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1.
Mol Cell ; 83(22): 4017-4031.e9, 2023 Nov 16.
Article in English | MEDLINE | ID: mdl-37820732

ABSTRACT

The MCM motor of the replicative helicase is loaded onto origin DNA as an inactive double hexamer before replication initiation. Recruitment of activators GINS and Cdc45 upon S-phase transition promotes the assembly of two active CMG helicases. Although work with yeast established the mechanism for origin activation, how CMG is formed in higher eukaryotes is poorly understood. Metazoan Downstream neighbor of Son (DONSON) has recently been shown to deliver GINS to MCM during CMG assembly. What impact this has on the MCM double hexamer is unknown. Here, we used cryoelectron microscopy (cryo-EM) on proteins isolated from replicating Xenopus egg extracts to identify a double CMG complex bridged by a DONSON dimer. We find that tethering elements mediating complex formation are essential for replication. DONSON reconfigures the MCM motors in the double CMG, and primordial dwarfism patients' mutations disrupting DONSON dimerization affect GINS and MCM engagement in human cells and DNA synthesis in Xenopus egg extracts.


Subject(s)
Cell Cycle Proteins , DNA Helicases , Nuclear Proteins , Animals , Humans , Cell Cycle Proteins/chemistry , Cell Cycle Proteins/metabolism , Cryoelectron Microscopy , DNA/genetics , DNA/metabolism , DNA Helicases/metabolism , DNA Replication , Minichromosome Maintenance Proteins/genetics , Minichromosome Maintenance Proteins/metabolism , Nuclear Proteins/chemistry , Nuclear Proteins/metabolism , Saccharomyces cerevisiae/genetics , Enzyme Activation
2.
Mol Cell ; 82(10): 1924-1939.e10, 2022 05 19.
Article in English | MEDLINE | ID: mdl-35439434

ABSTRACT

The 53BP1-RIF1-shieldin pathway maintains genome stability by suppressing nucleolytic degradation of DNA ends at double-strand breaks (DSBs). Although RIF1 interacts with damaged chromatin via phospho-53BP1 and facilitates recruitment of the shieldin complex to DSBs, it is unclear whether other regulatory cues contribute to this response. Here, we implicate methylation of histone H3 at lysine 4 by SETD1A-BOD1L in the recruitment of RIF1 to DSBs. Compromising SETD1A or BOD1L expression or deregulating H3K4 methylation allows uncontrolled resection of DNA ends, impairs end-joining of dysfunctional telomeres, and abrogates class switch recombination. Moreover, defects in RIF1 localization to DSBs are evident in patient cells bearing loss-of-function mutations in SETD1A. Loss of SETD1A-dependent RIF1 recruitment in BRCA1-deficient cells restores homologous recombination and leads to resistance to poly(ADP-ribose)polymerase inhibition, reinforcing the clinical relevance of these observations. Mechanistically, RIF1 binds directly to methylated H3K4, facilitating its recruitment to, or stabilization at, DSBs.


Subject(s)
DNA Breaks, Double-Stranded , Telomere-Binding Proteins , BRCA1 Protein/genetics , DNA/metabolism , DNA End-Joining Repair , DNA Repair , Histone-Lysine N-Methyltransferase/genetics , Histone-Lysine N-Methyltransferase/metabolism , Humans , Methylation , Telomere-Binding Proteins/genetics , Telomere-Binding Proteins/metabolism , Tumor Suppressor p53-Binding Protein 1/genetics , Tumor Suppressor p53-Binding Protein 1/metabolism
3.
Am J Hum Genet ; 110(3): 499-515, 2023 03 02.
Article in English | MEDLINE | ID: mdl-36724785

ABSTRACT

Telomere maintenance 2 (TELO2), Tel2 interacting protein 2 (TTI2), and Tel2 interacting protein 1 (TTI1) are the three components of the conserved Triple T (TTT) complex that modulates activity of phosphatidylinositol 3-kinase-related protein kinases (PIKKs), including mTOR, ATM, and ATR, by regulating the assembly of mTOR complex 1 (mTORC1). The TTT complex is essential for the expression, maturation, and stability of ATM and ATR in response to DNA damage. TELO2- and TTI2-related bi-allelic autosomal-recessive (AR) encephalopathies have been described in individuals with moderate to severe intellectual disability (ID), short stature, postnatal microcephaly, and a movement disorder (in the case of variants within TELO2). We present clinical, genomic, and functional data from 11 individuals in 9 unrelated families with bi-allelic variants in TTI1. All present with ID, and most with microcephaly, short stature, and a movement disorder. Functional studies performed in HEK293T cell lines and fibroblasts and lymphoblastoid cells derived from 4 unrelated individuals showed impairment of the TTT complex and of mTOR pathway activity which is improved by treatment with Rapamycin. Our data delineate a TTI1-related neurodevelopmental disorder and expand the group of disorders related to the TTT complex.


