1
|
Saldanha J, Rageul J, Patel JA, Phi AL, Lo N, Park JJ, Kim H. The TIMELESS and PARP1 interaction suppresses replication-associated DNA gap accumulation. Nucleic Acids Res 2024:gkae445. [PMID: 38801073 DOI: 10.1093/nar/gkae445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/09/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024] Open
Abstract
TIMELESS (TIM) in the fork protection complex acts as a scaffold of the replisome to prevent its uncoupling and ensure efficient DNA replication fork progression. Nevertheless, its underlying basis for coordinating leading and lagging strand synthesis to limit single-stranded DNA (ssDNA) exposure remains elusive. Here, we demonstrate that acute degradation of TIM at ongoing DNA replication forks induces the accumulation of ssDNA gaps stemming from defective Okazaki fragment (OF) processing. Cells devoid of TIM fail to support the poly(ADP-ribosyl)ation necessary for backing up the canonical OF processing mechanism mediated by LIG1 and FEN1. Consequently, recruitment of XRCC1, a known effector of PARP1-dependent single-strand break repair, to post-replicative ssDNA gaps behind replication forks is impaired. Physical disruption of the TIM-PARP1 complex phenocopies the rapid loss of TIM, indicating that the TIM-PARP1 interaction is critical for the activation of this compensatory pathway. Accordingly, combined deficiency of FEN1 and the TIM-PARP1 interaction leads to synergistic DNA damage and cytotoxicity. We propose that TIM is essential for the engagement of PARP1 to the replisome to coordinate lagging strand synthesis with replication fork progression. Our study identifies TIM as a synthetic lethal target of OF processing enzymes that can be exploited for cancer therapy.
Collapse
Affiliation(s)
- Joanne Saldanha
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
- The Graduate program in Genetics, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Julie Rageul
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Jinal A Patel
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Amy L Phi
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Natalie Lo
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Jennifer J Park
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Hyungjin Kim
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
- The Graduate program in Genetics, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
- Stony Brook Cancer Center, Renaissance School of Medicine at Stony Brook University, Stony Brook, NY 11794, USA
| |
Collapse
|
2
|
Herr LM, Schaffer ED, Fuchs KF, Datta A, Brosh RM. Replication stress as a driver of cellular senescence and aging. Commun Biol 2024; 7:616. [PMID: 38777831 PMCID: PMC11111458 DOI: 10.1038/s42003-024-06263-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Replication stress refers to slowing or stalling of replication fork progression during DNA synthesis that disrupts faithful copying of the genome. While long considered a nexus for DNA damage, the role of replication stress in aging is under-appreciated. The consequential role of replication stress in promotion of organismal aging phenotypes is evidenced by an extensive list of hereditary accelerated aging disorders marked by molecular defects in factors that promote replication fork progression and operate uniquely in the replication stress response. Additionally, recent studies have revealed cellular pathways and phenotypes elicited by replication stress that align with designated hallmarks of aging. Here we review recent advances demonstrating the role of replication stress as an ultimate driver of cellular senescence and aging. We discuss clinical implications of the intriguing links between cellular senescence and aging including application of senotherapeutic approaches in the context of replication stress.
Collapse
Affiliation(s)
- Lauren M Herr
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Ethan D Schaffer
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Kathleen F Fuchs
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Arindam Datta
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Robert M Brosh
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
| |
Collapse
|
3
|
Nasheuer HP, Meaney AM. Starting DNA Synthesis: Initiation Processes during the Replication of Chromosomal DNA in Humans. Genes (Basel) 2024; 15:360. [PMID: 38540419 PMCID: PMC10969946 DOI: 10.3390/genes15030360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 06/14/2024] Open
Abstract
The initiation reactions of DNA synthesis are central processes during human chromosomal DNA replication. They are separated into two main processes: the initiation events at replication origins, the start of the leading strand synthesis for each replicon, and the numerous initiation events taking place during lagging strand DNA synthesis. In addition, a third mechanism is the re-initiation of DNA synthesis after replication fork stalling, which takes place when DNA lesions hinder the progression of DNA synthesis. The initiation of leading strand synthesis at replication origins is regulated at multiple levels, from the origin recognition to the assembly and activation of replicative helicase, the Cdc45-MCM2-7-GINS (CMG) complex. In addition, the multiple interactions of the CMG complex with the eukaryotic replicative DNA polymerases, DNA polymerase α-primase, DNA polymerase δ and ε, at replication forks play pivotal roles in the mechanism of the initiation reactions of leading and lagging strand DNA synthesis. These interactions are also important for the initiation of signalling at unperturbed and stalled replication forks, "replication stress" events, via ATR (ATM-Rad 3-related protein kinase). These processes are essential for the accurate transfer of the cells' genetic information to their daughters. Thus, failures and dysfunctions in these processes give rise to genome instability causing genetic diseases, including cancer. In their influential review "Hallmarks of Cancer: New Dimensions", Hanahan and Weinberg (2022) therefore call genome instability a fundamental function in the development process of cancer cells. In recent years, the understanding of the initiation processes and mechanisms of human DNA replication has made substantial progress at all levels, which will be discussed in the review.
Collapse
Affiliation(s)
- Heinz Peter Nasheuer
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, Biochemistry, University of Galway, H91 TK33 Galway, Ireland;
| | | |
Collapse
|
4
|
Boavida A, Napolitano LM, Santos D, Cortone G, Jegadesan NK, Onesti S, Branzei D, Pisani FM. FANCJ DNA helicase is recruited to the replisome by AND-1 to ensure genome stability. EMBO Rep 2024; 25:876-901. [PMID: 38177925 PMCID: PMC10897178 DOI: 10.1038/s44319-023-00044-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/05/2023] [Accepted: 12/15/2023] [Indexed: 01/06/2024] Open
Abstract
FANCJ, a DNA helicase linked to Fanconi anemia and frequently mutated in cancers, counteracts replication stress by dismantling unconventional DNA secondary structures (such as G-quadruplexes) that occur at the DNA replication fork in certain sequence contexts. However, how FANCJ is recruited to the replisome is unknown. Here, we report that FANCJ directly binds to AND-1 (the vertebrate ortholog of budding yeast Ctf4), a homo-trimeric protein adaptor that connects the CDC45/MCM2-7/GINS replicative DNA helicase with DNA polymerase α and several other factors at DNA replication forks. The interaction between FANCJ and AND-1 requires the integrity of an evolutionarily conserved Ctf4-interacting protein (CIP) box located between the FANCJ helicase motifs IV and V. Disruption of the CIP box significantly reduces FANCJ association with the replisome, causing enhanced DNA damage, decreased replication fork recovery and fork asymmetry in cells unchallenged or treated with Pyridostatin, a G-quadruplex-binder, or Mitomycin C, a DNA inter-strand cross-linking agent. Cancer-relevant FANCJ CIP box variants display reduced AND-1-binding and enhanced DNA damage, a finding that suggests their potential role in cancer predisposition.
Collapse
Affiliation(s)
- Ana Boavida
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples, Italy
- Università degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy
| | | | - Diana Santos
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples, Italy
- Università degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy
| | - Giuseppe Cortone
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples, Italy
| | | | - Silvia Onesti
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste, Trieste, Italy
| | - Dana Branzei
- IFOM ETS-The AIRC Institute of Molecular Oncology, Milan, Italy
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy
| | - Francesca M Pisani
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples, Italy.
| |
Collapse
|
5
|
Vipat S, Moiseeva TN. The TIMELESS Roles in Genome Stability and Beyond. J Mol Biol 2024; 436:168206. [PMID: 37481157 DOI: 10.1016/j.jmb.2023.168206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/20/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
TIMELESS protein (TIM) protects replication forks from stalling at difficult-to-replicate regions and plays an important role in DNA damage response, including checkpoint signaling, protection of stalled replication forks and DNA repair. Loss of TIM causes severe replication stress, while its overexpression is common in various types of cancer, providing protection from DNA damage and resistance to chemotherapy. Although TIM has mostly been studied for its part in replication stress response, its additional roles in supporting genome stability and a wide variety of other cellular pathways are gradually coming to light. This review discusses the diverse functions of TIM and its orthologs in healthy and cancer cells, open questions, and potential future directions.
Collapse
Affiliation(s)
- Sameera Vipat
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn 12618, Estonia
| | - Tatiana N Moiseeva
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn 12618, Estonia.
| |
Collapse
|
6
|
Cao K, Wang R, Li L, Liao Y, Hu X, Li R, Liu X, Xiong XD, Wang Y, Liu X. Targeting DDX11 promotes PARP inhibitor sensitivity in hepatocellular carcinoma by attenuating BRCA2-RAD51 mediated homologous recombination. Oncogene 2024; 43:35-46. [PMID: 38007537 DOI: 10.1038/s41388-023-02898-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/06/2023] [Accepted: 11/14/2023] [Indexed: 11/27/2023]
Abstract
Homologous recombination (HR) is a major DNA double-strand break (DSB) repair pathway of clinical interest because of treatment with poly(ADP-ribose) polymerase inhibitors (PARPi). Cooperation between RAD51 and BRCA2 is pivotal for DNA DSB repair, and its dysfunction induces HR deficiency and sensitizes cancer cells to PARPi. The depletion of the DEAD-box protein DDX11 was found to suppress HR in hepatocellular carcinoma (HCC) cells. The HR ability of HCC cells is not always dependent on the DDX11 level because of natural DDX11 mutations. In Huh7 cells, natural DDX11 mutations were detected, increasing the susceptibility of Huh7 cells to olaparib in vitro and in vivo. The HR deficiency of Huh7 cells was restored when CRISPR/Cas9-mediated knock-in genomic editing was used to revert the DDX11 Q238H mutation to wild type. The DDX11 Q238H mutation impeded the phosphorylation of DDX11 by ATM at serine 237, preventing the recruitment of RAD51 to damaged DNA sites by disrupting the interaction between RAD51 and BRCA2. Clinically, a high level of DDX11 correlated with advanced clinical characteristics and a poor prognosis and served as an independent risk factor for overall and disease-free survival in patients with HCC. We propose that HCC with a high level of wild-type DDX11 tends to be more resistant to PARPi because of enhanced recombination repair, and the key mutation of DDX11 (Q238H) is potentially exploitable.
Collapse
Affiliation(s)
- Kun Cao
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China.
| | - Ruonan Wang
- Scientific Research Platform Service Management Center, Guangdong Medical University, Dongguan, 523808, China
| | - Lianhai Li
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China
| | - Yuting Liao
- Department of Radiotherapy, General Hospital of Southern Theater Command of the Chinese People's Liberation Army, Guangzhou, 510016, China
| | - Xiao Hu
- Department of Surgery, The Second People's Hospital of Guangdong Province, Guangzhou, 510317, China
| | - Ruixue Li
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China
| | - Xiuwen Liu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China
| | - Xing-Dong Xiong
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China.
| | - Yanjie Wang
- Department of Anesthesiology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
| | - Xinguang Liu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China.
| |
Collapse
|
7
|
Pellegrini L. The CMG DNA helicase and the core replisome. Curr Opin Struct Biol 2023; 81:102612. [PMID: 37244171 DOI: 10.1016/j.sbi.2023.102612] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/19/2023] [Accepted: 04/25/2023] [Indexed: 05/29/2023]
Abstract
Eukaryotic DNA replication is performed by the replisome, a large and dynamic multi-protein machine endowed with the required enzymatic components for the synthesis of new DNA. Recent cryo-electron microscopy (cryoEM) analyses have revealed the conserved architecture of the core eukaryotic replisome, comprising the CMG (Cdc45-MCM-GINS) DNA helicase, the leading-strand DNA polymerase epsilon, the Timeless-Tipin heterodimer, the hub protein AND-1 and the checkpoint protein Claspin. These results bid well for arriving soon at an integrated understanding of the structural basis of semi-discontinuous DNA replication. They further set the scene for the characterisation of the mechanisms that interface DNA synthesis with concurrent processes such as DNA repair, propagation of chromatin structure and establishment of sister chromatid cohesion.
