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Nature Cell Biology Feb 2021The response to poly(ADP-ribose) polymerase inhibitors (PARPi) is dictated by homologous recombination (HR) DNA repair and the abundance of lesions that trap PARP...
The response to poly(ADP-ribose) polymerase inhibitors (PARPi) is dictated by homologous recombination (HR) DNA repair and the abundance of lesions that trap PARP enzymes. It remains unclear, however, if the established role of PARP in promoting chromatin accessibility impacts viability in these settings. Using a CRISPR-based screen, we identified the PAR-binding chromatin remodeller ALC1/CHD1L as a key determinant of PARPi toxicity in HR-deficient cells. ALC1 loss reduced viability of breast cancer gene (BRCA)-mutant cells and enhanced sensitivity to PARPi by up to 250-fold, while overcoming several resistance mechanisms. ALC1 deficiency reduced chromatin accessibility concomitant with a decrease in the association of base damage repair factors. This resulted in an accumulation of replication-associated DNA damage, increased PARP trapping and a reliance on HR. These findings establish PAR-dependent chromatin remodelling as a mechanistically distinct aspect of PARPi responses and therapeutic target in HR-deficient cancers.
Topics: BRCA1 Protein; BRCA2 Protein; CRISPR-Cas Systems; Cell Line, Tumor; Cell Proliferation; Chromatin; Chromatin Assembly and Disassembly; Chromosome Aberrations; DNA Helicases; DNA Repair; DNA-Binding Proteins; Epistasis, Genetic; Genomic Instability; Green Fluorescent Proteins; Homologous Recombination; Humans; Methyl Methanesulfonate; Mutation; Phthalazines; Piperazines; Poly Adenosine Diphosphate Ribose; Poly(ADP-ribose) Polymerase Inhibitors; Poly(ADP-ribose) Polymerases; Protein Domains
PubMed: 33462394
DOI: 10.1038/s41556-020-00624-3 -
Current Genetics Oct 2020Histone proteins regulate cellular factors' accessibility to DNA, and histone dosage has previously been linked with DNA damage susceptibility and efficiency of DNA... (Review)
Review
Histone proteins regulate cellular factors' accessibility to DNA, and histone dosage has previously been linked with DNA damage susceptibility and efficiency of DNA repair pathways. Surplus histones are known to impede the DNA repair process by interfering with the homologous recombination-mediated DNA repair in Saccharomyces cerevisiae. Here, we discuss the recent finding of association of methyl methanesulfonate (MMS) resistance with the reduced histone H4 gene dosage in the pathogenic yeast Candida glabrata. We have earlier shown that while the low histone H3 gene dosage led to MMS susceptibility, the lack of two H4-encoding ORFs, CgHHF1 and CgHHF2, led to resistance to MMS-induced DNA damage. This resistance was linked with a higher rate of homologous recombination (HR). Taking these findings further, we review the interactome analysis of histones H3 and H4 in C. glabrata. We also report that the arginine residue present at the 95th position in the C-terminal tail of histone H4 protein is required for complementation of the MMS resistance in the Cghhf1Δhhf2Δ mutant, thereby pointing out a probable role of this residue in association with HR factors. Additionally, we present evidence that reduction in H4 protein levels may constitute an important part of varied stress responses in C. glabrata. Altogether, we present an overview of histone H4 dosage, HR-mediated repair of damaged DNA and stress resistance in this opportunistic human fungal pathogen.
Topics: Acetylation; Candida glabrata; DNA Repair; Fungal Proteins; Gene Expression Regulation, Fungal; Genome, Fungal; Histones; Homologous Recombination; Humans
PubMed: 32556547
DOI: 10.1007/s00294-020-01088-6 -
The EMBO Journal Dec 2023R-loops represent a major source of replication stress, but the mechanism by which these structures impede fork progression remains unclear. To address this question, we...
R-loops represent a major source of replication stress, but the mechanism by which these structures impede fork progression remains unclear. To address this question, we monitored fork progression, arrest, and restart in Saccharomyces cerevisiae cells lacking RNase H1 and H2, two enzymes responsible for degrading RNA:DNA hybrids. We found that while RNase H-deficient cells could replicate their chromosomes normally under unchallenged growth conditions, their replication was impaired when exposed to hydroxyurea (HU) or methyl methanesulfonate (MMS). Treated cells exhibited increased levels of RNA:DNA hybrids at stalled forks and were unable to generate RPA-coated single-stranded (ssDNA), an important postreplicative intermediate in resuming replication. Similar impairments in nascent DNA resection and ssDNA formation at HU-arrested forks were observed in human cells lacking RNase H2. However, fork resection was fully restored by addition of triptolide, an inhibitor of transcription that induces RNA polymerase degradation. Taken together, these data indicate that RNA:DNA hybrids not only act as barriers to replication forks, but also interfere with postreplicative fork repair mechanisms if not promptly degraded by RNase H.