Subject(s)
Microcephaly , Movement Disorders , Neurodevelopmental Disorders , Humans , Intracellular Signaling Peptides and Proteins , HEK293 Cells , TOR Serine-Threonine Kinases
4.
Mol Cell ; 71(1): 25-41.e6, 2018 07 05.
Article in English | MEDLINE | ID: mdl-29937342

ABSTRACT

Components of the Fanconi anemia and homologous recombination pathways play a vital role in protecting newly replicated DNA from uncontrolled nucleolytic degradation, safeguarding genome stability. Here we report that histone methylation by the lysine methyltransferase SETD1A is crucial for protecting stalled replication forks from deleterious resection. Depletion of SETD1A sensitizes cells to replication stress and leads to uncontrolled DNA2-dependent resection of damaged replication forks. The ability of SETD1A to prevent degradation of these structures is mediated by its ability to catalyze methylation on Lys4 of histone H3 (H3K4) at replication forks, which enhances FANCD2-dependent histone chaperone activity. Suppressing H3K4 methylation or expression of a chaperone-defective FANCD2 mutant leads to loss of RAD51 nucleofilament stability and severe nucleolytic degradation of replication forks. Our work identifies epigenetic modification and histone mobility as critical regulatory mechanisms in maintaining genome stability by restraining nucleases from irreparably damaging stalled replication forks.


Subject(s)
DNA/biosynthesis , Fanconi Anemia Complementation Group D2 Protein/metabolism , Histone-Lysine N-Methyltransferase/metabolism , Histones/metabolism , Molecular Chaperones/metabolism , Nucleosomes/metabolism , A549 Cells , DNA/genetics , DNA Replication/physiology , Epigenesis, Genetic/physiology , Fanconi Anemia Complementation Group D2 Protein/genetics , HeLa Cells , Histone-Lysine N-Methyltransferase/genetics , Histones/genetics , Humans , Methylation , Molecular Chaperones/genetics , Nucleosomes/genetics , Rad51 Recombinase/genetics , Rad51 Recombinase/metabolism
5.
Nature ; 571(7766): 521-527, 2019 07.
Article in English | MEDLINE | ID: mdl-31270457

ABSTRACT

The integrity of genomes is constantly threatened by problems encountered by the replication fork. BRCA1, BRCA2 and a subset of Fanconi anaemia proteins protect stalled replication forks from degradation by nucleases, through pathways that involve RAD51. The contribution and regulation of BRCA1 in replication fork protection, and how this role relates to its role in homologous recombination, is unclear. Here we show that BRCA1 in complex with BARD1, and not the canonical BRCA1-PALB2 interaction, is required for fork protection. BRCA1-BARD1 is regulated by a conformational change mediated by the phosphorylation-directed prolyl isomerase PIN1. PIN1 activity enhances BRCA1-BARD1 interaction with RAD51, thereby increasing the presence of RAD51 at stalled replication structures. We identify genetic variants of BRCA1-BARD1 in patients with cancer that exhibit poor protection of nascent strands but retain homologous recombination proficiency, thus defining domains of BRCA1-BARD1 that are required for fork protection and associated with cancer development. Together, these findings reveal a BRCA1-mediated pathway that governs replication fork protection.


Subject(s)
BRCA1 Protein/chemistry , BRCA1 Protein/metabolism , DNA Replication , Tumor Suppressor Proteins/metabolism , Ubiquitin-Protein Ligases/metabolism , BRCA1 Protein/genetics , Cell Line, Tumor , DNA Replication/genetics , Genomic Instability/genetics , Humans , Isomerism , Mutation , NIMA-Interacting Peptidylprolyl Isomerase/metabolism , Phosphorylation , Phosphoserine/metabolism , Protein Binding , Rad51 Recombinase/metabolism
6.
Mol Cell ; 65(5): 900-916.e7, 2017 Mar 02.
Article in English | MEDLINE | ID: mdl-28238654

ABSTRACT

Protein post-translation modification plays an important role in regulating DNA repair; however, the role of arginine methylation in this process is poorly understood. Here we identify the arginine methyltransferase PRMT5 as a key regulator of homologous recombination (HR)-mediated double-strand break (DSB) repair, which is mediated through its ability to methylate RUVBL1, a cofactor of the TIP60 complex. We show that PRMT5 targets RUVBL1 for methylation at position R205, which facilitates TIP60-dependent mobilization of 53BP1 from DNA breaks, promoting HR. Mechanistically, we demonstrate that PRMT5-directed methylation of RUVBL1 is critically required for the acetyltransferase activity of TIP60, promoting histone H4K16 acetylation, which facilities 53BP1 displacement from DSBs. Interestingly, RUVBL1 methylation did not affect the ability of TIP60 to facilitate ATM activation. Taken together, our findings reveal the importance of PRMT5-mediated arginine methylation during DSB repair pathway choice through its ability to regulate acetylation-dependent control of 53BP1 localization.