Collapse
|
8
|
Saldanha J, Rageul J, Patel JA, Kim H. The Adaptive Mechanisms and Checkpoint Responses to a Stressed DNA Replication Fork. Int J Mol Sci 2023; 24:10488. [PMID: 37445667 PMCID: PMC10341514 DOI: 10.3390/ijms241310488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
DNA replication is a tightly controlled process that ensures the faithful duplication of the genome. However, DNA damage arising from both endogenous and exogenous assaults gives rise to DNA replication stress associated with replication fork slowing or stalling. Therefore, protecting the stressed fork while prompting its recovery to complete DNA replication is critical for safeguarding genomic integrity and cell survival. Specifically, the plasticity of the replication fork in engaging distinct DNA damage tolerance mechanisms, including fork reversal, repriming, and translesion DNA synthesis, enables cells to overcome a variety of replication obstacles. Furthermore, stretches of single-stranded DNA generated upon fork stalling trigger the activation of the ATR kinase, which coordinates the cellular responses to replication stress by stabilizing the replication fork, promoting DNA repair, and controlling cell cycle and replication origin firing. Deregulation of the ATR checkpoint and aberrant levels of chronic replication stress is a common characteristic of cancer and a point of vulnerability being exploited in cancer therapy. Here, we discuss the various adaptive responses of a replication fork to replication stress and the roles of ATR signaling that bring fork stabilization mechanisms together. We also review how this knowledge is being harnessed for the development of checkpoint inhibitors to trigger the replication catastrophe of cancer cells.
Collapse
Affiliation(s)
- Joanne Saldanha
- The Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Julie Rageul
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jinal A Patel
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Hyungjin Kim
- The Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| |
Collapse
|
9
|
Carney SV, Banerjee K, Mujeeb A, Zhu B, Haase S, Varela ML, Kadiyala P, Tronrud CE, Zhu Z, Mukherji D, Gorla P, Sun Y, Tagett R, Núñez FJ, Luo M, Luo W, Ljungman M, Liu Y, Xia Z, Schwendeman A, Qin T, Sartor MA, Costello JF, Cahill DP, Lowenstein PR, Castro MG. Zinc Finger MYND-Type Containing 8 (ZMYND8) Is Epigenetically Regulated in Mutant Isocitrate Dehydrogenase 1 (IDH1) Glioma to Promote Radioresistance. Clin Cancer Res 2023; 29:1763-1782. [PMID: 36692427 PMCID: PMC10159884 DOI: 10.1158/1078-0432.ccr-22-1896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/27/2022] [Accepted: 12/22/2022] [Indexed: 01/25/2023]
Abstract
PURPOSE Mutant isocitrate dehydrogenase 1 (mIDH1) alters the epigenetic regulation of chromatin, leading to a hypermethylation phenotype in adult glioma. This work focuses on identifying gene targets epigenetically dysregulated by mIDH1 to confer therapeutic resistance to ionizing radiation (IR). EXPERIMENTAL DESIGN We evaluated changes in the transcriptome and epigenome in a radioresistant mIDH1 patient-derived glioma cell culture (GCC) following treatment with an mIDH1-specific inhibitor, AGI-5198. We identified Zinc Finger MYND-Type Containing 8 (ZMYND8) as a potential target of mIDH1 reprogramming. We suppressed ZMYND8 expression by shRNA knockdown and genetic knockout (KO) in mIDH1 glioma cells and then assessed cellular viability to IR. We assessed the sensitivity of mIDH1 GCCS to pharmacologic inhibition of ZMYND8-interacting partners: HDAC, BRD4, and PARP. RESULTS Inhibition of mIDH1 leads to an upregulation of gene networks involved in replication stress. We found that the expression of ZMYND8, a regulator of DNA damage response, was decreased in three patient-derived mIDH1 GCCs after treatment with AGI-5198. Knockdown of ZMYND8 expression sensitized mIDH1 GCCs to radiotherapy marked by decreased cellular viability. Following IR, mIDH1 glioma cells with ZMYND8 KO exhibit significant phosphorylation of ATM and sustained γH2AX activation. ZMYND8 KO mIDH1 GCCs were further responsive to IR when treated with either BRD4 or HDAC inhibitors. PARP inhibition further enhanced the efficacy of radiotherapy in ZMYND8 KO mIDH1 glioma cells. CONCLUSIONS These findings indicate the impact of ZMYND8 in the maintenance of genomic integrity and repair of IR-induced DNA damage in mIDH1 glioma. See related commentary by Sachdev et al., p. 1648.
Collapse
Affiliation(s)
- Stephen V. Carney
- Cancer Biology Training Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kaushik Banerjee
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Anzar Mujeeb
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Brandon Zhu
- Graduate Program in Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI, USA
| | - Santiago Haase
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maria L. Varela
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Padma Kadiyala
- Graduate Program in Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Claire E. Tronrud
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ziwen Zhu
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Devarshi Mukherji
- Neuroscience, University of Michigan College of Literature, Science, the Arts (LSA), Ann Arbor, MI 48109, USA
| | - Preethi Gorla
- Neuroscience, University of Michigan College of Literature, Science, the Arts (LSA), Ann Arbor, MI 48109, USA
| | - Yilun Sun
- Department of Radiation Oncology, University Hospitals/Case Western Reserve University, Cleveland, OH, USA
| | - Rebecca Tagett
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Felipe J. Núñez
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maowu Luo
- Department of Pathology, UT Southwestern Medical Center, Dallas TX 75390, USA
| | - Weibo Luo
- Department of Pathology, UT Southwestern Medical Center, Dallas TX 75390, USA
- Department of Pharmacology, UT Southwestern Medical Center, Dallas TX 75390, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Environmental Health Science, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yayuan Liu
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ziyun Xia
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anna Schwendeman
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Joseph F. Costello
- Department of Neurological Surgery, University of California, San Francisco, California, 94143 USA
| | - Daniel P. Cahill
- Department of Neurosurgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston Massachusetts, 02114, USA
| | - Pedro R. Lowenstein
- Cancer Biology Training Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Graduate Program in Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Biosciences Initiative in Brain Cancer, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maria G. Castro
- Cancer Biology Training Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Graduate Program in Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Biosciences Initiative in Brain Cancer, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| |
Collapse
|
10
|
Patel JA, Kim H. The TIMELESS effort for timely DNA replication and protection. Cell Mol Life Sci 2023; 80:84. [PMID: 36892674 PMCID: PMC9998586 DOI: 10.1007/s00018-023-04738-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/16/2023] [Accepted: 02/24/2023] [Indexed: 03/10/2023]
Abstract
Accurate replication of the genome is fundamental to cellular survival and tumor prevention. The DNA replication fork is vulnerable to DNA lesions and damages that impair replisome progression, and improper control over DNA replication stress inevitably causes fork stalling and collapse, a major source of genome instability that fuels tumorigenesis. The integrity of the DNA replication fork is maintained by the fork protection complex (FPC), in which TIMELESS (TIM) constitutes a key scaffold that couples the CMG helicase and replicative polymerase activities, in conjunction with its interaction with other proteins associated with the replication machinery. Loss of TIM or the FPC in general results in impaired fork progression, elevated fork stalling and breakage, and a defect in replication checkpoint activation, thus underscoring its pivotal role in protecting the integrity of both active and stalled replication forks. TIM is upregulated in multiple cancers, which may represent a replication vulnerability of cancer cells that could be exploited for new therapies. Here, we discuss recent advances on our understanding of the multifaceted roles of TIM in DNA replication and stalled fork protection, and how its complex functions are engaged in collaboration with other genome surveillance and maintenance factors.
Collapse
Affiliation(s)
- Jinal A Patel
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Basic Sciences Tower 8-125, 101 Nicolls Rd, Stony Brook, NY, 11794, USA
| | - Hyungjin Kim
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Basic Sciences Tower 8-125, 101 Nicolls Rd, Stony Brook, NY, 11794, USA.
- Stony Brook Cancer Center and Renaissance School of Medicine, Stony Brook University, Basic Sciences Tower 8-125, 101 Nicolls Rd, Stony Brook, NY, 11794, USA.
| |
Collapse
|
11
|
Ma C, Li C, Ma H, Yu D, Zhang Y, Zhang D, Su T, Wu J, Wang X, Zhang L, Chen CL, Zhang YE. Pan-cancer surveys indicate cell cycle-related roles of primate-specific genes in tumors and embryonic cerebrum. Genome Biol 2022; 23:251. [PMID: 36474250 PMCID: PMC9724437 DOI: 10.1186/s13059-022-02821-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/24/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Despite having been extensively studied, it remains largely unclear why humans bear a particularly high risk of cancer. The antagonistic pleiotropy hypothesis predicts that primate-specific genes (PSGs) tend to promote tumorigenesis, while the molecular atavism hypothesis predicts that PSGs involved in tumors may represent recently derived duplicates of unicellular genes. However, these predictions have not been tested. RESULTS By taking advantage of pan-cancer genomic data, we find the upregulation of PSGs across 13 cancer types, which is facilitated by copy-number gain and promoter hypomethylation. Meta-analyses indicate that upregulated PSGs (uPSGs) tend to promote tumorigenesis and to play cell cycle-related roles. The cell cycle-related uPSGs predominantly represent derived duplicates of unicellular genes. We prioritize 15 uPSGs and perform an in-depth analysis of one unicellular gene-derived duplicate involved in the cell cycle, DDX11. Genome-wide screening data and knockdown experiments demonstrate that DDX11 is broadly essential across cancer cell lines. Importantly, non-neutral amino acid substitution patterns and increased expression indicate that DDX11 has been under positive selection. Finally, we find that cell cycle-related uPSGs are also preferentially upregulated in the highly proliferative embryonic cerebrum. CONCLUSIONS Consistent with the predictions of the atavism and antagonistic pleiotropy hypotheses, primate-specific genes, especially those PSGs derived from cell cycle-related genes that emerged in unicellular ancestors, contribute to the early proliferation of the human cerebrum at the cost of hitchhiking by similarly highly proliferative cancer cells.
