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1.
Oncogene ; 43(11): 804-820, 2024 03.
Article in English | MEDLINE | ID: mdl-38279062

ABSTRACT

HJURP is overexpressed in several cancer types and strongly correlates with patient survival. However, the mechanistic basis underlying the association of HJURP with cancer aggressiveness is not well understood. HJURP promotes the loading of the histone H3 variant, CENP-A, at the centromeric chromatin, epigenetically defining the centromeres and supporting proper chromosome segregation. In addition, HJURP is associated with DNA repair but its function in this process is still scarcely explored. Here, we demonstrate that HJURP is recruited to DSBs through a mechanism requiring chromatin PARylation and promotes epigenetic alterations that favor the execution of DNA repair. Incorporation of HJURP at DSBs promotes turnover of H3K9me3 and HP1, facilitating DNA damage signaling and DSB repair. Moreover, HJURP overexpression in glioma cell lines also affected global structure of heterochromatin independently of DNA damage induction, promoting genome-wide reorganization and assisting DNA damage response. HJURP overexpression therefore extensively alters DNA damage signaling and DSB repair, and also increases radioresistance of glioma cells. Importantly, HJURP expression levels in tumors are also associated with poor response of patients to radiation. Thus, our results enlarge the understanding of HJURP involvement in DNA repair and highlight it as a promising target for the development of adjuvant therapies that sensitize tumor cells to irradiation.


Subject(s)
Chromatin , Glioma , Humans , Centromere/metabolism , Centromere Protein A/genetics , Centromere Protein A/metabolism , Chromatin/genetics , Chromosomal Proteins, Non-Histone/genetics , Chromosomal Proteins, Non-Histone/metabolism , DNA Repair/genetics , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Glioma/genetics
2.
Cell Rep ; 41(12): 111866, 2022 12 20.
Article in English | MEDLINE | ID: mdl-36543120

ABSTRACT

DNA damage leads to rapid synthesis of poly(ADP-ribose) (pADPr), which is important for damage signaling and repair. pADPr chains are removed by poly(ADP-ribose) glycohydrolase (PARG), releasing free mono(ADP-ribose) (mADPr). Here, we show that the NUDIX hydrolase NUDT5, which can hydrolyze mADPr to ribose-5-phosphate and either AMP or ATP, is recruited to damage sites through interaction with PARG. NUDT5 does not regulate PARP or PARG activity. Instead, loss of NUDT5 reduces basal cellular ATP levels and exacerbates the decrease in cellular ATP that occurs during DNA repair. Further, loss of NUDT5 activity impairs RAD51 recruitment, attenuates the phosphorylation of key DNA-repair proteins, and reduces both H2A.Z exchange at damage sites and repair by homologous recombination. The ability of NUDT5 to hydrolyze mADPr, and/or regulate cellular ATP, may therefore be important for efficient DNA repair. Targeting NUDT5 to disrupt PAR/mADPr and energy metabolism may be an effective anti-cancer strategy.


Subject(s)
Adenosine Diphosphate Ribose , DNA Repair , Adenosine Diphosphate Ribose/metabolism , Poly Adenosine Diphosphate Ribose/metabolism , Glycoside Hydrolases/metabolism , DNA Damage , Adenosine Triphosphate
3.
Mol Oncol ; 15(8): 2065-2083, 2021 08.
Article in English | MEDLINE | ID: mdl-33931939

ABSTRACT

Resistance to adjuvant chemotherapy is a major clinical problem in the treatment of colorectal cancer (CRC). The aim of this study was to elucidate the role of an epithelial to mesenchymal transition (EMT)-inducing protein, ZEB2, in chemoresistance of CRC, and to uncover the underlying mechanism. We performed IHC for ZEB2 and association analyses with clinical outcomes on primary CRC and matched CRC liver metastases in compliance with observational biomarker study guidelines. ZEB2 expression in primary tumours was an independent prognostic marker of reduced overall survival and disease-free survival in patients who received adjuvant FOLFOX chemotherapy. ZEB2 expression was retained in 96% of liver metastases. The ZEB2-dependent EMT transcriptional programme activated nucleotide excision repair (NER) pathway largely via upregulation of the ERCC1 gene and other components in NER pathway, leading to enhanced viability of CRC cells upon oxaliplatin treatment. ERCC1-overexpressing CRC cells did not respond to oxaliplatin in vivo, as assessed using a murine orthotopic model in a randomised and blinded preclinical study. Our findings show that ZEB2 is a biomarker of tumour response to chemotherapy and risk of recurrence in CRC patients. We propose that the ZEB2-ERCC1 axis is a key determinant of chemoresistance in CRC.


