Ontology highlight
ABSTRACT:
PROVIDER: PRJNA776127 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16632442.fastq.gz | Fastqsanger.gz | |||
| SRR16632443.fastq.gz | Fastqsanger.gz | |||
| SRR16632444.fastq.gz | Fastqsanger.gz | |||
| SRR16632445.fastq.gz | Fastqsanger.gz | |||
| SRR16632446.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:CRISPR-Cas constitutes an adaptive prokaryotic defence system against invasive nucleic acids like viruses and plasmids. Beyond their role in immunity, CRISPR-Cas systems have been shown to closely interact with components of cellular DNA repair pathways either by regulating their expression or via direct protein-protein contact or enzymatic activity. The integrase Cas1 is usually involved in the adaptation phase of CRISPR-Cas immunity but its function in cellular DNA repair pathways has been proposed before. Here, we analysed the capacity of an archaeal Cas1 from Haloferax volcanii to compensate DNA damage induced by oxidative stress and found that a deletion of the cas1 gene led to severe growth defects after stress induction. In addition, our results indicate that Cas1 is directly involved in DNA damage repair as the enzymatically active site of the protein is crucial for growth rescue under oxidative conditions. Based on biochemical cleavage assays, we propose a mechanism in which Cas1 exerts a similar function like the DNA repair protein Fen1 by resolving branched repair intermediate structures. Overall, the present study broadens our understanding of the functional link between CRISPR-Cas immunity and DNA repair by demonstrating that Cas1 and Fen1 display commutable roles during archaeal DNA damage repair.
2022-05-20 | PXD029952 | Pride
Project description:Comprehensive Model Description
Overview
This model simulates the cellular response to DNA damage under conditions of ATM/ATR deficiency—such as in ataxia telangiectasia—and predicts the potential benefits of drug repositioning with Omaveloxolone and spermidine. It integrates several interconnected modules: DNA damage production and repair, ATM/ATR–p53 signaling, NRF2/KEAP1 regulation, spermidine-induced autophagy (with additional positive modulation of ATR signaling), and downstream p53 effectors involved in cell fate decisions.
1. DNA Damage Production and Repair Module
Basal DNA Damage Production:
DNA damage is continuously generated at a constant rate, representing both endogenous processes and low-level environmental stress. This reaction acts as a source term for the DNA_damage species.
Repair Pathways:
Several mechanisms work to reduce DNA damage:
ATM-Mediated Repair: Active ATM facilitates the direct repair of DNA damage.
ATR-Mediated Repair: Active ATR, in cooperation with CHK1, repairs DNA damage.
NRF2-Mediated Repair: Active NRF2 triggers antioxidant responses that reduce DNA damage.
Autophagy-Mediated Repair: The autophagy pathway, induced by spermidine, repairs DNA damage in a saturable manner (modeled using Michaelis–Menten kinetics). This ensures that even a significant pulse of damage is only partially repaired, leaving a nonzero steady-state level.
2. ATM/ATR–p53 Signaling Module
ATM and ATR Activation:
DNA damage, along with a positive input from TOPBP1, converts inactive ATM and ATR to their active forms. Under ATM/ATR-deficient conditions (as in ataxia telangiectasia), the activation is severely reduced, resulting in higher levels of unrepaired DNA damage.
p53 Activation:
Both ATM_active and ATR_active phosphorylate and activate p53. Active p53 then acts as a central integrator of the DNA damage signal.
Regulatory Proteins:
HDAC4:
HDAC4 cycles between inactive and active states. Its active form can attenuate p53 activity.
TOPBP1:
TOPBP1 is activated in a DNA damage–dependent manner and helps promote ATR activation.
CK2:
CK2 is a constitutively active kinase that supports TOPBP1 activation.
3. NRF2/KEAP1 Module and Omaveloxolone
NRF2 Activation:
DNA damage stimulates the conversion of NRF2_inactive to NRF2_active. Active NRF2 enhances antioxidant defenses and promotes DNA repair.
KEAP1-Mediated Degradation:
Under normal conditions, KEAP1 targets NRF2_inactive for degradation, keeping NRF2 activity low.
Modulation by Omaveloxolone:
Omaveloxolone is modeled as a constant (boundary) species. It inhibits KEAP1’s activity, thereby reducing NRF2 degradation. This shifts the balance in favor of increased NRF2_active, which boosts the cell’s antioxidant and repair responses.