Topics: Humans; DNA Replication; RNA; Ribonucleases; DNA; Hydroxyurea; Ribonuclease H
PubMed: 37855233
DOI: 10.15252/embj.2022113104 -
Molecular Cell Feb 2021Chromatin is a barrier to efficient DNA repair, as it hinders access and processing of certain DNA lesions. ALC1/CHD1L is a nucleosome-remodeling enzyme that responds to...
Chromatin is a barrier to efficient DNA repair, as it hinders access and processing of certain DNA lesions. ALC1/CHD1L is a nucleosome-remodeling enzyme that responds to DNA damage, but its precise function in DNA repair remains unknown. Here we report that loss of ALC1 confers sensitivity to PARP inhibitors, methyl-methanesulfonate, and uracil misincorporation, which reflects the need to remodel nucleosomes following base excision by DNA glycosylases but prior to handover to APEX1. Using CRISPR screens, we establish that ALC1 loss is synthetic lethal with homologous recombination deficiency (HRD), which we attribute to chromosome instability caused by unrepaired DNA gaps at replication forks. In the absence of ALC1 or APEX1, incomplete processing of BER intermediates results in post-replicative DNA gaps and a critical dependence on HR for repair. Hence, targeting ALC1 alone or as a PARP inhibitor sensitizer could be employed to augment existing therapeutic strategies for HRD cancers.
Topics: Animals; Chromatin Assembly and Disassembly; DNA Helicases; DNA Replication; DNA-(Apurinic or Apyrimidinic Site) Lyase; DNA-Binding Proteins; Homologous Recombination; Mice; Mice, Knockout; Neoplasm Proteins; Neoplasms, Experimental; Nucleosomes; Poly(ADP-ribose) Polymerase Inhibitors; Poly(ADP-ribose) Polymerases
PubMed: 33333017
DOI: 10.1016/j.molcel.2020.12.006 -
ELife Jun 2023The replication checkpoint is essential for accurate DNA replication and repair, and maintenance of genomic integrity when a cell is challenged with genotoxic stress....
The replication checkpoint is essential for accurate DNA replication and repair, and maintenance of genomic integrity when a cell is challenged with genotoxic stress. Several studies have defined the complement of proteins that change subcellular location in the budding yeast following chemically induced DNA replication stress using methyl methanesulfonate (MMS) or hydroxyurea (HU). How these protein movements are regulated remains largely unexplored. We find that the essential checkpoint kinases Mec1 and Rad53 are responsible for regulating the subcellular localization of 159 proteins during MMS-induced replication stress. Unexpectedly, Rad53 regulation of the localization of 52 proteins is independent of its known kinase activator Mec1, and in some scenarios independent of Tel1 or the mediator proteins Rad9 and Mrc1. We demonstrate that Rad53 is phosphorylated and active following MMS exposure in cells lacking Mec1 and Tel1. This noncanonical mode of Rad53 activation depends partly on the retrograde signaling transcription factor Rtg3, which also facilitates proper DNA replication dynamics. We conclude that there are biologically important modes of Rad53 protein kinase activation that respond to replication stress and operate in parallel to Mec1 and Tel1.
Topics: Protein Serine-Threonine Kinases; Cell Cycle Proteins; Saccharomyces cerevisiae Proteins; Intracellular Signaling Peptides and Proteins; Checkpoint Kinase 2; Saccharomyces cerevisiae; Phosphorylation; DNA Damage; Methyl Methanesulfonate; DNA Replication
PubMed: 37278514
DOI: 10.7554/eLife.82483 -
Genes Feb 2022The identification of mutants through forward genetic screens is the backbone of genetics research, yet many mutants identified through these screens have yet to be...