Subject(s)
Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Colorectal Neoplasms/genetics , DNA Repair/genetics , DNA-Binding Proteins/genetics , Endonucleases/genetics , Epithelial-Mesenchymal Transition/genetics , Transcription, Genetic , Zinc Finger E-box Binding Homeobox 2/physiology , Animals , Cell Line, Tumor , Colorectal Neoplasms/drug therapy , Colorectal Neoplasms/pathology , Drug Resistance, Neoplasm , Fluorouracil/therapeutic use , Humans , Leucovorin/therapeutic use , Liver Neoplasms/secondary , Mice , Organoplatinum Compounds/therapeutic use , Xenograft Model Antitumor Assays
4.
PLoS One ; 15(12): e0237759, 2020.
Article in English | MEDLINE | ID: mdl-33332350

ABSTRACT

DNA repair requires reorganization of the local chromatin structure to facilitate access to and repair of the DNA. Studying DNA double-strand break (DSB) repair in specific chromatin domains has been aided by the use of sequence-specific endonucleases to generate targeted breaks. Here, we describe a new approach that combines KillerRed, a photosensitizer that generates reactive oxygen species (ROS) when exposed to light, and the genome-targeting properties of the CRISPR/Cas9 system. Fusing KillerRed to catalytically inactive Cas9 (dCas9) generates dCas9-KR, which can then be targeted to any desired genomic region with an appropriate guide RNA. Activation of dCas9-KR with green light generates a local increase in reactive oxygen species, resulting in "clustered" oxidative damage, including both DNA breaks and base damage. Activation of dCas9-KR rapidly (within minutes) increases both γH2AX and recruitment of the KU70/80 complex. Importantly, this damage is repaired within 10 minutes of termination of light exposure, indicating that the DNA damage generated by dCas9-KR is both rapid and transient. Further, repair is carried out exclusively through NHEJ, with no detectable contribution from HR-based mechanisms. Surprisingly, sequencing of repaired DNA damage regions did not reveal any increase in either mutations or INDELs in the targeted region, implying that NHEJ has high fidelity under the conditions of low level, limited damage. The dCas9-KR approach for creating targeted damage has significant advantages over the use of endonucleases, since the duration and intensity of DNA damage can be controlled in "real time" by controlling light exposure. In addition, unlike endonucleases that carry out multiple cut-repair cycles, dCas9-KR produces a single burst of damage, more closely resembling the type of damage experienced during acute exposure to reactive oxygen species or environmental toxins. dCas9-KR is a promising system to induce DNA damage and measure site-specific repair kinetics at clustered DNA lesions.


Subject(s)
CRISPR-Cas Systems/genetics , Clustered Regularly Interspaced Short Palindromic Repeats/genetics , DNA Damage/genetics , DNA Repair/genetics , DNA/genetics , Oxidative Stress/genetics , Cell Line , Chromatin/genetics , DNA Breaks, Double-Stranded , Endonucleases/genetics , Genome/genetics , HEK293 Cells , Humans , Light , RNA, Guide, Kinetoplastida/genetics
5.
Proc Natl Acad Sci U S A ; 117(44): 27566-27577, 2020 11 03.
Article in English | MEDLINE | ID: mdl-33077594

ABSTRACT

Recent studies have implicated DNA polymerases θ (Pol θ) and ß (Pol ß) as mediators of alternative nonhomologous end-joining (Alt-NHEJ) events, including chromosomal translocations. Here we identify subunits of the replicative DNA polymerase δ (Pol δ) as promoters of Alt-NHEJ that results in more extensive intrachromosomal mutations at a single double-strand break (DSB) and more frequent translocations between two DSBs. Depletion of the Pol δ accessory subunit POLD2 destabilizes the complex, resulting in degradation of both POLD1 and POLD3 in human cells. POLD2 depletion markedly reduces the frequency of translocations with sequence modifications but does not affect the frequency of translocations with exact joins. Using separation-of-function mutants, we show that both the DNA synthesis and exonuclease activities of the POLD1 subunit contribute to translocations. As described in yeast and unlike Pol θ, Pol δ also promotes homology-directed repair. Codepletion of POLD2 with 53BP1 nearly eliminates translocations. POLD1 and POLD2 each colocalize with phosphorylated H2AX at ionizing radiation-induced DSBs but not with 53BP1. Codepletion of POLD2 with either ligase 3 (LIG3) or ligase 4 (LIG4) does not further reduce translocation frequency compared to POLD2 depletion alone. Together, these data support a model in which Pol δ promotes Alt-NHEJ in human cells at DSBs, including translocations.