Collapse
Affiliation(s)
- Chenyu Ma
- grid.458458.00000 0004 1792 6416Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Chunyan Li
- grid.64939.310000 0000 9999 1211School of Engineering Medicine, Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), and Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, 100191 China
| | - Huijing Ma
- grid.458458.00000 0004 1792 6416Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Daqi Yu
- grid.458458.00000 0004 1792 6416Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yufei Zhang
- grid.458458.00000 0004 1792 6416Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China ,grid.41156.370000 0001 2314 964XSchool of Life Sciences, Nanjing University, Nanjing, 210093 China
| | - Dan Zhang
- grid.458458.00000 0004 1792 6416Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Tianhan Su
- grid.458458.00000 0004 1792 6416Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jianmin Wu
- grid.412474.00000 0001 0027 0586Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Center for Cancer Bioinformatics, Peking University Cancer Hospital & Institute, Beijing, 100142 China
| | - Xiaoyue Wang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Li Zhang
- grid.510934.a0000 0005 0398 4153Chinese Institute for Brain Research, Beijing, 102206 China
| | - Chun-Long Chen
- grid.462584.90000 0004 0367 1475Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, 75005 Paris, France
| | - Yong E. Zhang
- grid.458458.00000 0004 1792 6416Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China ,grid.510934.a0000 0005 0398 4153Chinese Institute for Brain Research, Beijing, 102206 China ,grid.9227.e0000000119573309CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223 China
| |
Collapse
|
12
|
Mellor C, Perez C, Sale JE. Creation and resolution of non-B-DNA structural impediments during replication. Crit Rev Biochem Mol Biol 2022; 57:412-442. [PMID: 36170051 PMCID: PMC7613824 DOI: 10.1080/10409238.2022.2121803] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 08/02/2022] [Accepted: 08/25/2022] [Indexed: 01/27/2023]
Abstract
During replication, folding of the DNA template into non-B-form secondary structures provides one of the most abundant impediments to the smooth progression of the replisome. The core replisome collaborates with multiple accessory factors to ensure timely and accurate duplication of the genome and epigenome. Here, we discuss the forces that drive non-B structure formation and the evidence that secondary structures are a significant and frequent source of replication stress that must be actively countered. Taking advantage of recent advances in the molecular and structural biology of the yeast and human replisomes, we examine how structures form and how they may be sensed and resolved during replication.
Collapse
Affiliation(s)
- Christopher Mellor
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Consuelo Perez
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Julian E Sale
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| |
Collapse
|
13
|
Batra S, Devbhandari S, Remus D. CMG helicase activity on G4-containing DNA templates. Methods Enzymol 2022; 672:233-260. [PMID: 35934477 PMCID: PMC9578012 DOI: 10.1016/bs.mie.2022.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
G-quadruplexes (G4s) are non-canonical nucleic acid structures that form in G-rich regions of the genome and threaten genome stability by interfering with DNA replication. However, the underlying mechanisms are poorly understood. We have recently found that G4s can stall eukaryotic replication forks by blocking the progression of replicative DNA helicase, CMG. In this paper, we detail the methodology of DNA unwinding assays to investigate the impact of G4s on CMG progression. The method details the purification of recombinantly expressed CMG from the budding yeast, Saccharomyces cerevisiae, purification of synthetic oligonucleotides, and covers various aspects of DNA substrate preparation, reaction setup and result interpretation. The use of synthetic oligonucleotides provides the advantage of allowing to control the formation of G4 structures in DNA substrates. The methods discussed here can be adapted for the study of other DNA helicases and provide a general template for the assembly of DNA substrates with distinct G4 structures.
Collapse
Affiliation(s)
- Sahil Batra
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Sujan Devbhandari
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Dirk Remus
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States.
| |
Collapse
|
14
|
Batté A, van der Horst SC, Tittel-Elmer M, Sun SM, Sharma S, van Leeuwen J, Chabes A, van Attikum H. Chl1 helicase controls replication fork progression by regulating dNTP pools. Life Sci Alliance 2022; 5:5/4/e202101153. [PMID: 35017203 PMCID: PMC8761496 DOI: 10.26508/lsa.202101153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 12/23/2021] [Accepted: 12/28/2021] [Indexed: 12/27/2022] Open
Abstract
Chl1 helicase affects RPA-dependent checkpoint activation after replication fork arrest by ensuring proper dNTP levels, thereby controlling replication fork progression under stress conditions. Eukaryotic cells have evolved a replication stress response that helps to overcome stalled/collapsed replication forks and ensure proper DNA replication. The replication checkpoint protein Mrc1 plays important roles in these processes, although its functional interactions are not fully understood. Here, we show that MRC1 negatively interacts with CHL1, which encodes the helicase protein Chl1, suggesting distinct roles for these factors during the replication stress response. Indeed, whereas Mrc1 is known to facilitate the restart of stalled replication forks, we uncovered that Chl1 controls replication fork rate under replication stress conditions. Chl1 loss leads to increased RNR1 gene expression and dNTP levels at the onset of S phase likely without activating the DNA damage response. This in turn impairs the formation of RPA-coated ssDNA and subsequent checkpoint activation. Thus, the Chl1 helicase affects RPA-dependent checkpoint activation in response to replication fork arrest by ensuring proper intracellular dNTP levels, thereby controlling replication fork progression under replication stress conditions.
Collapse
Affiliation(s)
- Amandine Batté
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Mireille Tittel-Elmer
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands.,Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, Netherlands
| | - Su Ming Sun
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Jolanda van Leeuwen
- Center for Integrative Genomics, Université de Lausanne, Lausanne-Dorigny, Switzerland
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| |
Collapse
|
15
|
Grabarczyk DB. The Fork Protection Complex: A Regulatory Hub at the Head of the Replisome. Subcell Biochem 2022; 99:83-107. [PMID: 36151374 DOI: 10.1007/978-3-031-00793-4_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
As well as accurately duplicating DNA, the eukaryotic replisome performs a variety of other crucial tasks to maintain genomic stability. For example, organizational elements, like cohesin, must be transferred from the front of the fork to the new strands, and when there is replication stress, forks need to be protected and checkpoint signalling activated. The Tof1-Csm3 (or Timeless-Tipin in humans) Fork Protection Complex (FPC) ensures efficient replisome progression and is required for a range of replication-associated activities. Recent studies have begun to reveal the structure of this complex, and how it functions within the replisome to perform its diverse roles. The core of the FPC acts as a DNA grip on the front of the replisome to regulate fork progression. Other flexibly linked domains and motifs mediate interactions with proteins and specific DNA structures, enabling the FPC to act as a hub at the head of the replication fork.
Collapse
Affiliation(s)
- Daniel B Grabarczyk
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, Würzburg, Germany.
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria.
| |
Collapse
|
16
|
van Schie JJM, de Lange J. The Interplay of Cohesin and the Replisome at Processive and Stressed DNA Replication Forks. Cells 2021; 10:3455. [PMID: 34943967 PMCID: PMC8700348 DOI: 10.3390/cells10123455] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 12/12/2022] Open
Abstract
The cohesin complex facilitates faithful chromosome segregation by pairing the sister chromatids after DNA replication until mitosis. In addition, cohesin contributes to proficient and error-free DNA replication. Replisome progression and establishment of sister chromatid cohesion are intimately intertwined processes. Here, we review how the key factors in DNA replication and cohesion establishment cooperate in unperturbed conditions and during DNA replication stress. We discuss the detailed molecular mechanisms of cohesin recruitment and the entrapment of replicated sister chromatids at the replisome, the subsequent stabilization of sister chromatid cohesion via SMC3 acetylation, as well as the role and regulation of cohesin in the response to DNA replication stress.
Collapse
Affiliation(s)
- Janne J. M. van Schie
- Cancer Center Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Job de Lange
- Cancer Center Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| |
Collapse
|
17
|
Cai YD, Chiu JC. Timeless in animal circadian clocks and beyond. FEBS J 2021; 289:6559-6575. [PMID: 34699674 PMCID: PMC9038958 DOI: 10.1111/febs.16253] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/09/2021] [Accepted: 10/26/2021] [Indexed: 12/13/2022]
Abstract
TIMELESS (TIM) was first identified as a molecular cog in the Drosophila circadian clock. Almost three decades of investigations have resulted in an insightful model describing the critical role of Drosophila TIM (dTIM) in circadian timekeeping in insects, including its function in mediating light entrainment and temperature compensation of the molecular clock. Furthermore, exciting discoveries on its sequence polymorphism and thermosensitive alternative RNA splicing have also established its role in regulating seasonal biology. Although mammalian TIM (mTIM), its mammalian paralog, was first identified as a potential circadian clock component in 1990s due to sequence similarity to dTIM, its role in clock regulation has been more controversial. Mammalian TIM has now been characterized as a DNA replication fork component and has been shown to promote fork progression and participate in cell cycle checkpoint signaling in response to DNA damage. Despite defective circadian rhythms displayed by mtim mutants, it remains controversial whether the regulation of circadian clocks by mTIM is direct, especially given the interconnection between the cell cycle and circadian clocks. In this review, we provide a historical perspective on the identification of animal tim genes, summarize the roles of TIM proteins in biological timing and genomic stability, and draw parallels between dTIM and mTIM despite apparent functional divergence.
Collapse
Affiliation(s)
- Yao D Cai
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, CA, USA
| | - Joanna C Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, CA, USA
| |
Collapse
|
18
|
Teng FY, Jiang ZZ, Guo M, Tan XZ, Chen F, Xi XG, Xu Y. G-quadruplex DNA: a novel target for drug design. Cell Mol Life Sci 2021; 78:6557-6583. [PMID: 34459951 PMCID: PMC11072987 DOI: 10.1007/s00018-021-03921-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/13/2021] [Accepted: 08/12/2021] [Indexed: 02/08/2023]
Abstract
G-quadruplex (G4) DNA is a type of quadruple helix structure formed by a continuous guanine-rich DNA sequence. Emerging evidence in recent years authenticated that G4 DNA structures exist both in cell-free and cellular systems, and function in different diseases, especially in various cancers, aging, neurological diseases, and have been considered novel promising targets for drug design. In this review, we summarize the detection method and the structure of G4, highlighting some non-canonical G4 DNA structures, such as G4 with a bulge, a vacancy, or a hairpin. Subsequently, the functions of G4 DNA in physiological processes are discussed, especially their regulation of DNA replication, transcription of disease-related genes (c-MYC, BCL-2, KRAS, c-KIT et al.), telomere maintenance, and epigenetic regulation. Typical G4 ligands that target promoters and telomeres for drug design are also reviewed, including ellipticine derivatives, quinoxaline analogs, telomestatin analogs, berberine derivatives, and CX-5461, which is currently in advanced phase I/II clinical trials for patients with hematologic cancer and BRCA1/2-deficient tumors. Furthermore, since the long-term stable existence of G4 DNA structures could result in genomic instability, we summarized the G4 unfolding mechanisms emerged recently by multiple G4-specific DNA helicases, such as Pif1, RecQ family helicases, FANCJ, and DHX36. This review aims to present a general overview of the field of G-quadruplex DNA that has progressed in recent years and provides potential strategies for drug design and disease treatment.
Collapse
Affiliation(s)
- Fang-Yuan Teng
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zong-Zhe Jiang
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Man Guo
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Xiao-Zhen Tan
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Feng Chen
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Xu-Guang Xi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- LBPA, Ecole Normale Supérieure Paris-Saclay, CNRS, Université Paris Saclay, 61, Avenue du Président Wilson, 94235, Cachan, France.
| | - Yong Xu
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
| |
Collapse
|
19
|
Kawasumi R, Abe T, Psakhye I, Miyata K, Hirota K, Branzei D. Vertebrate CTF18 and DDX11 essential function in cohesion is bypassed by preventing WAPL-mediated cohesin release. Genes Dev 2021; 35:1368-1382. [PMID: 34503989 PMCID: PMC8494208 DOI: 10.1101/gad.348581.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/16/2021] [Indexed: 01/26/2023]
Abstract
The alternative PCNA loader containing CTF18-DCC1-CTF8 facilitates sister chromatid cohesion (SCC) by poorly defined mechanisms. Here we found that in DT40 cells, CTF18 acts complementarily with the Warsaw breakage syndrome DDX11 helicase in mediating SCC and proliferation. We uncover that the lethality and cohesion defects of ctf18 ddx11 mutants are associated with reduced levels of chromatin-bound cohesin and rescued by depletion of WAPL, a cohesin-removal factor. On the contrary, high levels of ESCO1/2 acetyltransferases that acetylate cohesin to establish SCC do not rescue ctf18 ddx11 phenotypes. Notably, the tight proximity of sister centromeres and increased anaphase bridges characteristic of WAPL-depleted cells are abrogated by loss of both CTF18 and DDX11 The results reveal that vertebrate CTF18 and DDX11 collaborate to provide sufficient amounts of chromatin-loaded cohesin available for SCC generation in the presence of WAPL-mediated cohesin-unloading activity. This process modulates chromosome structure and is essential for cellular proliferation in vertebrates.