Subject(s)
Carrier Proteins/metabolism , DNA Breaks, Double-Stranded , DNA Helicases/metabolism , Histone Acetyltransferases/metabolism , Protein Processing, Post-Translational , Protein-Arginine N-Methyltransferases/metabolism , Recombinational DNA Repair , ATPases Associated with Diverse Cellular Activities , Acetylation , Animals , Arginine , Ataxia Telangiectasia Mutated Proteins/metabolism , Carrier Proteins/genetics , DNA Helicases/genetics , Genomic Instability , HEK293 Cells , HeLa Cells , Histone Acetyltransferases/genetics , Histones/metabolism , Humans , Lysine Acetyltransferase 5 , Methylation , Mice , Mice, Transgenic , Protein-Arginine N-Methyltransferases/genetics , RNA Interference , Time Factors , Transfection , Tumor Suppressor p53-Binding Protein 1/genetics , Tumor Suppressor p53-Binding Protein 1/metabolism
7.
Biochem J ; 481(14): 923-944, 2024 Jul 17.
Article in English | MEDLINE | ID: mdl-38985307

ABSTRACT

Maintenance of genome stability is of paramount importance for the survival of an organism. However, genomic integrity is constantly being challenged by various endogenous and exogenous processes that damage DNA. Therefore, cells are heavily reliant on DNA repair pathways that have evolved to deal with every type of genotoxic insult that threatens to compromise genome stability. Notably, inherited mutations in genes encoding proteins involved in these protective pathways trigger the onset of disease that is driven by chromosome instability e.g. neurodevelopmental abnormalities, neurodegeneration, premature ageing, immunodeficiency and cancer development. The ability of cells to regulate the recruitment of specific DNA repair proteins to sites of DNA damage is extremely complex but is primarily mediated by protein post-translational modifications (PTMs). Ubiquitylation is one such PTM, which controls genome stability by regulating protein localisation, protein turnover, protein-protein interactions and intra-cellular signalling. Over the past two decades, numerous ubiquitin (Ub) E3 ligases have been identified to play a crucial role not only in the initiation of DNA replication and DNA damage repair but also in the efficient termination of these processes. In this review, we discuss our current understanding of how different Ub E3 ligases (RNF168, TRAIP, HUWE1, TRIP12, FANCL, BRCA1, RFWD3) function to regulate DNA repair and replication and the pathological consequences arising from inheriting deleterious mutations that compromise the Ub-dependent DNA damage response.


Subject(s)
DNA Damage , DNA Repair , DNA Replication , Ubiquitin-Protein Ligases , Humans , Ubiquitin-Protein Ligases/metabolism , Ubiquitin-Protein Ligases/genetics , Ubiquitination , Neoplasms/genetics , Neoplasms/metabolism , Genomic Instability , Protein Processing, Post-Translational , Animals , Tumor Suppressor Proteins/genetics , Tumor Suppressor Proteins/metabolism
8.
Nucleic Acids Res ; 51(12): 6337-6354, 2023 07 07.
Article in English | MEDLINE | ID: mdl-37224534

ABSTRACT

Accurate genome replication is essential for all life and a key mechanism of disease prevention, underpinned by the ability of cells to respond to replicative stress (RS) and protect replication forks. These responses rely on the formation of Replication Protein A (RPA)-single stranded (ss) DNA complexes, yet this process remains largely uncharacterized. Here, we establish that actin nucleation-promoting factors (NPFs) associate with replication forks, promote efficient DNA replication and facilitate association of RPA with ssDNA at sites of RS. Accordingly, their loss leads to deprotection of ssDNA at perturbed forks, impaired ATR activation, global replication defects and fork collapse. Supplying an excess of RPA restores RPA foci formation and fork protection, suggesting a chaperoning role for actin nucleators (ANs) (i.e. Arp2/3, DIAPH1) and NPFs (i.e, WASp, N-WASp) in regulating RPA availability upon RS. We also discover that ß-actin interacts with RPA directly in vitro, and in vivo a hyper-depolymerizing ß-actin mutant displays a heightened association with RPA and the same dysfunctional replication phenotypes as loss of ANs/NPFs, which contrasts with the phenotype of a hyper-polymerizing ß-actin mutant. Thus, we identify components of actin polymerization pathways that are essential for preventing ectopic nucleolytic degradation of perturbed forks by modulating RPA activity.


