulation of the cytoplasmic exonuclease TREX1 enhances ISG expression in BS fibroblasts, and cytoplasmic micronuclei positive for cGAS are increased in BLM-deficient fibroblasts. Finally, BS patients demonstrate elevated ISG expression in peripheral blood. We conclude that BLM is essential to limit the expression of pro-inflammatory genes resulting from the sensing of DNA damage products by the cGAS-STING-IRF3 pathway. These results reveal an unexpected role for BLM in limiting ISG induction, thus connecting DNA damage to innate immunity, which may contribute to human pathogenesis.
2019-03-26 | GSE123447 | GEO
Project description:Preblastoderm Drosophila embryos replicate their genomes at maximal speed. The assembly of chromatin on the newly synthesized chromosomes relies entirely on high concentrations of maternal nucleosome assembly and remodelling factors. Extracts from preblastoderm embryos can be turned into a system for highly efficient assembly of complex chromatin. We serendipitously discovered that this chromatin assembly system contains numerous activities that recognise unprotected DNA ends and initiate DNA damage signalling cascades. Within minutes the phosphorylation of H2A.V (homologous to H2A.X) initiates from DNA breaks and spreads over tens of thousands DNA base pairs. The phosphorylation of H2A.V remains tightly associated with the damaged DNA in cis and does not spread to intact DNA circles in the same reaction. The ultrafast cycles of syncytial nuclei divisions of cleavage-stage embryos do not allow sufficient time to repair DNA breaks. Rather, fatally damaged nuclei are eliminated by a programmed ‘mitotic catastrophe’. Our descriptions of the damage-related proteome and DNA break-dependent phospho-proteome suggest that certain aspects of the DNA damage checkpoint that leads to the elimination of nuclei can be studied in this cell-free system. Our data provide a rich resource for in-depth mechanistic analyses of the DNA break response in this model system.
2019-10-14 | PXD013130 | Pride
Project description:Single Centre, open label assignment phase II clinical study.
To evaluate the effect of oral 200mg Methylene Blue tablets (administered 8x25mg) prior to endoscopy on double stranded DNA breaks in colonic biopsy samples assessed by histone gamma H2AX analysis, compared to control biopsies.
| 2178654 | ecrin-mdr-crc
Project description:Bloom syndrome protein restrains innate immune sensing of DNA damage by cGAS.
| PRJNA508771 | ENA