Collapse
Affiliation(s)
- Ryotaro Kawasumi
- International Foundation of Medicine (IFOM), the Fondazione Italiana per la Ricerca sul Cancro (FIRC) Institute for Molecular Oncology Foundation, Milan 20139, Italy
| | - Takuya Abe
- International Foundation of Medicine (IFOM), the Fondazione Italiana per la Ricerca sul Cancro (FIRC) Institute for Molecular Oncology Foundation, Milan 20139, Italy
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan
| | - Ivan Psakhye
- International Foundation of Medicine (IFOM), the Fondazione Italiana per la Ricerca sul Cancro (FIRC) Institute for Molecular Oncology Foundation, Milan 20139, Italy
| | - Keiji Miyata
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan
| | - Dana Branzei
- International Foundation of Medicine (IFOM), the Fondazione Italiana per la Ricerca sul Cancro (FIRC) Institute for Molecular Oncology Foundation, Milan 20139, Italy
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Pavia 27100, Italy
| |
Collapse
|
20
|
Park JS, Lee ME, Jang WS, Rha KH, Lee SH, Lee J, Ham WS. The DEAD/DEAH Box Helicase, DDX11, Is Essential for the Survival of Advanced Clear Cell Renal Cell Carcinoma and Is a Determinant of PARP Inhibitor Sensitivity. Cancers (Basel) 2021; 13:cancers13112574. [PMID: 34073906 PMCID: PMC8197413 DOI: 10.3390/cancers13112574] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/13/2021] [Accepted: 05/20/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary DDX11, a helicase involved in sister chromatid cohesion, was identified as a significant biomarker of aggressive renal cell carcinoma (RCC) in our previous studies. In this study, we evaluated the molecular pathways through which DDX11 is involved in RCC cell survival. Furthermore, we assessed the sensitivity of poly (ADP-ribose) polymerase (PARP) inhibitors, which have not been used in RCC treatment, in association with DDX11 expression. DDX11-deficient RCC inhibited RCC proliferation, caused defects in segregation, and increased apoptosis. DDX11-deficient RCC was associated with increased sensitivity to PARP inhibition. DDX11 could be a novel therapeutic and prognostic biomarker for RCC patients, and this study is the first to suggest the use of PARP inhibitors in DDX11-deficient RCC patients. Abstract Genes associated with the DEAD-box helicase DDX11 are significant biomarkers of aggressive renal cell carcinoma (RCC), but their molecular function is poorly understood. We analyzed the molecular pathways through which DDX11 is involved in RCC cell survival and poly (ADP-ribose) polymerase (PARP) inhibitor sensitivity. Immunohistochemistry and immunoblotting determined DDX11 expression in normal kidney tissues, benign renal tumors, and RCC tissues and cell lines. Quantitative polymerase chain reaction validated the downregulation of DDX11 in response to transfection with DDX11-specific small interfering RNA. Proliferation analysis and apoptosis assays were performed to determine the impact of DDX11 knockdown on RCC cells, and the relevant effects of sunitinib, olaparib, and sunitinib plus olaparib were evaluated. DDX11 was upregulated in high-grade, advanced RCC compared to low-grade, localized RCC, and DDX11 was not expressed in normal kidney tissues or benign renal tumors. DDX11 knockdown resulted in the inhibition of RCC cell proliferation, segregation defects, and rapid apoptosis. DDX11-deficient RCC cells exhibited significantly increased sensitivity to olaparib compared to sunitinib alone or sunitinib plus olaparib combination treatments. Moreover, DDX11 could determine PARP inhibitor sensitivity in RCC. DDX11 could serve as a novel therapeutic biomarker for RCC patients who are refractory to conventional targeted therapies and immunotherapies.
Collapse
Affiliation(s)
- Jee Soo Park
- Department of Urology and Urological Science Institute, Yonsei University College of Medicine, Seoul 03722, Korea; (J.S.P.); (M.E.L.); (W.S.J.); (K.H.R.); (S.H.L.); (J.L.)
- Department of Urology, Sorokdo National Hospital, Goheung 59562, Korea
| | - Myung Eun Lee
- Department of Urology and Urological Science Institute, Yonsei University College of Medicine, Seoul 03722, Korea; (J.S.P.); (M.E.L.); (W.S.J.); (K.H.R.); (S.H.L.); (J.L.)
| | - Won Sik Jang
- Department of Urology and Urological Science Institute, Yonsei University College of Medicine, Seoul 03722, Korea; (J.S.P.); (M.E.L.); (W.S.J.); (K.H.R.); (S.H.L.); (J.L.)
| | - Koon Ho Rha
- Department of Urology and Urological Science Institute, Yonsei University College of Medicine, Seoul 03722, Korea; (J.S.P.); (M.E.L.); (W.S.J.); (K.H.R.); (S.H.L.); (J.L.)
| | - Seung Hwan Lee
- Department of Urology and Urological Science Institute, Yonsei University College of Medicine, Seoul 03722, Korea; (J.S.P.); (M.E.L.); (W.S.J.); (K.H.R.); (S.H.L.); (J.L.)
| | - Jongsoo Lee
- Department of Urology and Urological Science Institute, Yonsei University College of Medicine, Seoul 03722, Korea; (J.S.P.); (M.E.L.); (W.S.J.); (K.H.R.); (S.H.L.); (J.L.)
| | - Won Sik Ham
- Department of Urology and Urological Science Institute, Yonsei University College of Medicine, Seoul 03722, Korea; (J.S.P.); (M.E.L.); (W.S.J.); (K.H.R.); (S.H.L.); (J.L.)
- Correspondence: ; Tel.: +82-10-6242-7938; Fax: +82-2-312-2538
| |
Collapse
|
21
|
Hodáková Z, Nans A, Kunzelmann S, Mehmood S, Taylor I, Uhlmann F, Cherepanov P, Singleton MR. Structural characterisation of the Chaetomium thermophilum Chl1 helicase. PLoS One 2021; 16:e0251261. [PMID: 33970942 PMCID: PMC8109800 DOI: 10.1371/journal.pone.0251261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/22/2021] [Indexed: 11/19/2022] Open
Abstract
Chl1 is a member of the XPD family of 5'-3' DNA helicases, which perform a variety of roles in genome maintenance and transmission. They possess a variety of unique structural features, including the presence of a highly variable, partially-ordered insertion in the helicase domain 1. Chl1 has been shown to be required for chromosome segregation in yeast due to its role in the formation of persistent chromosome cohesion during S-phase. Here we present structural and biochemical data to show that Chl1 has the same overall domain organisation as other members of the XPD family, but with some conformational alterations. We also present data suggesting the insert domain in Chl1 regulates its DNA binding.
Collapse
Affiliation(s)
- Zuzana Hodáková
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, London, United Kingdom
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Shahid Mehmood
- Proteomics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Ian Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Martin R. Singleton
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, London, United Kingdom
| |
Collapse
|
22
|
DDX11 loss causes replication stress and pharmacologically exploitable DNA repair defects. Proc Natl Acad Sci U S A 2021; 118:2024258118. [PMID: 33879618 PMCID: PMC8092582 DOI: 10.1073/pnas.2024258118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Replication stress can affect development and is a hallmark of cancers. Warsaw breakage syndrome is a developmental disorder caused by mutations in the conserved DDX11 DNA helicase. Here, using human cellular models of DDX11 deficiency, we report that DDX11 helicase prevents replication stress and mediates homology-directed repair via homologous recombination. Mechanistically, DDX11 promotes resection, enabling RPA and RAD51 focus formation, and acts nonredundantly with the RAD51 mediators BRCA1 and BRCA2. As a result, targeting DDX11 confers improved chemotherapy responsiveness in both chemotherapy-sensitive and drug-resistant BRCA1/2-mutated cancers that regained homologous recombination proficiency by suppressor mutation or somatic reversion. The results pinpoint DDX11 as a critical replication stress mitigating factor whose targeting can improve chemotherapeutic response in a range of cancers. DDX11 encodes an iron–sulfur cluster DNA helicase required for development, mutated, and overexpressed in cancers. Here, we show that loss of DDX11 causes replication stress and sensitizes cancer cells to DNA damaging agents, including poly ADP ribose polymerase (PARP) inhibitors and platinum drugs. We find that DDX11 helicase activity prevents chemotherapy drug hypersensitivity and accumulation of DNA damage. Mechanistically, DDX11 acts downstream of 53BP1 to mediate homology-directed repair and RAD51 focus formation in manners nonredundant with BRCA1 and BRCA2. As a result, DDX11 down-regulation aggravates the chemotherapeutic sensitivity of BRCA1/2-mutated cancers and resensitizes chemotherapy drug–resistant BRCA1/2-mutated cancer cells that regained homologous recombination proficiency. The results further indicate that DDX11 facilitates recombination repair by assisting double strand break resection and the loading of both RPA and RAD51 on single-stranded DNA substrates. We propose DDX11 as a potential target in cancers by creating pharmacologically exploitable DNA repair vulnerabilities.
Collapse
|
23
|
The Genome Stability Maintenance DNA Helicase DDX11 and Its Role in Cancer. Genes (Basel) 2021; 12:genes12030395. [PMID: 33802088 PMCID: PMC8000936 DOI: 10.3390/genes12030395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 12/12/2022] Open
Abstract
DDX11/ChlR1 is a super-family two iron–sulfur cluster containing DNA helicase with roles in DNA replication and sister chromatid cohesion establishment, and general chromosome architecture. Bi-allelic mutations of the DDX11 gene cause a rare hereditary disease, named Warsaw breakage syndrome, characterized by a complex spectrum of clinical manifestations (pre- and post-natal growth defects, microcephaly, intellectual disability, heart anomalies and sister chromatid cohesion loss at cellular level) in accordance with the multifaceted, not yet fully understood, physiological functions of this DNA helicase. In the last few years, a possible role of DDX11 in the onset and progression of many cancers is emerging. Herein we summarize the results of recent studies, carried out either in tumoral cell lines or in xenograft cancer mouse models, suggesting that DDX11 may have an oncogenic role. The potential of DDX11 DNA helicase as a pharmacological target for novel anti-cancer therapeutic interventions, as inferred from these latest developments, is also discussed.
Collapse
|
24
|
Santos D, Mahtab M, Boavida A, Pisani FM. Role of the DDX11 DNA Helicase in Warsaw Breakage Syndrome Etiology. Int J Mol Sci 2021; 22:2308. [PMID: 33669056 PMCID: PMC7956524 DOI: 10.3390/ijms22052308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/13/2021] [Accepted: 02/23/2021] [Indexed: 12/23/2022] Open
Abstract
Warsaw breakage syndrome (WABS) is a genetic disorder characterized by sister chromatid cohesion defects, growth retardation, microcephaly, hearing loss and other variable clinical manifestations. WABS is due to biallelic mutations of the gene coding for the super-family 2 DNA helicase DDX11/ChlR1, orthologous to the yeast chromosome loss protein 1 (Chl1). WABS is classified in the group of "cohesinopathies", rare hereditary diseases that are caused by mutations in genes coding for subunits of the cohesin complex or protein factors having regulatory roles in the sister chromatid cohesion process. In fact, among the cohesion regulators, an important player is DDX11, which is believed to be important for the functional coupling of DNA synthesis and cohesion establishment at the replication forks. Here, we will review what is known about the molecular and cellular functions of human DDX11 and its role in WABS etiopathogenesis, even in light of recent findings on the role of cohesin and its regulator network in promoting chromatin loop formation and regulating chromatin spatial organization.