Subject(s)
DNA End-Joining Repair , DNA Polymerase III/metabolism , Translocation, Genetic , DNA Breaks, Double-Stranded , DNA Polymerase III/genetics , Gene Knockdown Techniques , HEK293 Cells , HeLa Cells , Humans , RNA, Small Interfering/metabolism
6.
Cancer Gene Ther ; 27(5): 319-329, 2020 05.
Article in English | MEDLINE | ID: mdl-31138900

ABSTRACT

The Holliday Junction-Recognition Protein (HJURP) was reported as overexpressed in several cancers and also strongly correlated with poor prognosis of patients, especially in glioblastoma (GBM), the most common and deadly type of primary brain tumor. HJURP is responsible for loading the histone H3 variant-the Centromeric Protein A (CENP-A)-at the centromeres in a cell cycle-regulated manner, being required for proper chromosome segregation. Here we investigated HJURP association with survival and radioresistance of different GBM cell lines. HJURP knockdown compromised the clonogenic capacity and severely impaired survival of five distinct GBM cells, while nontumor astrocytes were not affected. U251MG cells showed a robust cell cycle arrest in G2/M phases followed by a drastic increment in cell death after HJURP silencing, while U138MG and U343MG cell lines presented augmented senescence with a comparable increase in cell death. Importantly, we verified that the impact on cell cycle dynamics and clonogenic survival were associated with loss CENP-A at the centromeres. Moreover, radiation resistance was also impacted by HJURP modulation in several GBM cell lines. U87MG, T98G, U138MG, and U343MG cells were all sensitized to ionizing radiation after HJURP reduction. These data reinforce the requirement of HJURP for proliferative capacity and radioresistance of tumor cells, underlining its potential as a promising therapeutic target for GBM.


Subject(s)
Brain Neoplasms/radiotherapy , Centromere Protein A/metabolism , DNA-Binding Proteins/metabolism , Glioblastoma/radiotherapy , Neoplastic Stem Cells/radiation effects , Brain Neoplasms/pathology , Cell Cycle Checkpoints/genetics , Cell Cycle Checkpoints/radiation effects , Cell Line, Tumor , Cell Proliferation/genetics , Cell Proliferation/radiation effects , Cell Survival/genetics , Cell Survival/radiation effects , Centromere/metabolism , Centromere/radiation effects , DNA-Binding Proteins/genetics , Gene Knockdown Techniques , Glioblastoma/pathology , Humans , Neoplastic Stem Cells/pathology , Radiation Tolerance/genetics , Tumor Stem Cell Assay
7.
Trends Genet ; 35(2): 159-172, 2019 02.
Article in English | MEDLINE | ID: mdl-30595401

ABSTRACT

Although stress-induced synthesis of mono(ADP-ribose) (mADPr) and poly(ADP-ribose) (pADPr) conjugates by pADPr polymerase (PARP) enzymes has been studied extensively, the removal and degradation of pADPr, as well as the fate of ADPr metabolites, have received less attention. The observations that stress-induced pADPr undergoes rapid turnover, and that deficiencies in ADPr degradation phenocopy loss of pADPr synthesis, suggest that ADPr degradation is fundamentally important to the cellular stress response. Recent work has identified several distinct families of pADPr hydrolases that can degrade pADPr to release pADPr or mADPr into the cytoplasm. Further, many stress-response proteins contain ADPr-binding domains that can interact with these metabolites. We discuss how pADPr metabolites generated during pADPr degradation can function as signaling intermediates in processes such as inflammation, apoptosis, and DNA damage responses. These studies highlight that the full cycle of ADPr metabolism, including both synthesis and degradation, is necessary for responses to genotoxic stress.