Subject(s)
Actins , DNA Replication , Actins/genetics , Replication Protein A/genetics , Replication Protein A/metabolism , DNA, Single-Stranded/genetics , Molecular Chaperones/genetics
9.
Nucleic Acids Res ; 51(9): 4341-4362, 2023 05 22.
Article in English | MEDLINE | ID: mdl-36928661

ABSTRACT

BRCA1 mutations are associated with increased breast and ovarian cancer risk. BRCA1-mutant tumors are high-grade, recurrent, and often become resistant to standard therapies. Herein, we performed a targeted CRISPR-Cas9 screen and identified MEPCE, a methylphosphate capping enzyme, as a synthetic lethal interactor of BRCA1. Mechanistically, we demonstrate that depletion of MEPCE in a BRCA1-deficient setting led to dysregulated RNA polymerase II (RNAPII) promoter-proximal pausing, R-loop accumulation, and replication stress, contributing to transcription-replication collisions. These collisions compromise genomic integrity resulting in loss of viability of BRCA1-deficient cells. We also extend these findings to another RNAPII-regulating factor, PAF1. This study identifies a new class of synthetic lethal partners of BRCA1 that exploit the RNAPII pausing regulation and highlight the untapped potential of transcription-replication collision-inducing factors as unique potential therapeutic targets for treating cancers associated with BRCA1 mutations.


Subject(s)
BRCA1 Protein , DNA Replication , Hereditary Breast and Ovarian Cancer Syndrome , Mutation , Transcription, Genetic , Humans , BRCA1 Protein/deficiency , BRCA1 Protein/genetics , DNA Replication/genetics , Hereditary Breast and Ovarian Cancer Syndrome/genetics , Hereditary Breast and Ovarian Cancer Syndrome/pathology , Hereditary Breast and Ovarian Cancer Syndrome/physiopathology , RNA Polymerase II/metabolism , Transcription, Genetic/genetics , Promoter Regions, Genetic , Methyltransferases/deficiency , Methyltransferases/genetics , R-Loop Structures , Cell Death
10.
Nucleic Acids Res ; 51(19): 10484-10505, 2023 10 27.
Article in English | MEDLINE | ID: mdl-37697435

ABSTRACT

Breast cancer linked with BRCA1/2 mutations commonly recur and resist current therapies, including PARP inhibitors. Given the lack of effective targeted therapies for BRCA1-mutant cancers, we sought to identify novel targets to selectively kill these cancers. Here, we report that loss of RNF8 significantly protects Brca1-mutant mice against mammary tumorigenesis. RNF8 deficiency in human BRCA1-mutant breast cancer cells was found to promote R-loop accumulation and replication fork instability, leading to increased DNA damage, senescence, and synthetic lethality. Mechanistically, RNF8 interacts with XRN2, which is crucial for transcription termination and R-loop resolution. We report that RNF8 ubiquitylates XRN2 to facilitate its recruitment to R-loop-prone genomic loci and that RNF8 deficiency in BRCA1-mutant breast cancer cells decreases XRN2 occupancy at R-loop-prone sites, thereby promoting R-loop accumulation, transcription-replication collisions, excessive genomic instability, and cancer cell death. Collectively, our work identifies a synthetic lethal interaction between RNF8 and BRCA1, which is mediated by a pathological accumulation of R-loops.


Subject(s)
BRCA1 Protein , Breast Neoplasms , Animals , Female , Humans , Mice , BRCA1 Protein/metabolism , BRCA2 Protein/genetics , Breast Neoplasms/genetics , DNA Damage , DNA-Binding Proteins/metabolism , Exoribonucleases/metabolism , Genomic Instability , Neoplasm Recurrence, Local , R-Loop Structures , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/metabolism , Ubiquitination
11.
Haematologica ; 2024 06 06.
Article in English | MEDLINE | ID: mdl-38841800