4. Spermidine-Induced Autophagy and Positive Modulation of ATR Signaling
Spermidine is modeled as a constant species and has two major effects:
Induction of Autophagy:
Spermidine promotes the conversion of Autophagy_inactive to Autophagy_active. The active autophagy machinery repairs DNA damage using a saturable (Michaelis–Menten) mechanism. This pathway helps clear DNA damage but is limited by its maximum capacity.
Enhancement of ATR Signaling:
Spermidine also positively modulates ATR signaling by enhancing the CK2-mediated activation of TOPBP1. In the model, the effective rate of TOPBP1 activation is increased proportionally to the concentration of spermidine. This is represented by a modulation factor, where the effective rate constant for TOPBP1 activation is multiplied by a term that increases with spermidine concentration. The boosted TOPBP1_active level in turn enhances ATR activation, partially compensating for the loss of ATM/ATR function.
5. Downstream p53 Targets: Cell Fate Decisions
Activated p53 regulates cell fate by inducing the production of several downstream effectors:
p21:
p21 is produced in response to p53 activation and is associated with cell cycle arrest and senescence. Its production is balanced by a degradation reaction.
BAX and PUMA:
Both BAX and PUMA are pro-apoptotic proteins. They are produced in proportion to p53_active and are subsequently degraded. Their relative levels help determine whether the cell will undergo apoptosis.
6. Reaction Kinetics (Qualitative Overview)
Mass-Action and Michaelis–Menten Kinetics:
Most reactions in the model are governed by mass-action kinetics. For example, activation and deactivation reactions (such as ATM activation by DNA damage or p53 activation by ATM/ATR) follow simple proportional relationships.
Saturable Repair Processes:
The autophagy-mediated DNA repair reaction uses Michaelis–Menten kinetics to reflect a saturation effect; when DNA damage is high, the repair rate approaches a maximum value, ensuring that not all damage is cleared immediately.
Modulatory Effects:
Spermidine increases the effective rate of TOPBP1 activation (and hence ATR activation) via a modulation term that is proportional to its concentration. Omaveloxolone reduces the degradation rate of NRF2 by inhibiting KEAP1.
Biological Implications and Model Utility
ATM/ATR Deficiency:
In ataxia telangiectasia, ATM/ATR functions are diminished, leading to increased DNA damage. The model simulates this scenario and examines how alternative pathways (NRF2-mediated repair, autophagy, and enhanced ATR signaling via spermidine) help mitigate the damage.
Drug Repositioning Predictions:
The model can be used to predict the outcomes of repositioning drugs:
Omaveloxolone is expected to stabilize NRF2, enhancing antioxidant defenses and reducing DNA damage.
Spermidine acts dually by promoting autophagy (with a saturable repair capacity) and by boosting ATR signaling via TOPBP1 activation.
Cell Fate Outcomes:
The downstream p53 targets (p21, BAX, and PUMA) serve as markers for cell cycle arrest/senescence and apoptosis. By simulating the dynamics of these proteins, the model can predict whether a cell is likely to survive, arrest its cycle, or undergo apoptosis based on the integrated response to DNA damage and drug interventions.
Conclusion
This detailed and comprehensive model integrates multiple layers of the cellular response to DNA damage in ATM/ATR-deficient conditions. It includes upstream damage sensing, multiple repair pathways (including direct kinase-mediated repair, antioxidant responses via NRF2, and autophagy-mediated repair), and downstream effectors that determine cell fate. Omaveloxolone and spermidine are modeled to specifically modulate the NRF2/KEAP1 pathway and ATR signaling (via TOPBP1 activation), respectively. This framework provides a robust platform for exploring drug repositioning strategies and predicting cellular outcomes in diseases such as ataxia telangiectasia.
2025-11-25 | MODEL2503190002 | BioModels
Project description:CRISPR loci are found in bacterial and archaeal genomes where they provide the molecular machinery for acquisition of immunity against foreign DNA. In addition to the cas genes fundamentally required for CRISPR activity, a second class of genes is associated with the CRISPR loci, of which many have no reported function in CRISPR-mediated immunity. Here, we characterize MM_0565 of Methanosarcina mazei Gö1 associated to the type I-B CRISPR-locus providing evidence for its relevance in regulating this system. We show that MM_0565 is composed of a modified Rossmann-like fold and a winged helix-turn-helix domain and forms a dimer in solution. While direct effects on CRISPR-Cas transcription were not detected by genetic approaches, binding to the leader region of both CRISPR-Cas systems was observed by microscale thermophoresis and electromobility shift assays. Overexpression of MM_0565 however, strongly induced transcription of the cas1-solo gene located in the recently reported casposon, the gene product of which shows high similarity to classical Cas1 proteins. Based on our findings we hypothesize that Cas1-solo is involved in the adaptation of CRISPR-mediated immunity in M. mazei, and that MM_0565 modulates the activity of the CRISPR systems amongst potential other hypnotized actions by activating the transcription of the cas1-solo gene.