Subject(s)
ADP-Ribosylation/genetics , Poly Adenosine Diphosphate Ribose/genetics , Proteins/genetics , Stress, Physiological/genetics , DNA Damage/genetics , Protein Domains/genetics , Protein Processing, Post-Translational/genetics , Signal Transduction/genetics
8.
Nucleic Acids Res ; 46(8): 3891-3905, 2018 05 04.
Article in English | MEDLINE | ID: mdl-29529298

ABSTRACT

CHD1 is a conserved chromatin remodeling enzyme required for development and linked to prostate cancer in adults, yet its role in human cells is poorly understood. Here, we show that targeted disruption of the CHD1 gene in human cells leads to a defect in early double-strand break (DSB) repair via homologous recombination (HR), resulting in hypersensitivity to ionizing radiation as well as PARP and PTEN inhibition. CHD1 knockout cells show reduced H2AX phosphorylation (γH2AX) and foci formation as well as impairments in CtIP recruitment to the damaged sites. Chromatin immunoprecipitation following a single DSB shows that the reduced levels of γH2AX accumulation at DSBs in CHD1-KO cells are due to both a global reduction in H2AX incorporation and poor retention of H2AX at the DSBs. We also identified a unique N-terminal region of CHD1 that inhibits the DNA binding, ATPase, and chromatin assembly and remodeling activities of CHD1. CHD1 lacking the N terminus was more active in rescuing the defects in γH2AX formation and CtIP recruitment in CHD1-KO cells than full-length CHD1, suggesting the N terminus is a negative regulator in cells. Our data point to a role for CHD1 in the DSB repair process and identify a novel regulatory region of the protein.


Subject(s)
DNA Damage , DNA Helicases/metabolism , DNA-Binding Proteins/metabolism , Adenosine Triphosphatases/chemistry , Adenosine Triphosphatases/genetics , Adenosine Triphosphatases/metabolism , Binding Sites , Carrier Proteins/metabolism , Cell Line , Chromatin Assembly and Disassembly , DNA Breaks, Double-Stranded , DNA Helicases/chemistry , DNA Helicases/genetics , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/genetics , Endodeoxyribonucleases , Gene Knockout Techniques , Histones/metabolism , Homologous Recombination , Humans , Nuclear Proteins/metabolism , Peptide Fragments/chemistry , Peptide Fragments/genetics , Peptide Fragments/metabolism , Phosphorylation , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Signal Transduction
9.
Sci Rep ; 7(1): 12921, 2017 10 10.
Article in English | MEDLINE | ID: mdl-29018219

ABSTRACT

The n-terminal tail of histone H4 recruits repair proteins, including 53BP1, to DNA double-strand breaks (DSB) and undergoes dynamic acetylation during DSB repair. However, how H4 acetylation (H4Ac) recruits repair proteins and reorganizes chromatin during DNA repair is unclear. Here, we show that the bromodomain protein BRD2 is recruited to DSBs. This recruitment requires binding of BRD2's tandem bromodomains to H4Ac, which is generated at DSBs by the Tip60/KAT5 acetyltransferase. Binding of BRD2 to H4Ac protects the underlying acetylated chromatin from attack by histone deacetylases and allows acetylation to spread along the flanking chromatin. However, BRD2 recruitment is spatially restricted to a chromatin domain extending only 2 kb either side of the DSB, and BRD2 does not spread into the chromatin domains flanking the break. Instead, BRD2 facilitates recruitment of a second bromodomain protein, ZMYND8, which spreads along the flanking chromatin, but is excluded from the DSB region. This creates a spatially restricted H4Ac/BRD2 domain which reorganizes chromatin at DSBs, limits binding of the L3MBTL1 repressor and promotes 53BP1 binding, while limiting end-resection of DSBs. BRD2 therefore creates a restricted chromatin environment surrounding DSBs which facilitates DSB repair and which is framed by extensive ZMYND8 domains on the flanking chromatin.


Subject(s)
DNA Breaks, Double-Stranded , DNA Repair , Histones/metabolism , Protein Serine-Threonine Kinases/metabolism , Acetylation , Cell Line, Tumor , Chromosomal Proteins, Non-Histone/metabolism , DNA End-Joining Repair , Humans , Protein Binding , Repressor Proteins/metabolism , Transcription Factors , Tumor Suppressor Proteins , Tumor Suppressor p53-Binding Protein 1 , Valosin Containing Protein/metabolism
10.
Sci Rep ; 7(1): 9674, 2017 08 29.
Article in English | MEDLINE | ID: mdl-28852018

ABSTRACT

Ape1 is the major apurinic/apyrimidinic (AP) endonuclease activity in mammalian cells, and a key factor in base-excision repair of DNA. High expression or aberrant subcellular distribution of Ape1 has been detected in many cancer types, correlated with drug response, tumor prognosis, or patient survival. Here we present evidence that Ape1 facilitates BRCA1-mediated homologous recombination repair (HR), while counteracting error-prone non-homologous end joining of DNA double-strand breaks. Furthermore, Ape1, coordinated with checkpoint kinase Chk2, regulates drug response of glioblastoma cells. Suppression of Ape1/Chk2 signaling in glioblastoma cells facilitates alternative means of damage site recruitment of HR proteins as part of a genomic defense system. Through targeting "HR-addicted" temozolomide-resistant glioblastoma cells via a chemical inhibitor of Rad51, we demonstrated that targeting HR is a promising strategy for glioblastoma therapy. Our study uncovers a critical role for Ape1 in DNA repair pathway choice, and provides a mechanistic understanding of DNA repair-supported chemoresistance in glioblastoma cells.