ABSTRACT

Diffuse large B-cell lymphoma (DLBCL) is the most common malignancy that develops in patients with ataxia-telangiectasia, a cancer-predisposing inherited syndrome characterized by inactivating germline ATM mutations. ATM is also frequently mutated in sporadic DLBCL. To investigate lymphomagenic mechanisms and lymphoma-specific dependencies underlying defective ATM, we applied ribonucleic acid (RNA)-seq and genome-scale loss-offunction clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 screens to systematically interrogate B-cell lymphomas arising in a novel murine model (Atm-/-nu-/-) with constitutional Atm loss, thymic aplasia but residual T-cell populations. Atm-/-nu-/-lymphomas, which phenotypically resemble either activated B-cell-like or germinal center Bcell-like DLBCL, harbor a complex karyotype, and are characterized by MYC pathway activation. In Atm-/-nu-/-lymphomas, we discovered nucleotide biosynthesis as a MYCdependent cellular vulnerability that can be targeted through the synergistic nucleotidedepleting actions of mycophenolate mofetil (MMF) and the WEE1 inhibitor, adavosertib (AZD1775). The latter is mediated through a synthetically lethal interaction between RRM2 suppression and MYC dysregulation that results in replication stress overload in Atm-/-nu-/-lymphoma cells. Validation in cell line models of human DLBCL confirmed the broad applicability of nucleotide depletion as a therapeutic strategy for MYC-driven DLBCL independent of ATM mutation status. Our findings extend current understanding of lymphomagenic mechanisms underpinning ATM loss and highlight nucleotide metabolism as a targetable therapeutic vulnerability in MYC-driven DLBCL.

12.
Cell ; 136(3): 420-34, 2009 Feb 06.
Article in English | MEDLINE | ID: mdl-19203578

ABSTRACT

The biological response to DNA double-strand breaks acts to preserve genome integrity. Individuals bearing inactivating mutations in components of this response exhibit clinical symptoms that include cellular radiosensitivity, immunodeficiency, and cancer predisposition. The archetype for such disorders is Ataxia-Telangiectasia caused by biallelic mutation in ATM, a central component of the DNA damage response. Here, we report that the ubiquitin ligase RNF168 is mutated in the RIDDLE syndrome, a recently discovered immunodeficiency and radiosensitivity disorder. We show that RNF168 is recruited to sites of DNA damage by binding to ubiquitylated histone H2A. RNF168 acts with UBC13 to amplify the RNF8-dependent histone ubiquitylation by targeting H2A-type histones and by promoting the formation of lysine 63-linked ubiquitin conjugates. These RNF168-dependent chromatin modifications orchestrate the accumulation of 53BP1 and BRCA1 to DNA lesions, and their loss is the likely cause of the cellular and developmental phenotypes associated with RIDDLE syndrome.


Subject(s)
DNA Damage , Immunologic Deficiency Syndromes/metabolism , Signal Transduction , Ubiquitin/metabolism , Cell Line , Histones/metabolism , Humans , Immunologic Deficiency Syndromes/genetics , Radiation Tolerance , Ubiquitin-Conjugating Enzymes/metabolism , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/metabolism
13.
PLoS Genet ; 17(11): e1009909, 2021 11.
Article in English | MEDLINE | ID: mdl-34780483

ABSTRACT

The ATRX ATP-dependent chromatin remodelling/helicase protein associates with the DAXX histone chaperone to deposit histone H3.3 over repetitive DNA regions. Because ATRX-protein interactions impart functions, such as histone deposition, we used proximity-dependent biotinylation (BioID) to identify proximal associations for ATRX. The proteomic screen captured known interactors, such as DAXX, NBS1, and PML, but also identified a range of new associating proteins. To gauge the scope of their roles, we examined three novel ATRX-associating proteins that likely differed in function, and for which little data were available. We found CCDC71 to associate with ATRX, but also HP1 and NAP1, suggesting a role in chromatin maintenance. Contrastingly, FAM207A associated with proteins involved in ribosome biosynthesis and localized to the nucleolus. ATRX proximal associations with the SLF2 DNA damage response factor help inhibit telomere exchanges. We further screened for the proteomic changes at telomeres when ATRX, SLF2, or both proteins were deleted. The loss caused important changes in the abundance of chromatin remodelling, DNA replication, and DNA repair factors at telomeres. Interestingly, several of these have previously been implicated in alternative lengthening of telomeres. Altogether, this study expands the repertoire of ATRX-associating proteins and functions.


Subject(s)
Co-Repressor Proteins/genetics , DNA-Binding Proteins/genetics , Intracellular Signaling Peptides and Proteins/genetics , Nuclear Proteins/genetics , X-linked Nuclear Protein/genetics , Biotinylation/genetics , Cell Cycle Proteins/genetics , Cell Line , Chromatin/genetics , Chromobox Protein Homolog 5/genetics , DNA Damage/genetics , DNA Repair/genetics , Histone Chaperones/genetics , Histones/genetics , Humans , Molecular Chaperones/genetics , Promyelocytic Leukemia Protein/genetics , Telomere/genetics , tRNA Methyltransferases
14.
EMBO Rep ; 22(5): e51120, 2021 05 05.
Article in English | MEDLINE | ID: mdl-33779025