Collapse
Affiliation(s)
- Diana Santos
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; (D.S.); (M.M.); (A.B.)
| | - Mohammad Mahtab
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; (D.S.); (M.M.); (A.B.)
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania Luigi Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ana Boavida
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; (D.S.); (M.M.); (A.B.)
| | - Francesca M. Pisani
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; (D.S.); (M.M.); (A.B.)
| |
Collapse
|
25
|
Su SG, Li QL, Zhang MF, Zhang PW, Shen H, Zhang CZ. An E2F1/DDX11/EZH2 Positive Feedback Loop Promotes Cell Proliferation in Hepatocellular Carcinoma. Front Oncol 2021; 10:593293. [PMID: 33614480 PMCID: PMC7892623 DOI: 10.3389/fonc.2020.593293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 12/15/2020] [Indexed: 12/26/2022] Open
Abstract
Hepatocellular carcinoma (HCC) accounts for one of the leading causes of cancer-related death, and is attributed to the dysregulation of genes involved in genome stability. DDX11, a DNA helicase, has been implicated in rare genetic disease and human cancers. Yet, its clinical value, biological function, and the underlying mechanism in HCC progression are not fully understood. Here, we show that DDX11 is upregulated in HCC and exhibits oncogenic activity via EZH2/p21 signaling. High expression of DDX11 is significantly correlated with poor outcomes of HCC patients in two independent cohorts. DDX11 overexpression increases HCC cell viabilities and colony formation, whereas DDX11 knockdown arrests cells at G1 phase without alteration of p53 expression. Ectopic expression of DDX11 reduces, while depletion of DDX11 induces the expression of p21. Treatment of p21 siRNA markedly attenuates the cell growth suppression caused by DDX11 silence. Further studies reveal that DDX11 interacts with EZH2 in HCC cells to protect it from ubiquitination-mediated protein degradation, consequently resulting in the downregulation of p21. In addition, E2F1 is identified as one of the upstream regulators of DDX11, and forms a positive feedback loop with EZH2 to upregulate DDX11 and facilitate cell proliferation. Collectively, our data suggest DDX11 as a promising prognostic factor and an oncogene in HCC via a E2F1/DDX11/EZH2 positive feedback loop.
Collapse
Affiliation(s)
- Shu-Guang Su
- Department of Pathology, The Affiliated Hexian Memorial Hospital of Southern Medical University, Guangzhou, China
| | - Qiu-Li Li
- Department of Head and Neck Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Mei-Fang Zhang
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Peng-Wei Zhang
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Huimin Shen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chris Zhiyi Zhang
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| |
Collapse
|
26
|
Bottega R, Ravera S, Napolitano LMR, Chiappetta V, Zini N, Crescenzi B, Arniani S, Faleschini M, Cortone G, Faletra F, Medagli B, Sirchia F, Moretti M, de Lange J, Cappelli E, Mecucci C, Onesti S, Pisani FM, Savoia A. Genomic integrity and mitochondrial metabolism defects in Warsaw syndrome cells: a comparison with Fanconi anemia. J Cell Physiol 2021; 236:5664-5675. [PMID: 33432587 DOI: 10.1002/jcp.30265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 12/25/2022]
Abstract
Warsaw breakage syndrome (WABS), is caused by biallelic mutations of DDX11, a gene coding a DNA helicase. We have recently reported two affected sisters, compound heterozygous for a missense (p.Leu836Pro) and a frameshift (p.Lys303Glufs*22) variant. By investigating the pathogenic mechanism, we demonstrate the inability of the DDX11 p.Leu836Pro mutant to unwind forked DNA substrates, while retaining DNA binding activity. We observed the accumulation of patient-derived cells at the G2/M phase and increased chromosomal fragmentation after mitomycin C treatment. The phenotype partially overlaps with features of the Fanconi anemia cells, which shows not only genomic instability but also defective mitochondria. This prompted us to examine mitochondrial functionality in WABS cells and revealed an altered aerobic metabolism. This opens the door to the further elucidation of the molecular and cellular basis of an impaired mitochondrial phenotype and sheds light on this fundamental process in cell physiology and the pathogenesis of these diseases.
Collapse
Affiliation(s)
- Roberta Bottega
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - Silvia Ravera
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | | | - Viviana Chiappetta
- Istituto di Biochimica e Biologia Cellulare (IBBC), Consiglio Nazionale delle Ricerche (CNR), Naples, Italy
| | - Nicoletta Zini
- CNR-National Research Council of Italy, Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza"-Unit of Bologna, Bologna, Italy.,IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Barbara Crescenzi
- Sezione di Ematologia ed Immunologia Clinica, Centro Ricerche Emato-Oncologiche, University of Perugia, Perugia, Italy
| | - Silvia Arniani
- Sezione di Ematologia ed Immunologia Clinica, Centro Ricerche Emato-Oncologiche, University of Perugia, Perugia, Italy
| | - Michela Faleschini
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - Giuseppe Cortone
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste, Trieste, Italy.,International School for Advanced Studies (SISSA), Trieste, Italy
| | - Flavio Faletra
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - Barbara Medagli
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste, Trieste, Italy.,Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Fabio Sirchia
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - Martina Moretti
- Sezione di Ematologia ed Immunologia Clinica, Centro Ricerche Emato-Oncologiche, University of Perugia, Perugia, Italy
| | - Job de Lange
- Amsterdam UMC, Clinical Genetics, Section Oncogenetics, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Enrico Cappelli
- UO Ematologia, IRCCS Istituto Giannina Gaslini, Genova, Italy, Genova, Italy
| | - Cristina Mecucci
- Sezione di Ematologia ed Immunologia Clinica, Centro Ricerche Emato-Oncologiche, University of Perugia, Perugia, Italy
| | - Silvia Onesti
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste, Trieste, Italy
| | - Francesca M Pisani
- Istituto di Biochimica e Biologia Cellulare (IBBC), Consiglio Nazionale delle Ricerche (CNR), Naples, Italy
| | - Anna Savoia
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy.,Department of Medical Sciences, University of Trieste, Trieste, Italy
| |
Collapse
|
27
|
Stokes K, Winczura A, Song B, Piccoli GD, Grabarczyk DB. Ctf18-RFC and DNA Pol ϵ form a stable leading strand polymerase/clamp loader complex required for normal and perturbed DNA replication. Nucleic Acids Res 2020; 48:8128-8145. [PMID: 32585006 PMCID: PMC7641331 DOI: 10.1093/nar/gkaa541] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/05/2020] [Accepted: 06/16/2020] [Indexed: 12/28/2022] Open
Abstract
The eukaryotic replisome must faithfully replicate DNA and cope with replication fork blocks and stalling, while simultaneously promoting sister chromatid cohesion. Ctf18-RFC is an alternative PCNA loader that links all these processes together by an unknown mechanism. Here, we use integrative structural biology combined with yeast genetics and biochemistry to highlight the specific functions that Ctf18-RFC plays within the leading strand machinery via an interaction with the catalytic domain of DNA Pol ϵ. We show that a large and unusually flexible interface enables this interaction to occur constitutively throughout the cell cycle and regardless of whether forks are replicating or stalled. We reveal that, by being anchored to the leading strand polymerase, Ctf18-RFC can rapidly signal fork stalling to activate the S phase checkpoint. Moreover, we demonstrate that, independently of checkpoint signaling or chromosome cohesion, Ctf18-RFC functions in parallel to Chl1 and Mrc1 to protect replication forks and cell viability.
Collapse
Affiliation(s)
- Katy Stokes
- University of Warwick, Warwick Medical School, Coventry, UK
| | | | - Boyuan Song
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, Josef-Schneider-Str. 2, Würzburg 97080, Germany.,Department of Biochemistry, Biocenter, University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | | | - Daniel B Grabarczyk
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, Josef-Schneider-Str. 2, Würzburg 97080, Germany
| |
Collapse
|
28
|
Freudenreich CH. A Timeless Tale: G4 structure recognition by the fork protection complex triggers unwinding by DDX11 helicase. EMBO J 2020; 39:e106305. [PMID: 32790898 DOI: 10.15252/embj.2020106305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
How the replisome senses and deals with DNA secondary structures has been a mystery. A new study from the Sale and Pellegrini laboratories finds that the Timeless protein has a G-quadruplex binding domain that works together with the DDX11 helicase to facilitate replication of G4 DNA structures.
Collapse
|
29
|
Lerner LK, Holzer S, Kilkenny ML, Šviković S, Murat P, Schiavone D, Eldridge CB, Bittleston A, Maman JD, Branzei D, Stott K, Pellegrini L, Sale JE. Timeless couples G-quadruplex detection with processing by DDX11 helicase during DNA replication. EMBO J 2020; 39:e104185. [PMID: 32705708 PMCID: PMC7506991 DOI: 10.15252/embj.2019104185] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/27/2022] Open
Abstract
Regions of the genome with the potential to form secondary DNA structures pose a frequent and significant impediment to DNA replication and must be actively managed in order to preserve genetic and epigenetic integrity. How the replisome detects and responds to secondary structures is poorly understood. Here, we show that a core component of the fork protection complex in the eukaryotic replisome, Timeless, harbours in its C-terminal region a previously unappreciated DNA-binding domain that exhibits specific binding to G-quadruplex (G4) DNA structures. We show that this domain contributes to maintaining processive replication through G4-forming sequences, and exhibits partial redundancy with an adjacent PARP-binding domain. Further, this function of Timeless requires interaction with and activity of the helicase DDX11. Loss of both Timeless and DDX11 causes epigenetic instability at G4-forming sequences and DNA damage. Our findings indicate that Timeless contributes to the ability of the replisome to sense replication-hindering G4 formation and ensures the prompt resolution of these structures by DDX11 to maintain processive DNA synthesis.
Collapse
Affiliation(s)
- Leticia K Lerner
- MRC Laboratory of Molecular BiologyCambridgeUK
- Present address:
Centre de Recherche des CordeliersCell Death and Drug Resistance in Hematological Disorders TeamINSERM UMRS 1138Sorbonne UniversitéParisFrance
| | - Sandro Holzer
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | | | | | | | | | | | - Joseph D Maman
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Dana Branzei
- IFOMFondazione Italiana per la Ricerca sul CancroInstitute of Molecular OncologyMilanItaly
| | - Katherine Stott
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Luca Pellegrini
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | |
Collapse
|
30
|
van Schie JJM, Faramarz A, Balk JA, Stewart GS, Cantelli E, Oostra AB, Rooimans MA, Parish JL, de Almeida Estéves C, Dumic K, Barisic I, Diderich KEM, van Slegtenhorst MA, Mahtab M, Pisani FM, Te Riele H, Ameziane N, Wolthuis RMF, de Lange J. Warsaw Breakage Syndrome associated DDX11 helicase resolves G-quadruplex structures to support sister chromatid cohesion. Nat Commun 2020; 11:4287. [PMID: 32855419 PMCID: PMC7452896 DOI: 10.1038/s41467-020-18066-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 07/30/2020] [Indexed: 02/01/2023] Open
Abstract
Warsaw Breakage Syndrome (WABS) is a rare disorder related to cohesinopathies and Fanconi anemia, caused by bi-allelic mutations in DDX11. Here, we report multiple compound heterozygous WABS cases, each displaying destabilized DDX11 protein and residual DDX11 function at the cellular level. Patient-derived cell lines exhibit sensitivity to topoisomerase and PARP inhibitors, defective sister chromatid cohesion and reduced DNA replication fork speed. Deleting DDX11 in RPE1-TERT cells inhibits proliferation and survival in a TP53-dependent manner and causes chromosome breaks and cohesion defects, independent of the expressed pseudogene DDX12p. Importantly, G-quadruplex (G4) stabilizing compounds induce chromosome breaks and cohesion defects which are strongly aggravated by inactivation of DDX11 but not FANCJ. The DNA helicase domain of DDX11 is essential for sister chromatid cohesion and resistance to G4 stabilizers. We propose that DDX11 is a DNA helicase protecting against G4 induced double-stranded breaks and concomitant loss of cohesion, possibly at DNA replication forks.