Subject(s)
DNA Repair , DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism , Drug Tolerance , Glioblastoma/pathology , Metabolic Networks and Pathways , Ubiquitin-Protein Ligases/metabolism , Checkpoint Kinase 2/metabolism , Homologous Recombination , Humans
11.
Philos Trans R Soc Lond B Biol Sci ; 372(1731)2017 Oct 05.
Article in English | MEDLINE | ID: mdl-28847821

ABSTRACT

The ability of cells to detect and repair DNA double-strand breaks (DSBs) within the complex architecture of the genome requires co-ordination between the DNA repair machinery and chromatin remodelling complexes. This co-ordination is essential to process damaged chromatin and create open chromatin structures which are required for repair. Initially, there is a PARP-dependent recruitment of repressors, including HP1 and several H3K9 methyltransferases, and exchange of histone H2A.Z by the NuA4-Tip60 complex. This creates repressive chromatin at the DSB in which the tail of histone H4 is bound to the acidic patch on the nucleosome surface. These repressor complexes are then removed, allowing rapid acetylation of the H4 tail by Tip60. H4 acetylation blocks interaction between the H4 tail and the acidic patch on adjacent nucleosomes, decreasing inter-nucleosomal interactions and creating open chromatin. Further, the H4 tail is now free to recruit proteins such as 53BP1 to DSBs, a process modulated by H4 acetylation, and provides binding sites for bromodomain proteins, including ZMYND8 and BRD4, which are important for DSB repair. Here, we will discuss how the H4 tail functions as a dynamic hub that can be programmed through acetylation to alter chromatin packing and recruit repair proteins to the break site.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.


Subject(s)
Chromatin/genetics , DNA Breaks, Double-Stranded , DNA Repair , Histones/metabolism , Acetylation , Animals , Humans
12.
J Cell Biol ; 216(7): 1871-1873, 2017 07 03.
Article in English | MEDLINE | ID: mdl-28572116

ABSTRACT

Repairing DNA breaks within the complexity of the cell chromatin is challenging. In this issue, Gong et al. (2017. J. Cell Biol. https://doi.org/10.1083/jcb.201611135) identify the histone demethylase KDM5A as a critical editor of the cells' "histone code" that is required to recruit DNA repair complexes to DNA breaks.


Subject(s)
Chromatin , Histone Code , DNA Breaks , DNA Repair , Histones/genetics
14.
Nat Commun ; 8: 15110, 2017 04 27.
Article in English | MEDLINE | ID: mdl-28447610

ABSTRACT

Chromosomal rearrangements are essential events in the pathogenesis of both malignant and nonmalignant disorders, yet the factors affecting their formation are incompletely understood. Here we develop a zinc-finger nuclease translocation reporter and screen for factors that modulate rearrangements in human cells. We identify UBC9 and RAD50 as suppressors and 53BP1, DDB1 and poly(ADP)ribose polymerase 3 (PARP3) as promoters of chromosomal rearrangements across human cell types. We focus on PARP3 as it is dispensable for murine viability and has druggable catalytic activity. We find that PARP3 regulates G quadruplex (G4) DNA in response to DNA damage, which suppresses repair by nonhomologous end-joining and homologous recombination. Chemical stabilization of G4 DNA in PARP3-/- cells leads to widespread DNA double-strand breaks and synthetic lethality. We propose a model in which PARP3 suppresses G4 DNA and facilitates DNA repair by multiple pathways.