ABSTRACT

Replication stress, a major cause of genome instability in cycling cells, is mainly prevented by the ATR-dependent replication stress response pathway in somatic cells. However, the replication stress response pathway in embryonic stem cells (ESCs) may be different due to alterations in cell cycle phase length. The transcription factor MYBL2, which is implicated in cell cycle regulation, is expressed a hundred to a thousand-fold more in ESCs compared with somatic cells. Here we show that MYBL2 activates ATM and suppresses replication stress in ESCs. Consequently, loss of MYBL2 or inhibition of ATM or Mre11 in ESCs results in replication fork slowing, increased fork stalling and elevated origin firing. Additionally, we demonstrate that inhibition of CDC7 activity rescues replication stress induced by MYBL2 loss and ATM inhibition, suggesting that uncontrolled new origin firing may underlie the replication stress phenotype resulting from loss/inhibition of MYBL2 and ATM. Overall, our study proposes that in addition to ATR, a MYBL2-MRN-ATM replication stress response pathway functions in ESCs to control DNA replication initiation and prevent genome instability.


Subject(s)
Cell Cycle Proteins , Pluripotent Stem Cells , Ataxia Telangiectasia Mutated Proteins/genetics , Ataxia Telangiectasia Mutated Proteins/metabolism , Cell Cycle Proteins/genetics , Cell Cycle Proteins/metabolism , DNA Damage , DNA Replication , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Pluripotent Stem Cells/metabolism
15.
Mol Cell ; 59(3): 462-77, 2015 Aug 06.
Article in English | MEDLINE | ID: mdl-26166705

ABSTRACT

Recognition and repair of damaged replication forks are essential to maintain genome stability and are coordinated by the combined action of the Fanconi anemia and homologous recombination pathways. These pathways are vital to protect stalled replication forks from uncontrolled nucleolytic activity, which otherwise causes irreparable genomic damage. Here, we identify BOD1L as a component of this fork protection pathway, which safeguards genome stability after replication stress. Loss of BOD1L confers exquisite cellular sensitivity to replication stress and uncontrolled resection of damaged replication forks, due to a failure to stabilize RAD51 at these forks. Blocking DNA2-dependent resection, or downregulation of the helicases BLM and FBH1, suppresses both catastrophic fork processing and the accumulation of chromosomal damage in BOD1L-deficient cells. Thus, our work implicates BOD1L as a critical regulator of genome integrity that restrains nucleolytic degradation of damaged replication forks.


Subject(s)
Cell Cycle Proteins/genetics , Cell Cycle Proteins/metabolism , DNA Replication , Rad51 Recombinase/genetics , Rad51 Recombinase/metabolism , Cell Line , Cell Survival , DNA Damage , DNA Helicases/metabolism , DNA-Binding Proteins/metabolism , Genome, Human , Genomic Instability , HeLa Cells , Humans , RecQ Helicases/metabolism
16.
Am J Hum Genet ; 104(3): 439-453, 2019 03 07.
Article in English | MEDLINE | ID: mdl-30773278

ABSTRACT

SPONASTRIME dysplasia is a rare, recessive skeletal dysplasia characterized by short stature, facial dysmorphism, and aberrant radiographic findings of the spine and long bone metaphysis. No causative genetic alterations for SPONASTRIME dysplasia have yet been determined. Using whole-exome sequencing (WES), we identified bi-allelic TONSL mutations in 10 of 13 individuals with SPONASTRIME dysplasia. TONSL is a multi-domain scaffold protein that interacts with DNA replication and repair factors and which plays critical roles in resistance to replication stress and the maintenance of genome integrity. We show here that cellular defects in dermal fibroblasts from affected individuals are complemented by the expression of wild-type TONSL. In addition, in vitro cell-based assays and in silico analyses of TONSL structure support the pathogenicity of those TONSL variants. Intriguingly, a knock-in (KI) Tonsl mouse model leads to embryonic lethality, implying the physiological importance of TONSL. Overall, these findings indicate that genetic variants resulting in reduced function of TONSL cause SPONASTRIME dysplasia and highlight the importance of TONSL in embryonic development and postnatal growth.


Subject(s)
Fibroblasts/pathology , Genes, Lethal , Mutation , NF-kappa B/genetics , Osteochondrodysplasias/pathology , Adolescent , Adult , Animals , Cells, Cultured , Child , Child, Preschool , DNA Damage , Dermis/metabolism , Dermis/pathology , Female , Fibroblasts/metabolism , Humans , Infant , Infant, Newborn , Mice , Mice, Inbred C57BL , Osteochondrodysplasias/genetics , Exome Sequencing/methods , Young Adult
17.
J Gen Virol ; 101(8): 873-883, 2020 08.
Article in English | MEDLINE | ID: mdl-32501196