The identification of mutants through forward genetic screens is the backbone of genetics research, yet many mutants identified through these screens have yet to be mapped to the genome. This is especially true of mutants that have been identified as mutagen-sensitive (), but have not yet been mapped to their associated molecular locus. Our study addressed the need for additional gene identification by determining the locus and exploring the function of the -linked mutagen-sensitive gene using three available mutant alleles: , , and . After first confirming that all three alleles were sensitive to methyl methanesulfonate (MMS) using complementation analysis, we used deletion mapping to narrow the candidate genes for Through DNA sequencing, we were able to determine that is the uncharacterized gene which encodes the ortholog of the highly conserved DNA2 protein that is important for DNA replication and repair. We further used the sequence and structure of DNA2 to predict the impact of the allele mutations on the final gene product. Together, these results provide a tool for researchers to further investigate the role of DNA2 in DNA repair processes in
Topics: Animals; DNA Repair; Drosophila; Drosophila melanogaster; Methyl Methanesulfonate; Mutagens
PubMed: 35205357
DOI: 10.3390/genes13020312 -
Royal Society Open Science Sep 2021The winged-helix domain of the methyl methanesulfonate and ultraviolet-sensitive 81 (MUS81) is a potential cancer drug target. In this context, marine fungi compounds...
The winged-helix domain of the methyl methanesulfonate and ultraviolet-sensitive 81 (MUS81) is a potential cancer drug target. In this context, marine fungi compounds were indicated to be able to prevent MUS81 structure via atomistic simulations. Eight compounds such as (), (), (), (), (), (), () and () were indicated that they are able to prevent the conformation of MUS81 via forming a strong binding affinity to the enzyme via perturbation approach. The electrostatic interaction is the dominant factor in the binding process of ligands to MUS81. The residues Trp55, Arg59, Leu62, His63 and Arg69 were found to frequently form non-bonded contacts and hydrogen bonds to inhibitors. Moreover, the influence of the ligand , which formed the lowest binding free energy to MUS81, on the structural change of enzyme was investigated using replica exchange molecular dynamics simulations. The obtained results indicated that , which forms a strong binding affinity, can modify the structure of MUS81. Overall, the marine compounds probably inhibit MUS81 due to forming a strong binding affinity to the enzyme as well as altering the enzymic conformation.
PubMed: 34527278
DOI: 10.1098/rsos.210974 -
Scientific Reports Mar 2021We evaluated the duloxetine DNA damaging capacity utilizing the comet assay applied to mouse brain and liver cells, as well as its DNA, lipid, protein, and nitric oxide...
We evaluated the duloxetine DNA damaging capacity utilizing the comet assay applied to mouse brain and liver cells, as well as its DNA, lipid, protein, and nitric oxide oxidative potential in the same cells. A kinetic time/dose strategy showed the effect of 2, 20, and 200 mg/kg of the drug administered intraperitoneally once in comparison with a control and a methyl methanesulfonate group. Each parameter was evaluated at 3, 9, 15, and 21 h postadministration in five mice per group, except for the DNA oxidation that was examined only at 9 h postadministration. Results showed a significant DNA damage mainly at 9 h postexposure in both organs. In the brain, with 20 and 200 mg/kg we found 50 and 80% increase over the control group (p ≤ 0.05), in the liver, the increase of 2, 20, and 200 mg/kg of duloxetine was 50, 80, and 135% in comparison with the control level (p ≤ 0.05). DNA, lipid, protein and nitric oxide oxidation increase was also observed in both organs. Our data established the DNA damaging capacity of duloxetine even with a dose from the therapeutic range (2 mg/kg), and suggest that this effect can be related with its oxidative potential.
Topics: Animals; Brain; DNA Damage; Duloxetine Hydrochloride; Liver; Male; Mice; Oxidation-Reduction; Oxidative Stress; Serotonin and Noradrenaline Reuptake Inhibitors
PubMed: 33767322
DOI: 10.1038/s41598-021-86366-0 -
Acta Crystallographica. Section E,... Oct 2021Nafamostat dimesylate {systematic name: [amino({6-[(4-{[amino(iminiumyl)methyl]amino}phenyl)carbonyloxy]naphthalen-2-yl})methylidene]azanium bis(methanesulfonate)}, CHNO...
Nafamostat dimesylate {systematic name: [amino({6-[(4-{[amino(iminiumyl)methyl]amino}phenyl)carbonyloxy]naphthalen-2-yl})methylidene]azanium bis(methanesulfonate)}, CHNO ·2CHOS, is a broad-spectrum serine protease inhibitor and has been applied clinically as an anti-coagulant agent during hemodialysis and for treatment of severe acute pancreatitis (SAP). Since nafamostat contains flexible moieties, it is necessary to determine the conformation to understand the structure-activity relationships. The divalent cation has a screw-like motif. The guanidinium group is approximately perpendicular to the naphthyl ring system, subtending a dihedral angle of 84.30 (14)°. In the crystal, the nafamostat mol-ecules form columnar structures surrounded by a hydro-philic region.
PubMed: 34667626
DOI: 10.1107/S2056989021009245