2020-09-08 | GSE151372 | GEO
Project description:Partial hepatectomy (PH) imposes increased protein synthesis demands on remaining hepatocytes. Activation of IRE1α, a key sensor of endoplasmic reticulum (ER) stress, elicits XBP1 mRNA splicing and production of XBP1 protein, a main trigger of the unfolded protein response (UPR). Using genome-wide ChIPseq analysis we have explored the role of XBP1 during liver regeneration. XBP1 was induced in liver at 6h after PH in an IL-6 dependent manner. After PH, XBP1 silencing caused persistent ER stress, defective acute phase response (APR), increased hepatocellular damage and regenerative delay. At 6h post-PH, XBP1 bound an increased number of genes implicated in proteostasis, APR, metabolism, antioxidant defense and DNA damage response (DDR). ). XBP1 was linked to regulatory sequences containing canonical UPR motifs as well as motifs characteristic of other nuclear factors suggesting molecular interactions during liver regeneration. Upon PH, XBP1 bound the promoter of STAT3, a molecule downregulated in XBP1-silenced livers. XBP1 was indispensable for ser727-STAT3 phosphorylation, a post-translational modification implicated in cell proliferation and DNA damage repair. During active DNA replication XBP1 deficient livers showed high levels of the DNA double-strand break marker γ-H2AX, in association with defective upregulation of Eme1 and Fen1, two main executors of DDR. In conclusion, XBP1 is induced after PH and co-regulates UPR, APR and DDR during liver regeneration.
2017-01-17 | GSE86048 | GEO
Project description:Transcriptome sequencing was carried out on an Illumina HiSeq platform to investigate the activation of CRISPR-Cas and DNA repair systems by Csa3a in Sulfolobus islandicus Rey15A. We compared the differently expressed genes in Sulfolobus islandicus Rey15A strain with csa3a overexpression vs. Sulfolobus islandicus Rey15A strain carrying an empty expression vector, cas1 deletion strain with csa3a overexpression vs. cas1 deletion strain carrying an empty expression vector, as well as interference-deficient strain with csa3a overexpression vs. interference-deficient strain carrying an empty expression vector. We find that cas genes (SiRe_0760, SiRe_0761, SiRe_0762, SiRe_0763), nucleotidyltransferase domain of DNA polymerase beta (SiRe_0459), chromosome segregation protein (SMC)-related ATPase (SiRe_0649), SMC-related protein (SiRe_1142) and three HerA helicases involved in DNA double break repair (encoded by SiRe_0064 and SiRe_0095 of nurA-herA operons, and SiRe_1857) were significantly up-regulated. Our data indicated that the Csa3a regulator couples transcriptional activation of spacer acquisition genes, CRISPR RNA transcription, DNA repair and genome stability genes.
2017-10-31 | GSE99099 | GEO
Project description:Background: Repair of DNA damage requires chromatin remodeling to permit removal of the lesions. How nucleosomes are remodelled to initiate repair of DNA damage remains largely unknown. Here, we describe how chromatin is altered during repair of UV-induced DNA damage at the level of the linear organisation of nucleosomes. Results: Using MNase-seq, we identified a subset of nucleosomes in the genome that are remodelled in UV-damaged wild-type yeast cells. We mapped the genomic location of these nucleosomes, showing that they contain the histone variant H2A.Z. The remodelling observed is consistent with histone exchange or eviction at these positions. This depends on the yeast SWI/SNF global genome nucleotide excision repair (GG-NER) chromatin-remodelling complex. Remarkably, we found that in the absence of DNA damage, the GG-NER complex occupies chromatin at nucleosome free regions separating adjacent nucleosomes. This establishes the nucleosome structure at these genomic locations, which we refer to as GG-NER complex binding sites (GCBS’s). We observed that these sites are frequently located precisely at certain boundary regions that delineate chromasomally interacting domains (CIDs). These boundaries define chromosomal domains of higher-order nucleosome-nucleosome interaction. We demonstrate that the GG-NER complex redistributes following remodelling of these nucleosomes after DNA damage taking up genomic positions located within the CIDs. This permits the efficient removal of DNA damage at these sites. Conclusions: We argue that organising DNA repair in the genome as described may define origins of DNA repair that greatly reduces the genomic search space for DNA damage recognition, thus ensuring the efficient repair of damage in chromatin.