ABSTRACT

Gammaherpesviruses establish lifelong latent infection in B lymphocytes and are the causative agent of several B-cell malignancies and lymphoproliferative disorders. While a quiescent latent infection allows these pathogens to evade immune detection, initiation of an alternative lifecycle stage, known as lytic replication, is an essential step in the production and dissemination of infectious progeny. Although cessation of cellular proliferation is an eventual consequence of lytic induction, exactly how gammaherpesviruses manipulate the cell cycle prior to amplification of viral DNA remains under debate. Here we show that the onset of Kaposi's sarcoma-associated herpesvirus (KSHV) lytic reactivation in B cells leads to S-phase accumulation and that exit from G1 is required for efficient viral DNA replication. We also show that lytic replication leads to an S-phase-specific activation of the DNA damage response (DDR) that is abrogated when lytic replication is restricted to G0/G1. Finally, we observe that expression of early lytic viral genes results in cellular replication stress with increased stalling of DNA replication forks. Overall, we demonstrate that S-phase entry is important for optimal KSHV replication, that G1 arresting compounds are effective inhibitors of viral propagation, and that lytic-induced cell-cycle arrest could occur through the obstruction of cellular replication forks and subsequent activation of the DDR.


Subject(s)
DNA Replication/genetics , Herpesviridae/genetics , Lymphoma, Primary Effusion/virology , S Phase/genetics , Virus Replication/genetics , Cell Line , DNA, Viral/genetics , G1 Phase/genetics , Gene Expression Regulation, Viral/genetics , Herpesvirus 8, Human/genetics , Humans , Virus Activation/genetics , Virus Latency/genetics
18.
Mol Cell ; 45(4): 505-16, 2012 Feb 24.
Article in English | MEDLINE | ID: mdl-22365830

ABSTRACT

DNA double-strand break (DSB) signaling and repair are critical for cell viability, and rely on highly coordinated pathways whose molecular organization is still incompletely understood. Here, we show that heterogeneous nuclear ribonucleoprotein U-like (hnRNPUL) proteins 1 and 2 play key roles in cellular responses to DSBs. We identify human hnRNPUL1 and -2 as binding partners for the DSB sensor complex MRE11-RAD50-NBS1 (MRN) and demonstrate that hnRNPUL1 and -2 are recruited to DNA damage in an interdependent manner that requires MRN. Moreover, we show that hnRNPUL1 and -2 stimulate DNA-end resection and promote ATR-dependent signaling and DSB repair by homologous recombination, thereby contributing to cell survival upon exposure to DSB-inducing agents. Finally, we establish that hnRNPUL1 and -2 function downstream of MRN and CtBP-interacting protein (CtIP) to promote recruitment of the BLM helicase to DNA breaks. Collectively, these results provide insights into how mammalian cells respond to DSBs.


Subject(s)
DNA Breaks, Double-Stranded , DNA End-Joining Repair , Heterogeneous-Nuclear Ribonucleoproteins/physiology , Nuclear Proteins/physiology , Transcription Factors/physiology , Acid Anhydride Hydrolases , Carrier Proteins/genetics , Carrier Proteins/metabolism , Carrier Proteins/physiology , Cell Cycle Proteins/metabolism , DNA Repair Enzymes/metabolism , DNA-Binding Proteins/metabolism , Endodeoxyribonucleases , Heterogeneous-Nuclear Ribonucleoproteins/genetics , Heterogeneous-Nuclear Ribonucleoproteins/metabolism , Humans , MRE11 Homologue Protein , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Signal Transduction , Transcription Factors/genetics , Transcription Factors/metabolism
19.
J Virol ; 92(12)2018 06 15.
Article in English | MEDLINE | ID: mdl-29593045