Collapse
Affiliation(s)
- Janne J M van Schie
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Atiq Faramarz
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Jesper A Balk
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Erika Cantelli
- Netherlands Cancer Institute, Division of Tumor Biology and Immunology, Amsterdam, The Netherlands
| | - Anneke B Oostra
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Martin A Rooimans
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Joanna L Parish
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | | | - Katja Dumic
- Department of Pediatric Endocrinology and Diabetes, University Hospital Centre Zagreb, University of Zagreb Medical School, Zagreb, Croatia
| | - Ingeborg Barisic
- Children's Hospital Zagreb, Center of Excellence for Reproductive and Regenerative Medicine, Medical School University of Zagreb, Zagreb, Croatia
| | - Karin E M Diderich
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Mohammad Mahtab
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Francesca M Pisani
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Hein Te Riele
- Netherlands Cancer Institute, Division of Tumor Biology and Immunology, Amsterdam, The Netherlands
| | - Najim Ameziane
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
- Centogene, Am Strande 7, 18055, Rostock, Germany
| | - Rob M F Wolthuis
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands.
| | - Job de Lange
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands.
| |
Collapse
|
31
|
Brosh RM, Matson SW. History of DNA Helicases. Genes (Basel) 2020; 11:genes11030255. [PMID: 32120966 PMCID: PMC7140857 DOI: 10.3390/genes11030255] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 12/13/2022] Open
Abstract
Since the discovery of the DNA double helix, there has been a fascination in understanding the molecular mechanisms and cellular processes that account for: (i) the transmission of genetic information from one generation to the next and (ii) the remarkable stability of the genome. Nucleic acid biologists have endeavored to unravel the mysteries of DNA not only to understand the processes of DNA replication, repair, recombination, and transcription but to also characterize the underlying basis of genetic diseases characterized by chromosomal instability. Perhaps unexpectedly at first, DNA helicases have arisen as a key class of enzymes to study in this latter capacity. From the first discovery of ATP-dependent DNA unwinding enzymes in the mid 1970's to the burgeoning of helicase-dependent pathways found to be prevalent in all kingdoms of life, the story of scientific discovery in helicase research is rich and informative. Over four decades after their discovery, we take this opportunity to provide a history of DNA helicases. No doubt, many chapters are left to be written. Nonetheless, at this juncture we are privileged to share our perspective on the DNA helicase field - where it has been, its current state, and where it is headed.
Collapse
Affiliation(s)
- Robert M. Brosh
- Section on DNA Helicases, Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
- Correspondence: (R.M.B.J.); (S.W.M.); Tel.: +1-410-558-8578 (R.M.B.J.); +1-919-962-0005 (S.W.M.)
| | - Steven W. Matson
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Correspondence: (R.M.B.J.); (S.W.M.); Tel.: +1-410-558-8578 (R.M.B.J.); +1-919-962-0005 (S.W.M.)
| |
Collapse
|
32
|
Simon AK, Kummer S, Wild S, Lezaja A, Teloni F, Jozwiakowski SK, Altmeyer M, Gari K. The iron-sulfur helicase DDX11 promotes the generation of single-stranded DNA for CHK1 activation. Life Sci Alliance 2020; 3:3/3/e201900547. [PMID: 32071282 PMCID: PMC7032568 DOI: 10.26508/lsa.201900547] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 02/06/2020] [Accepted: 02/06/2020] [Indexed: 12/12/2022] Open
Abstract
The iron–sulfur cluster helicase DDX11 promotes the generation of ssDNA and the phosphorylation of CHK1 at serine-345, possibly by unwinding replication-dependent DNA secondary structures. The iron–sulfur (FeS) cluster helicase DDX11 is associated with a human disorder termed Warsaw Breakage Syndrome. Interestingly, one disease-associated mutation affects the highly conserved arginine-263 in the FeS cluster-binding motif. Here, we demonstrate that the FeS cluster in DDX11 is required for DNA binding, ATP hydrolysis, and DNA helicase activity, and that arginine-263 affects FeS cluster binding, most likely because of its positive charge. We further show that DDX11 interacts with the replication factors DNA polymerase delta and WDHD1. In vitro, DDX11 can remove DNA obstacles ahead of Pol δ in an ATPase- and FeS domain-dependent manner, and hence generate single-stranded DNA. Accordingly, depletion of DDX11 causes reduced levels of single-stranded DNA, a reduction of chromatin-bound replication protein A, and impaired CHK1 phosphorylation at serine-345. Taken together, we propose that DDX11 plays a role in dismantling secondary structures during DNA replication, thereby promoting CHK1 activation.
Collapse
Affiliation(s)
- Anna K Simon
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Sandra Kummer
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Sebastian Wild
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Aleksandra Lezaja
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Federico Teloni
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | | | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Kerstin Gari
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| |
Collapse
|
33
|
Delamarre A, Barthe A, de la Roche Saint-André C, Luciano P, Forey R, Padioleau I, Skrzypczak M, Ginalski K, Géli V, Pasero P, Lengronne A. MRX Increases Chromatin Accessibility at Stalled Replication Forks to Promote Nascent DNA Resection and Cohesin Loading. Mol Cell 2020; 77:395-410.e3. [PMID: 31759824 DOI: 10.1016/j.molcel.2019.10.029] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/09/2019] [Accepted: 10/17/2019] [Indexed: 01/04/2023]
Abstract
The recovery of stalled replication forks depends on the controlled resection of nascent DNA and on the loading of cohesin. These processes operate in the context of nascent chromatin, but the impact of nucleosome structure on a fork restart remains poorly understood. Here, we show that the Mre11-Rad50-Xrs2 (MRX) complex acts together with the chromatin modifiers Gcn5 and Set1 and the histone remodelers RSC, Chd1, and Isw1 to promote chromatin remodeling at stalled forks. Increased chromatin accessibility facilitates the resection of nascent DNA by the Exo1 nuclease and the Sgs1 and Chl1 DNA helicases. Importantly, increased ssDNA promotes the recruitment of cohesin to arrested forks in a Scc2-Scc4-dependent manner. Altogether, these results indicate that MRX cooperates with chromatin modifiers to orchestrate the action of remodelers, nucleases, and DNA helicases, promoting the resection of nascent DNA and the loading of cohesin, two key processes involved in the recovery of arrested forks.
Collapse
Affiliation(s)
- Axel Delamarre
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
| | - Antoine Barthe
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
| | - Christophe de la Roche Saint-André
- Marseille Cancer Research Center (CRCM), CNRS, INSERM, Aix Marseille University, Institut Paoli-Calmettes, Equipe Labélisée Ligue contre le Cancer, 13273 Marseille, France
| | - Pierre Luciano
- Marseille Cancer Research Center (CRCM), CNRS, INSERM, Aix Marseille University, Institut Paoli-Calmettes, Equipe Labélisée Ligue contre le Cancer, 13273 Marseille, France
| | - Romain Forey
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
| | - Ismaël Padioleau
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
| | - Magdalena Skrzypczak
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Vincent Géli
- Marseille Cancer Research Center (CRCM), CNRS, INSERM, Aix Marseille University, Institut Paoli-Calmettes, Equipe Labélisée Ligue contre le Cancer, 13273 Marseille, France.
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France.
| | - Armelle Lengronne
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France.
| |
Collapse
|
34
|
Faramarz A, Balk JA, van Schie JJM, Oostra AB, Ghandour CA, Rooimans MA, Wolthuis RMF, de Lange J. Non-redundant roles in sister chromatid cohesion of the DNA helicase DDX11 and the SMC3 acetyl transferases ESCO1 and ESCO2. PLoS One 2020; 15:e0220348. [PMID: 31935221 PMCID: PMC6959578 DOI: 10.1371/journal.pone.0220348] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 12/30/2019] [Indexed: 12/30/2022] Open
Abstract
In a process linked to DNA replication, duplicated chromosomes are entrapped in large, circular cohesin complexes and functional sister chromatid cohesion (SCC) is established by acetylation of the SMC3 cohesin subunit. Roberts Syndrome (RBS) and Warsaw Breakage Syndrome (WABS) are rare human developmental syndromes that are characterized by defective SCC. RBS is caused by mutations in the SMC3 acetyltransferase ESCO2, whereas mutations in the DNA helicase DDX11 lead to WABS. We found that WABS-derived cells predominantly rely on ESCO2, not ESCO1, for residual SCC, growth and survival. Reciprocally, RBS-derived cells depend on DDX11 to maintain low levels of SCC. Synthetic lethality between DDX11 and ESCO2 correlated with a prolonged delay in mitosis, and was rescued by knockdown of the cohesin remover WAPL. Rescue experiments using human or mouse cDNAs revealed that DDX11, ESCO1 and ESCO2 act on different but related aspects of SCC establishment. Furthermore, a DNA binding DDX11 mutant failed to correct SCC in WABS cells and DDX11 deficiency reduced replication fork speed. We propose that DDX11, ESCO1 and ESCO2 control different fractions of cohesin that are spatially and mechanistically separated.
Collapse
Affiliation(s)
- Atiq Faramarz
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Jesper A. Balk
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Janne J. M. van Schie
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Anneke B. Oostra
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Cherien A. Ghandour
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Martin A. Rooimans
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Rob M. F. Wolthuis
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Job de Lange
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| |
Collapse
|
35
|
Pisani FM. Spotlight on Warsaw Breakage Syndrome. APPLICATION OF CLINICAL GENETICS 2019; 12:239-248. [PMID: 31824187 PMCID: PMC6901054 DOI: 10.2147/tacg.s186476] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/13/2019] [Indexed: 12/14/2022]
Abstract
Warsaw breakage syndrome (WABS) is a very rare recessive hereditary disease caused by mutations in the gene coding for the DNA helicase DDX11, involved in genome stability maintenance and sister cohesion establishment. Typical clinical features observed in WABS patients include growth retardation, facial dysmorphia, microcephaly, hearing loss due to cochlear malformations and, at cytological level, sister chromatid cohesion defects. Molecular bases of WABS have not yet been elucidated, due to lack of disease animal model systems and limited knowledge of the DDX11 physiological functions. However, WABS is considered to belong to the group of cohesinopathies, genetic disorders due to mutations of subunits or regulators of cohesin, the protein complex responsible for tethering sister chromatids from the time of their synthesis till they separate in mitosis. Recent evidences suggest that cohesin and its regulators have additional key roles in chromatin organization by promoting the formation of chromatin loops. This “non-canonical” function of cohesin is expected to impact gene transcription during cell differentiation and embryonic development and its dis-regulation, caused by mutation/loss of genes encoding cohesin subunits or regulators, could originate the developmental defects observed in cohesinopathies. Ethiopathogenesis of WABS is discussed in line with these recent findings and evidence of a possible role of DDX11 as a cohesin regulator.