Subject(s)
Cell Cycle Proteins/genetics , DNA Repair Enzymes/genetics , DNA-Binding Proteins/genetics , DNA/metabolism , G-Quadruplexes , Poly(ADP-ribose) Polymerases/genetics , Translocation, Genetic/genetics , Tumor Suppressor p53-Binding Protein 1/genetics , Ubiquitin-Conjugating Enzymes/genetics , A549 Cells , Acid Anhydride Hydrolases , Cell Line, Tumor , Chromosomes/metabolism , DNA Breaks, Double-Stranded , DNA Damage , DNA End-Joining Repair/genetics , Gene Knockout Techniques , HEK293 Cells , HeLa Cells , Homologous Recombination , Humans , Models, Genetic , Synthetic Lethal Mutations
15.
Oncotarget ; 8(15): 24518-24532, 2017 Apr 11.
Article in English | MEDLINE | ID: mdl-28445939

ABSTRACT

Radiation therapy is widely used to treat human malignancies, but many tumor types, including gliomas, exhibit significant radioresistance. Radiation therapy creates DNA double-strand breaks (DSBs), and DSB repair is linked to rapid changes in epigenetic modifications, including increased histone methylation. This increased histone methylation recruits DNA repair proteins which can then alter the local chromatin structure and promote repair. Consequently, combining inhibitors of specific histone methyltransferases with radiation therapy may increase tumor radiosensitivity, particularly in tumors with significant therapeutic resistance. Here, we demonstrate that inhibitors of the H4K20 methyltransferase SETD8 (UNC-0379) and the H3K9 methyltransferase G9a (BIX-01294) are effective radiosensitizers of human glioma cells. UNC-0379 blocked H4K20 methylation and reduced recruitment of the 53BP1 protein to DSBs, although this loss of 53BP1 caused only limited changes in radiosensitivity. In contrast, loss of H3K9 methylation through G9a inhibition with BIX-01294 increased radiosensitivity of a panel of glioma cells (SER2Gy range: 1.5 - 2.9). Further, loss of H3K9 methylation reduced DSB signaling dependent on H3K9, including reduced activation of the Tip60 acetyltransferase, loss of ATM signaling and reduced phosphorylation of the KAP-1 repressor. In addition, BIX-0194 inhibited DSB repair through both the homologous recombination and nonhomologous end-joining pathways. Inhibition of G9a and loss of H3K9 methylation is therefore an effective approach for increasing radiosensitivity of glioma cells. These results suggest that combining inhibitors of histone methyltransferases which are critical for DSB repair with radiation therapy may provide a new therapeutic route for sensitizing gliomas and other tumors to radiation therapy.


Subject(s)
DNA Damage/genetics , Glioma/genetics , Histones/metabolism , Glioma/metabolism , Glioma/pathology , Humans , Methylation , Radiation-Sensitizing Agents , Signal Transduction
16.
J Mol Biol ; 428(9 Pt B): 1846-60, 2016 05 08.
Article in English | MEDLINE | ID: mdl-26625977

ABSTRACT

The ability of cells to detect and repair DNA double-strand breaks (DSBs) is dependent on reorganization of the surrounding chromatin structure by chromatin remodeling complexes. These complexes promote access to the site of DNA damage, facilitate processing of the damaged DNA and, importantly, are essential to repackage the repaired DNA. Here, we will review the chromatin remodeling steps that occur immediately after DSB production and that prepare the damaged chromatin template for processing by the DSB repair machinery. DSBs promote rapid accumulation of repressive complexes, including HP1, the NuRD complex, H2A.Z and histone methyltransferases at the DSB. This shift to a repressive chromatin organization may be important to inhibit local transcription and limit mobility of the break and to maintain the DNA ends in close contact. Subsequently, the repressive chromatin is rapidly dismantled through a mechanism involving dynamic exchange of the histone variant H2A.Z. H2A.Z removal at DSBs alters the acidic patch on the nucleosome surface, promoting acetylation of the H4 tail (by the NuA4-Tip60 complex) and shifting the chromatin to a more open structure. Further, H2A.Z removal promotes chromatin ubiquitination and recruitment of additional DSB repair proteins to the break. Modulation of the nucleosome surface and nucleosome function during DSB repair therefore plays a vital role in processing of DNA breaks. Further, the nucleosome surface may function as a central hub during DSB repair, directing specific patterns of histone modification, recruiting DNA repair proteins and modulating chromatin packing during processing of the damaged DNA template.