ABSTRACT

Infection by most DNA viruses activates a cellular DNA damage response (DDR), which may be to the detriment or advantage of the virus. In the case of adenoviruses, they neutralize antiviral effects of DDR activation by targeting a number of proteins for rapid proteasome-mediated degradation. We have now identified a novel DDR protein, tankyrase 1 binding protein 1 (TNKS1BP1) (also known as Tab182), which is degraded during infection by adenovirus serotype 5 and adenovirus serotype 12. In both cases, degradation requires the action of the early region 1B55K (E1B55K) and early region 4 open reading frame 6 (E4orf6) viral proteins and is mediated through the proteasome by the action of cullin-based cellular E3 ligases. The degradation of Tab182 appears to be serotype specific, as the protein remains relatively stable following infection with adenovirus serotypes 4, 7, 9, and 11. We have gone on to confirm that Tab182 is an integral component of the CNOT complex, which has transcriptional regulatory, deadenylation, and E3 ligase activities. The levels of at least 2 other members of the complex (CNOT3 and CNOT7) are also reduced during adenovirus infection, whereas the levels of CNOT4 and CNOT1 remain stable. The depletion of Tab182 with small interfering RNA (siRNA) enhances the expression of early region 1A proteins (E1As) to a limited extent during adenovirus infection, but the depletion of CNOT1 is particularly advantageous to the virus and results in a marked increase in the expression of adenovirus early proteins. In addition, the depletion of Tab182 and CNOT1 results in a limited increase in the viral DNA level during infection. We conclude that the cellular CNOT complex is a previously unidentified major target for adenoviruses during infection.IMPORTANCE Adenoviruses target a number of cellular proteins involved in the DNA damage response for rapid degradation. We have now shown that Tab182, which we have confirmed to be an integral component of the mammalian CNOT complex, is degraded following infection by adenovirus serotypes 5 and 12. This requires the viral E1B55K and E4orf6 proteins and is mediated by cullin-based E3 ligases and the proteasome. In addition to Tab182, the levels of other CNOT proteins are also reduced during adenovirus infection. Thus, CNOT3 and CNOT7, for example, are degraded, whereas CNOT4 and CNOT1 are not. The siRNA-mediated depletion of components of the complex enhances the expression of adenovirus early proteins and increases the concentration of viral DNA produced during infection. This study highlights a novel protein complex, CNOT, which is targeted for adenovirus-mediated protein degradation. To our knowledge, this is the first time that the CNOT complex has been identified as an adenoviral target.


Subject(s)
Adenoviridae Infections/metabolism , Adenovirus E4 Proteins/metabolism , Telomeric Repeat Binding Protein 1/chemistry , Transcription Factors/metabolism , Viral Proteins/metabolism , Adenoviridae/immunology , Adenoviridae/pathogenicity , Adenoviridae Infections/virology , Cullin Proteins/metabolism , Exoribonucleases , HEK293 Cells , HeLa Cells , Humans , Proteasome Endopeptidase Complex/metabolism , Proteolysis , Repressor Proteins , Serogroup
20.
Blood ; 130(2): 156-166, 2017 07 13.
Article in English | MEDLINE | ID: mdl-28495793

ABSTRACT

The role of deubiquitylase ubiquitin-specific protease 7 (USP7) in the regulation of the p53-dependent DNA damage response (DDR) pathway is well established. Whereas previous studies have mostly focused on the mechanisms underlying how USP7 directly controls p53 stability, we recently showed that USP7 modulates the stability of the DNA damage responsive E3 ubiquitin ligase RAD18. This suggests that targeting USP7 may have therapeutic potential even in tumors with defective p53 or ibrutinib resistance. To test this hypothesis, we studied the effect of USP7 inhibition in chronic lymphocytic leukemia (CLL) where the ataxia telangiectasia mutated (ATM)-p53 pathway is inactivated with relatively high frequency, leading to treatment resistance and poor clinical outcome. We demonstrate that USP7 is upregulated in CLL cells, and its loss or inhibition disrupts homologous recombination repair (HRR). Consequently, USP7 inhibition induces significant tumor-cell killing independently of ATM and p53 through the accumulation of genotoxic levels of DNA damage. Moreover, USP7 inhibition sensitized p53-defective, chemotherapy-resistant CLL cells to clinically achievable doses of HRR-inducing chemotherapeutic agents in vitro and in vivo in a murine xenograft model. Together, these results identify USP7 as a promising therapeutic target for the treatment of hematological malignancies with DDR defects, where ATM/p53-dependent apoptosis is compromised.


Subject(s)
Gene Expression Regulation, Neoplastic , Leukemia, Lymphocytic, Chronic, B-Cell/genetics , Recombinational DNA Repair/drug effects , Tumor Suppressor Protein p53/genetics , Ubiquitin-Specific Proteases/genetics , Adenine/analogs & derivatives , Animals , Antineoplastic Agents/pharmacology , Ataxia Telangiectasia Mutated Proteins/genetics , Ataxia Telangiectasia Mutated Proteins/metabolism , Cell Line, Tumor , DNA Damage , Drug Resistance, Neoplasm/genetics , Humans , Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy , Leukemia, Lymphocytic, Chronic, B-Cell/metabolism , Leukemia, Lymphocytic, Chronic, B-Cell/pathology , Mice , Mice, Inbred NOD , Piperidines , Primary Cell Culture , Pyrazoles/pharmacology , Pyrimidines/pharmacology , RNA, Small Interfering/genetics , RNA, Small Interfering/metabolism , Signal Transduction , Tumor Suppressor Protein p53/metabolism , Ubiquitin-Specific Peptidase 7 , Ubiquitin-Specific Proteases/antagonists & inhibitors , Ubiquitin-Specific Proteases/metabolism , Xenograft Model Antitumor Assays
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