Collapse
Affiliation(s)
- Francesca M Pisani
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples 80131, Italy
| |
Collapse
|
36
|
Bianco JN, Bergoglio V, Lin YL, Pillaire MJ, Schmitz AL, Gilhodes J, Lusque A, Mazières J, Lacroix-Triki M, Roumeliotis TI, Choudhary J, Moreaux J, Hoffmann JS, Tourrière H, Pasero P. Overexpression of Claspin and Timeless protects cancer cells from replication stress in a checkpoint-independent manner. Nat Commun 2019; 10:910. [PMID: 30796221 PMCID: PMC6385232 DOI: 10.1038/s41467-019-08886-8] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/05/2019] [Indexed: 12/31/2022] Open
Abstract
Oncogene-induced replication stress (RS) promotes cancer development but also impedes tumor growth by activating anti-cancer barriers. To determine how cancer cells adapt to RS, we have monitored the expression of different components of the ATR-CHK1 pathway in primary tumor samples. We show that unlike upstream components of the pathway, the checkpoint mediators Claspin and Timeless are overexpressed in a coordinated manner. Remarkably, reducing the levels of Claspin and Timeless in HCT116 cells to pretumoral levels impeded fork progression without affecting checkpoint signaling. These data indicate that high level of Claspin and Timeless increase RS tolerance by protecting replication forks in cancer cells. Moreover, we report that primary fibroblasts adapt to oncogene-induced RS by spontaneously overexpressing Claspin and Timeless, independently of ATR signaling. Altogether, these data indicate that enhanced levels of Claspin and Timeless represent a gain of function that protects cancer cells from of oncogene-induced RS in a checkpoint-independent manner.
Collapse
Affiliation(s)
- Julien N Bianco
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, 34396, Montpellier, France.,Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Valérie Bergoglio
- Cancer Research Center of Toulouse, INSERM U1037, CNRS ERL5294, University of Toulouse 3, 31037, Toulouse, France
| | - Yea-Lih Lin
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, 34396, Montpellier, France
| | - Marie-Jeanne Pillaire
- Cancer Research Center of Toulouse, INSERM U1037, CNRS ERL5294, University of Toulouse 3, 31037, Toulouse, France
| | - Anne-Lyne Schmitz
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, 34396, Montpellier, France
| | - Julia Gilhodes
- Clinical trials Office - Biostatistics Unit, Institute Claudius Regaud, Institute Universitaire du Cancer Toulouse-Oncopole (IUCT-O), 31100, Toulouse, France
| | - Amelie Lusque
- Clinical trials Office - Biostatistics Unit, Institute Claudius Regaud, Institute Universitaire du Cancer Toulouse-Oncopole (IUCT-O), 31100, Toulouse, France
| | - Julien Mazières
- Thoracic Oncology Department, Toulouse University Hospital, University Paul Sabatier, 31062, Toulouse, France
| | | | | | | | - Jérôme Moreaux
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, 34396, Montpellier, France
| | - Jean-Sébastien Hoffmann
- Cancer Research Center of Toulouse, INSERM U1037, CNRS ERL5294, University of Toulouse 3, 31037, Toulouse, France
| | - Hélène Tourrière
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, 34396, Montpellier, France.
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, 34396, Montpellier, France.
| |
Collapse
|
37
|
Lerner LK, Sale JE. Replication of G Quadruplex DNA. Genes (Basel) 2019; 10:genes10020095. [PMID: 30700033 PMCID: PMC6409989 DOI: 10.3390/genes10020095] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 01/03/2023] Open
Abstract
A cursory look at any textbook image of DNA replication might suggest that the complex machine that is the replisome runs smoothly along the chromosomal DNA. However, many DNA sequences can adopt non-B form secondary structures and these have the potential to impede progression of the replisome. A picture is emerging in which the maintenance of processive DNA replication requires the action of a significant number of additional proteins beyond the core replisome to resolve secondary structures in the DNA template. By ensuring that DNA synthesis remains closely coupled to DNA unwinding by the replicative helicase, these factors prevent impediments to the replisome from causing genetic and epigenetic instability. This review considers the circumstances in which DNA forms secondary structures, the potential responses of the eukaryotic replisome to these impediments in the light of recent advances in our understanding of its structure and operation and the mechanisms cells deploy to remove secondary structure from the DNA. To illustrate the principles involved, we focus on one of the best understood DNA secondary structures, G quadruplexes (G4s), and on the helicases that promote their resolution.
Collapse
Affiliation(s)
- Leticia Koch Lerner
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Julian E Sale
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| |
Collapse
|
38
|
Single-Molecule DNA Fiber Analyses to Characterize Replication Fork Dynamics in Living Cells. Methods Mol Biol 2019; 1999:307-318. [PMID: 31127587 DOI: 10.1007/978-1-4939-9500-4_21] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Understanding the molecular dynamics of DNA replication in vivo has been a formidable challenge requiring the development of advanced technologies. Over the past 50 years or so, studies involving DNA autoradiography in bacterial cells have led to sophisticated DNA tract analyses in human cells to characterize replication dynamics at the single-molecule level. Our own lab has used DNA fiber analysis to characterize replication in helicase-deficient human cells. This work led us to propose a model in which the human DNA helicase RECQ1 acts as a governor of the single-stranded DNA binding protein RPA and regulates its bioavailability for DNA synthesis. We have also used the DNA fiber approach to investigate the interactive role of DDX11 helicase with a replication fork protection protein (Timeless) in human cells when they are under pharmacologically induced stress. In this methods chapter, we present a step-by-step protocol for the single-molecule DNA fiber assay. We describe experimental designs to study replication stress and staining patterns from pulse-chase labeling experiments to address the dynamics of replication forks in stressed cells.
Collapse
|
39
|
Pisani FM, Napolitano E, Napolitano LMR, Onesti S. Molecular and Cellular Functions of the Warsaw Breakage Syndrome DNA Helicase DDX11. Genes (Basel) 2018; 9:genes9110564. [PMID: 30469382 PMCID: PMC6266566 DOI: 10.3390/genes9110564] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/17/2018] [Accepted: 11/19/2018] [Indexed: 12/23/2022] Open
Abstract
DDX11/ChlR1 (Chl1 in yeast) is a DNA helicase involved in sister chromatid cohesion and in DNA repair pathways. The protein belongs to the family of the iron–sulphur cluster containing DNA helicases, whose deficiencies have been linked to a number of diseases affecting genome stability. Mutations of human DDX11 are indeed associated with the rare genetic disorder named Warsaw breakage syndrome, showing both chromosomal breakages and chromatid cohesion defects. Moreover, growing evidence of a potential role in oncogenesis further emphasizes the clinical relevance of DDX11. Here, we illustrate the biochemical and structural features of DDX11 and how it cooperates with multiple protein partners in the cell, acting at the interface of DNA replication/repair/recombination and sister chromatid cohesion to preserve genome stability.
Collapse
Affiliation(s)
- Francesca M Pisani
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via P. Castellino, 111, 80131 Napoli, Italy.
| | - Ettore Napolitano
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via P. Castellino, 111, 80131 Napoli, Italy.
| | - Luisa M R Napolitano
- Elettra⁻Sincrotrone Trieste S.C.p.A., AREA Science Park Basovizza, 34149 Trieste, Italy.
| | - Silvia Onesti
- Elettra⁻Sincrotrone Trieste S.C.p.A., AREA Science Park Basovizza, 34149 Trieste, Italy.
| |
Collapse
|
40
|
Rajkumar MS, Garg R, Jain M. Genome-wide discovery of DNA polymorphisms among chickpea cultivars with contrasting seed size/weight and their functional relevance. Sci Rep 2018; 8:16795. [PMID: 30429540 PMCID: PMC6235875 DOI: 10.1038/s41598-018-35140-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 10/31/2018] [Indexed: 12/16/2022] Open
Abstract
Seed size/weight is a major agronomic trait which determine crop productivity in legumes. To understand the genetic basis of seed size determination, we sought to identify DNA polymorphisms between two small (Himchana 1 and Pusa 362) and two large-seeded (JGK 3 and PG 0515) chickpea cultivars via whole genome resequencing. We identified a total of 75535 single nucleotide polymorphisms (SNPs), 6486 insertions and deletions (InDels), 1938 multi-nucleotide polymorphisms (MNPs) and 5025 complex variants between the two small and two large-seeded chickpea cultivars. Our analysis revealed 814, 244 and 72 seed-specific genes harboring DNA polymorphisms in promoter or non-synonymous and large-effect DNA polymorphisms, respectively. Gene ontology analysis revealed enrichment of cell growth and division related terms in these genes. Among them, at least 22 genes associated with quantitative trait loci, and those involved in cell growth and division and encoding transcription factors harbored promoter and/or large-effect/non-synonymous DNA polymorphisms. These also showed higher expression at late-embryogenesis and/or mid-maturation stages of seed development in the large-seeded cultivar, suggesting their role in seed size/weight determination in chickpea. Altogether, this study provided a valuable resource for large-scale genotyping applications and a few putative candidate genes that might play crucial role in governing seed size/weight in chickpea.
Collapse
Affiliation(s)
- Mohan Singh Rajkumar
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, 201314, India
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India. .,National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
| |
Collapse
|
41
|
Cortone G, Zheng G, Pensieri P, Chiappetta V, Tatè R, Malacaria E, Pichierri P, Yu H, Pisani FM. Interaction of the Warsaw breakage syndrome DNA helicase DDX11 with the replication fork-protection factor Timeless promotes sister chromatid cohesion. PLoS Genet 2018; 14:e1007622. [PMID: 30303954 PMCID: PMC6179184 DOI: 10.1371/journal.pgen.1007622] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 08/13/2018] [Indexed: 12/19/2022] Open
Abstract
Establishment of sister chromatid cohesion is coupled to DNA replication, but the underlying molecular mechanisms are incompletely understood. DDX11 (also named ChlR1) is a super-family 2 Fe-S cluster-containing DNA helicase implicated in Warsaw breakage syndrome (WABS). Herein, we examined the role of DDX11 in cohesion establishment in human cells. We demonstrated that DDX11 interacts with Timeless, a component of the replication fork-protection complex, through a conserved peptide motif. The DDX11-Timeless interaction is critical for sister chromatid cohesion in interphase and mitosis. Immunofluorescence studies further revealed that cohesin association with chromatin requires DDX11. Finally, we demonstrated that DDX11 localises at nascent DNA by SIRF analysis. Moreover, we found that DDX11 promotes cohesin binding to the DNA replication forks in concert with Timeless and that recombinant purified cohesin interacts with DDX11 in vitro. Collectively, our results establish a critical role for the DDX11-Timeless interaction in coordinating DNA replication with sister chromatid cohesion, and have important implications for understanding the molecular basis of WABS.