Subject(s)
DNA Breaks, Double-Stranded , DNA Repair Enzymes/metabolism , DNA Repair , Multienzyme Complexes/metabolism , Nucleosomes/chemistry , Nucleosomes/metabolism , Chromatin Assembly and Disassembly , Models, Biological
17.
Proc Natl Acad Sci U S A ; 112(24): 7507-12, 2015 Jun 16.
Article in English | MEDLINE | ID: mdl-26034280

ABSTRACT

The repair of DNA double-strand breaks (DSBs) requires open, flexible chromatin domains. The NuA4-Tip60 complex creates these flexible chromatin structures by exchanging histone H2A.Z onto nucleosomes and promoting acetylation of histone H4. Here, we demonstrate that the accumulation of H2A.Z on nucleosomes at DSBs is transient, and that rapid eviction of H2A.Z is required for DSB repair. Anp32e, an H2A.Z chaperone that interacts with the C-terminal docking domain of H2A.Z, is rapidly recruited to DSBs. Anp32e functions to remove H2A.Z from nucleosomes, so that H2A.Z levels return to basal within 10 min of DNA damage. Further, H2A.Z removal by Anp32e disrupts inhibitory interactions between the histone H4 tail and the nucleosome surface, facilitating increased acetylation of histone H4 following DNA damage. When H2A.Z removal by Anp32e is blocked, nucleosomes at DSBs retain elevated levels of H2A.Z, and assume a more stable, hypoacetylated conformation. Further, loss of Anp32e leads to increased CtIP-dependent end resection, accumulation of single-stranded DNA, and an increase in repair by the alternative nonhomologous end joining pathway. Exchange of H2A.Z onto the chromatin and subsequent rapid removal by Anp32e are therefore critical for creating open, acetylated nucleosome structures and for controlling end resection by CtIP. Dynamic modulation of H2A.Z exchange and removal by Anp32e reveals the importance of the nucleosome surface and nucleosome dynamics in processing the damaged chromatin template during DSB repair.


Subject(s)
DNA Breaks, Double-Stranded , DNA Repair , Histone Chaperones/metabolism , Histones/metabolism , Nuclear Proteins/metabolism , Nucleosomes/metabolism , Phosphoproteins/metabolism , Acetylation , Amino Acid Sequence , Carrier Proteins/metabolism , Cell Line , DNA End-Joining Repair , Endodeoxyribonucleases , HEK293 Cells , HeLa Cells , Histone Chaperones/chemistry , Histones/chemistry , Histones/genetics , Humans , Molecular Chaperones , Molecular Sequence Data , Nuclear Proteins/chemistry , Phosphoproteins/chemistry , Protein Interaction Domains and Motifs
18.
Proc Natl Acad Sci U S A ; 111(25): 9169-74, 2014 Jun 24.
Article in English | MEDLINE | ID: mdl-24927542

ABSTRACT

Dynamic changes in histone modification are critical for regulating DNA double-strand break (DSB) repair. Activation of the Tip60 acetyltransferase by DSBs requires interaction of Tip60 with histone H3 methylated on lysine 9 (H3K9me3). However, how H3K9 methylation is regulated during DSB repair is not known. Here, we demonstrate that a complex containing kap-1, HP1, and the H3K9 methyltransferase suv39h1 is rapidly loaded onto the chromatin at DSBs. Suv39h1 methylates H3K9, facilitating loading of additional kap-1/HP1/suv39h1 through binding of HP1's chromodomain to the nascent H3K9me3. This process initiates cycles of kap-1/HP1/suv39h1 loading and H3K9 methylation that facilitate spreading of H3K9me3 and kap-1/HP1/suv39h1 complexes for tens of kilobases away from the DSB. These domains of H3K9me3 function to activate the Tip60 acetyltransferase, allowing Tip60 to acetylate both ataxia telangiectasia-mutated (ATM) kinase and histone H4. Consequently, cells lacking suv39h1 display defective activation of Tip60 and ATM, decreased DSB repair, and increased radiosensitivity. Importantly, activated ATM rapidly phosphorylates kap-1, leading to release of the repressive kap-1/HP1/suv39h1 complex from the chromatin. ATM activation therefore functions as a negative feedback loop to remove repressive suv39h1 complexes at DSBs, which may limit DSB repair. Recruitment of kap-1/HP1/suv39h1 to DSBs therefore provides a mechanism for transiently increasing the levels of H3K9me3 in open chromatin domains that lack H3K9me3 and thereby promoting efficient activation of Tip60 and ATM in these regions. Further, transient formation of repressive chromatin may be critical for stabilizing the damaged chromatin and for remodeling the chromatin to create an efficient template for the DNA repair machinery.