2018-12-06 | E-MTAB-6569 | biostudies-arrayexpress
Project description:Here, we identify the transcription factor IRX5 as a promoter of HFSC activation. Irx5-/- mice display delayed onset of first postnatal anagen, with increased DNA damage and diminished HFSC proliferation. Through transcriptomic and epigenetic analysis, we discover the formation of open chromatin regions near key cell cycle progression- and DNA damage repair genes in Irx5-/- HFSC. We also identify DNA damage repair factors BRCA1 and BARD1 as IRX5 downstream targets. Inhibition of FGF18 kinase signaling partially rescues the anagen delay in Irx5-/- mice, indicating that the Irx5-/- HFSC quiescent phenotype is in part due to failure to suppress Fgf18 expression. Our findings identify IRX5 as a required promoter of DNA damage repair in HFSC activation and hair cycle initiation.
2022-11-01 | GSE202085 | GEO
Project description:Mastl is commonly overexpressed in cancer, appearing as an alternative therapeutic anticancer target. Loss of Mastl induces multiple chromosomal mitotic errors that lead to the accumulation of micronuclei and multilobulated cells with polyploidy. Our detailed analyses display that loss of Mastl quickly lead to chromosomes breakage and abnormalities impairing correct segregation. Phosphoproteomic data of mouse embryonic fibroblasts revealed defects in kinetochores, perichromosomes, and centrosomes but also on RNA binding proteins and double strand DNA damage repair.In our study, Rad51ap1, a well-known homologous recombination regulator, appeared to be effectively phosphorylated by Nek2 and CDK1, but also efficiently depshosphorylated by PP2A/B55. Taken together, these results suggest that Mastl loss induces a multitude of alteration even in noncancerous cells that lead to the disruption of DNA damage repair triggering chromosomes breakage and in consequence, creates an accumulative disequilibrium in the phosphoproteome.
2020-10-15 | PXD019297 | JPOST Repository
Project description:As a central component during Okazaki fragment maturation, flap endonuclease 1 (FEN1) removes the 5â flap and maintains genomic stability. Here, FEN1 was cloned as a suppressor of transcriptional gene silencing (TGS) from a forward genetic screen. FEN1 is abundant in the root and shoot apical meristems and FEN1-GFP shows a nucleolus-localized signal in tobacco cells. Arabidopsis fen1-1 mutant is hypersensitive to MMS and shows reduced telomere length. Interestingly, genome-wide ChIP-seq and RNA-seq results demonstrate that FEN1 mutation leads to a decrease in the H3K27me3 level and an increase in the expression of a subset of genes marked with H3K27me3. Overall, these results uncover a role for FEN1 in mediating TGS besides maintaining genome stability in Arabidopsis. To characterized the role of FEN1 in epigenetic silencing, we examine histone modification and RNA expression changes by whole-genome RNA sequencing; H3K27me3-, H3K4me3-, H3K9me2-, H3-ChIP-seq in A. thaliana transgenic wild type (TWT) and fen1 mutant
2016-05-28 | E-GEOD-79738 | biostudies-arrayexpress
Project description:DNA double strand breaks (DSBs) in B lymphocytes are thought to arise stochastically during replication (S phase) or as a result of targeted DNA damage by activation induced cytidine deaminase (AID) in G1. Here we identify a novel class of recurrent, early replicating and AID independent DNA lesions, termed early replication fragile sites (ERFS), by genome-wide localization of DNA repair proteins DNA double strand breaks (DSBs) in B lymphocytes are thought to arise stochastically during replication (S phase) or as a result of targeted DNA damage by activation induced cytidine deaminase (AID) in G1. Here we identify a novel class of recurrent, early replicating and AID independent DNA lesions, termed early replication fragile sites (ERFS), by genome-wide localization of DNA repair proteins DNA double strand breaks (DSBs) in B lymphocytes are thought to arise stochastically during replication (S phase) or as a result of targeted DNA damage by activation induced cytidine deaminase (AID) in G1. Here we identify a novel class of recurrent, early replicating and AID independent DNA lesions, termed early replication fragile sites (ERFS), by genome-wide localization of DNA repair proteins RPA, SMC5, gamma-H2AX, and BRCA1 in B cells subjected to replication stress. Protein-DNA association for four DNA damage response proteins (RPA, SMC5, g-H2AX, BRCA1), BrdU incorporation, and gene transcription in B lymphocytes with and without hydroxyurea treatment were examined.
2013-02-04 | E-GEOD-43504 | biostudies-arrayexpress