Subject(s)
Chromatin Assembly and Disassembly , Chromatin/metabolism , DNA Breaks, Double-Stranded , Histones/metabolism , Ataxia Telangiectasia Mutated Proteins/genetics , Ataxia Telangiectasia Mutated Proteins/metabolism , Chromatin/genetics , HEK293 Cells , HeLa Cells , Histone Acetyltransferases/genetics , Histone Acetyltransferases/metabolism , Histones/genetics , Humans , Lysine/genetics , Lysine/metabolism , Lysine Acetyltransferase 5 , Methylation , Methyltransferases/genetics , Methyltransferases/metabolism , Phosphorylation , Protein Structure, Tertiary , Repressor Proteins/genetics , Repressor Proteins/metabolism , Tripartite Motif-Containing Protein 28
19.
Proc Natl Acad Sci U S A ; 110(44): 17844-9, 2013 Oct 29.
Article in English | MEDLINE | ID: mdl-24127576

ABSTRACT

The major mammalian apurinic/apyrimidinic endonuclease Ape1 is a multifunctional protein operating in protection of cells from oxidative stress via its DNA repair, redox, and transcription regulatory activities. The importance of Ape1 has been marked by previous work demonstrating its requirement for viability in mammalian cells. However, beyond a requirement for Ape1-dependent DNA repair activity, deeper molecular mechanisms of the fundamental role of Ape1 in cell survival have not been defined. Here, we report that Ape1 is an essential factor stabilizing telomeric DNA, and its deficiency is associated with telomere dysfunction and segregation defects in immortalized cells maintaining telomeres by either the alternative lengthening of telomeres pathway (U2OS) or telomerase expression (BJ-hTERT), or in normal human fibroblasts (IMR90). Through the expression of Ape1 derivatives with site-specific changes, we found that the DNA repair and N-terminal acetylation domains are required for the Ape1 function at telomeres. Ape1 associates with telomere proteins in U2OS cells, and Ape1 depletion causes dissociation of TRF2 protein from telomeres. Consistent with this effect, we also observed that Ape1 depletion caused telomere shortening in both BJ-hTERT and in HeLa cells. Thus, our study describes a unique and unpredicted role for Ape1 in telomere protection, providing a direct link between base excision DNA repair activities and telomere metabolism.


Subject(s)
DNA Repair/physiology , DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism , Telomere Homeostasis/genetics , Blotting, Western , Cell Line, Tumor , Chromatin Immunoprecipitation , DNA Primers/genetics , DNA-(Apurinic or Apyrimidinic Site) Lyase/genetics , Fluorescent Antibody Technique , Humans , Immunoprecipitation , In Situ Hybridization, Fluorescence , Telomerase/metabolism , Telomere Homeostasis/physiology
20.
Mol Cell ; 50(6): 908-18, 2013 Jun 27.
Article in English | MEDLINE | ID: mdl-23806336

ABSTRACT

Fanconi anemia (FA) is a rare genetic disorder characterized by an increased susceptibility to squamous cell cancers. Fifteen FA genes are known, and the encoded proteins cooperate in a common DNA repair pathway. A critical step is the monoubiquitination of the FANCD2 protein, and cells from most FA patients are deficient in this step. How monoubiquitinated FANCD2 suppresses squamous cell cancers is unknown. Here we show that Fancd2-deficient mice are prone to Ras-oncogene-driven skin carcinogenesis, while Usp1-deficient mice, expressing elevated cellular levels of Fancd2-Ub, are resistant to skin tumors. Moreover, Fancd2-Ub activates the transcription of the tumor suppressor TAp63, thereby promoting cellular senescence and blocking skin tumorigenesis. For FA patients, the reduction of FANCD2-Ub and TAp63 protein levels may account for their susceptibility to squamous cell neoplasia. Taken together, Usp1 inhibition may be a useful strategy for upregulating TAp63 and preventing or treating squamous cell cancers in the general non-FA population.


Subject(s)
Cell Transformation, Neoplastic/genetics , Fanconi Anemia Complementation Group D2 Protein/physiology , Genes, Tumor Suppressor , Phosphoproteins/genetics , Trans-Activators/genetics , Transcriptional Activation , Animals , Arabidopsis Proteins , Cell Proliferation , Cells, Cultured , Cellular Senescence , DNA Damage , Disease Resistance/genetics , Endopeptidases/deficiency , Endopeptidases/genetics , Fanconi Anemia/genetics , Female , Genes, ras , Genetic Predisposition to Disease , Humans , Mice , Mice, Inbred C57BL , Mice, Knockout , Neoplasms, Squamous Cell/chemically induced , Neoplasms, Squamous Cell/genetics , Neoplasms, Squamous Cell/pathology , Phosphoproteins/metabolism , Promoter Regions, Genetic , Protein Binding , Skin Neoplasms/chemically induced , Skin Neoplasms/genetics , Skin Neoplasms/pathology , Trans-Activators/metabolism , Ubiquitin-Specific Proteases , Ubiquitination
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