Collapse
Affiliation(s)
- Giuseppe Cortone
- Istituto di Biochimica delle Proteine, Consiglio Nazionale Ricerche, Naples, Italy
| | - Ge Zheng
- Howard Hughes Medical Institute, Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Pasquale Pensieri
- Istituto di Biochimica delle Proteine, Consiglio Nazionale Ricerche, Naples, Italy
| | - Viviana Chiappetta
- Istituto di Biochimica delle Proteine, Consiglio Nazionale Ricerche, Naples, Italy
| | - Rosarita Tatè
- Istituto di Genetica e Biofisica "Adriano Buzzati Traverso", Consiglio Nazionale Ricerche, Naples, Italy
| | - Eva Malacaria
- Istituto Superiore di Sanità, Dipartimento Ambiente e Salute, Rome, Italy
| | - Pietro Pichierri
- Istituto Superiore di Sanità, Dipartimento Ambiente e Salute, Rome, Italy
| | - Hongtao Yu
- Howard Hughes Medical Institute, Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
- * E-mail: (HY); (FMP)
| | - Francesca M. Pisani
- Istituto di Biochimica delle Proteine, Consiglio Nazionale Ricerche, Naples, Italy
- * E-mail: (HY); (FMP)
| |
Collapse
|
42
|
Warsaw breakage syndrome DDX11 helicase acts jointly with RAD17 in the repair of bulky lesions and replication through abasic sites. Proc Natl Acad Sci U S A 2018; 115:8412-8417. [PMID: 30061412 PMCID: PMC6099846 DOI: 10.1073/pnas.1803110115] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Warsaw breakage syndrome, a developmental disorder caused by mutations in the conserved DDX11/ChlR1 DNA helicase, shows features of genome instability partly overlapping with those of Fanconi anemia (FA). Here, using avian cellular models of DDX11 deficiency, we find that DDX11 functions as backup to the FA pathway and facilitates, jointly with the checkpoint clamp 9-1-1, a homologous recombination pathway of DNA bulky-lesion repair that does not affect replication fork speed and stalled fork stability. DDX11 also promotes diversification of the immunoglobulin-variable gene locus by facilitating hypermutation and gene conversion at programmed abasic sites that constitute endogenous replication blocks. The results suggest commonality between postreplicative gap filling and replication through abasic sites and pinpoint DDX11 as a critical player in both these processes. Warsaw breakage syndrome, a developmental disorder caused by mutations in the DDX11/ChlR1 helicase, shows cellular features of genome instability similar to Fanconi anemia (FA). Here we report that DDX11-deficient avian DT40 cells exhibit interstrand crosslink (ICL)-induced chromatid breakage, with DDX11 functioning as backup for the FA pathway in regard to ICL repair. Importantly, we establish that DDX11 acts jointly with the 9-1-1 checkpoint clamp and its loader, RAD17, primarily in a postreplicative fashion, to promote homologous recombination repair of bulky lesions, but is not required for intra-S checkpoint activation or efficient fork progression. Notably, we find that DDX11 also promotes diversification of the chicken Ig-variable gene, a process triggered by programmed abasic sites, by facilitating both hypermutation and homeologous recombination-mediated gene conversion. Altogether, our results uncover that DDX11 orchestrates jointly with 9-1-1 and its loader, RAD17, DNA damage tolerance at sites of bulky lesions, and endogenous abasic sites. These functions may explain the essential roles of DDX11 and its similarity with 9-1-1 during development.
Collapse
|
43
|
Abe T, Kawasumi R, Arakawa H, Hori T, Shirahige K, Losada A, Fukagawa T, Branzei D. Chromatin determinants of the inner-centromere rely on replication factors with functions that impart cohesion. Oncotarget 2018; 7:67934-67947. [PMID: 27636994 PMCID: PMC5356530 DOI: 10.18632/oncotarget.11982] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 09/06/2016] [Indexed: 01/08/2023] Open
Abstract
Replication fork-associated factors promote genome integrity and protect against cancer. Mutations in the DDX11 helicase and the ESCO2 acetyltransferase also cause related developmental disorders classified as cohesinopathies. Here we generated vertebrate model cell lines of these disorders and cohesinopathies-related genes. We found that vertebrate DDX11 and Tim-Tipin are individually needed to compensate for ESCO2 loss in chromosome segregation, with DDX11 also playing complementary roles with ESCO2 in centromeric cohesion. Our study reveals that overt centromeric cohesion loss does not necessarily precede chromosome missegregation, while both these problems correlate with, and possibly originate from, inner-centromere defects involving reduced phosphorylation of histone H3T3 (pH3T3) in the region. Interestingly, the mitotic pH3T3 mark was defective in all analyzed replication-related mutants with functions in cohesion. The results pinpoint mitotic pH3T3 as a postreplicative chromatin mark that is sensitive to replication stress and conducts with different kinetics to robust centromeric cohesion and correct chromosome segregation.
Collapse
Affiliation(s)
- Takuya Abe
- IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy
| | - Ryotaro Kawasumi
- IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy.,Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa, Hachioji-shi, Tokyo, Japan
| | - Hiroshi Arakawa
- IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy
| | - Tetsuya Hori
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Katsuhiko Shirahige
- Laboratory of Genome Structure and Function, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, Yayoi Bunkyo-Ku, Tokyo, Japan
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Program, Spanish National Cancer Research Centre, Madrid, Spain
| | - Tatsuo Fukagawa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Dana Branzei
- IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy
| |
Collapse
|
44
|
RecQ and Fe-S helicases have unique roles in DNA metabolism dictated by their unwinding directionality, substrate specificity, and protein interactions. Biochem Soc Trans 2017; 46:77-95. [PMID: 29273621 DOI: 10.1042/bst20170044] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/15/2017] [Accepted: 11/17/2017] [Indexed: 12/11/2022]
Abstract
Helicases are molecular motors that play central roles in nucleic acid metabolism. Mutations in genes encoding DNA helicases of the RecQ and iron-sulfur (Fe-S) helicase families are linked to hereditary disorders characterized by chromosomal instabilities, highlighting the importance of these enzymes. Moreover, mono-allelic RecQ and Fe-S helicase mutations are associated with a broad spectrum of cancers. This review will discuss and contrast the specialized molecular functions and biological roles of RecQ and Fe-S helicases in DNA repair, the replication stress response, and the regulation of gene expression, laying a foundation for continued research in these important areas of study.
Collapse
|
45
|
Liang GC, Zheng HF, Chen YX, Li TC, Liu W, Fang YQ. Light of DNA-alkylating agents in castration-resistant prostate cancer cells: a novel mixed EGFR/DNA targeting combi-molecule. Am J Transl Res 2017; 9:3245-3257. [PMID: 28804543 PMCID: PMC5553875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/05/2017] [Indexed: 06/07/2023]
Abstract
OBJECTIVE The mechanism underlying the therapeutic effects of combi-molecule JDF12 on prostate cancer (PCa) DU145 cells remains still unclear. This study aimed to investigate the proteomic profile after JDF12 treatment in DU145 cells by comparing with that in Iressa treated cells and untreated cells. METHODS MTT was used to evaluate drug cytotoxicity, DAPI staining was done to assess apoptosis of cells, and flow cytometry was used to analyze cell cycle. iTRAQ and qPCR were employed to obtain the proteomic profiles of JDF12 treated, Iressa treated, and untreated DU145 cells, and validate the expression of selected differentially expressed proteins, respectively. RESULTS JDF12 could significantly inhibit the proliferation and increase the apoptosis of DU145 cells when compared with Iressa or blank group. In total, 5071 proteins were obtained, out of which, 42, including 21 up-regulated and 21 down-regulated proteins, were differentially expressed in JDF12 group when compared with Iressa and blank groups. The up-regulated proteins were mainly involved in DNA damage/repair and energy metabolism; while the down-regulated proteins were mainly associated with cell apoptosis. qPCR confirmed the expression of several biologically important proteins in DU145 cells after JDF12 treatment. CONCLUSION The molecular mechanisms of DNA alkylating agents on PCa therapy that with the assistant of EGFR-blocker were revealed on proteomic level, which may increase the possible applications of DNA alkylating agents and JDF12 on PCa therapy.
Collapse
Affiliation(s)
- Guan-Can Liang
- Department of Urology, The Third Affiliated Hospital of Sun Yat-sen UniversityGuangzhou 510630, China
| | - Hao-Feng Zheng
- Department of Urology, The Third Affiliated Hospital of Sun Yat-sen UniversityGuangzhou 510630, China
| | - Yan-Xiong Chen
- Department of Urology, The Third Affiliated Hospital of Sun Yat-sen UniversityGuangzhou 510630, China
| | - Teng-Cheng Li
- Department of Urology, The Third Affiliated Hospital of Sun Yat-sen UniversityGuangzhou 510630, China
| | - Wei Liu
- Guangdong Provincial Key Laboratory of Liver Disease, The Third Affiliated Hospital of Sun Yat-sen UniversityGuangzhou 510630, China
| | - You-Qiang Fang
- Department of Urology, The Third Affiliated Hospital of Sun Yat-sen UniversityGuangzhou 510630, China
| |
Collapse
|
46
|
Pai CC, Kearsey SE. A Critical Balance: dNTPs and the Maintenance of Genome Stability. Genes (Basel) 2017; 8:genes8020057. [PMID: 28146119 PMCID: PMC5333046 DOI: 10.3390/genes8020057] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 01/24/2017] [Indexed: 01/14/2023] Open
Abstract
A crucial factor in maintaining genome stability is establishing deoxynucleoside triphosphate (dNTP) levels within a range that is optimal for chromosomal replication. Since DNA replication is relevant to a wide range of other chromosomal activities, these may all be directly or indirectly affected when dNTP concentrations deviate from a physiologically normal range. The importance of understanding these consequences is relevant to genetic disorders that disturb dNTP levels, and strategies that inhibit dNTP synthesis in cancer chemotherapy and for treatment of other disorders. We review here how abnormal dNTP levels affect DNA replication and discuss the consequences for genome stability.
Collapse
Affiliation(s)
- Chen-Chun Pai
- CRUK-MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK.
| | - Stephen E Kearsey
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
| |
Collapse
|
47
|
Samora CP, Saksouk J, Goswami P, Wade BO, Singleton MR, Bates PA, Lengronne A, Costa A, Uhlmann F. Ctf4 Links DNA Replication with Sister Chromatid Cohesion Establishment by Recruiting the Chl1 Helicase to the Replisome. Mol Cell 2016; 63:371-84. [PMID: 27397686 PMCID: PMC4980427 DOI: 10.1016/j.molcel.2016.05.036] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 04/24/2016] [Accepted: 05/26/2016] [Indexed: 12/02/2022]
Abstract
DNA replication during S phase is accompanied by establishment of sister chromatid cohesion to ensure faithful chromosome segregation. The Eco1 acetyltransferase, helped by factors including Ctf4 and Chl1, concomitantly acetylates the chromosomal cohesin complex to stabilize its cohesive links. Here we show that Ctf4 recruits the Chl1 helicase to the replisome via a conserved interaction motif that Chl1 shares with GINS and polymerase α. We visualize recruitment by EM analysis of a reconstituted Chl1-Ctf4-GINS assembly. The Chl1 helicase facilitates replication fork progression under conditions of nucleotide depletion, partly independently of Ctf4 interaction. Conversely, Ctf4 interaction, but not helicase activity, is required for Chl1's role in sister chromatid cohesion. A physical interaction between Chl1 and the cohesin complex during S phase suggests that Chl1 contacts cohesin to facilitate its acetylation. Our results reveal how Ctf4 forms a replisomal interaction hub that coordinates replication fork progression and sister chromatid cohesion establishment.
Collapse
MESH Headings
- Acetyltransferases/metabolism
- Acylation
- Cell Cycle Proteins/metabolism
- Chromatids/enzymology
- Chromatids/genetics
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomal Proteins, Non-Histone/ultrastructure
- Chromosomes, Fungal/enzymology
- Chromosomes, Fungal/genetics
- DNA, Fungal/biosynthesis
- DNA, Fungal/genetics
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- DNA-Binding Proteins/ultrastructure
- Microscopy, Electron, Transmission
- Models, Molecular
- Multiprotein Complexes
- Nuclear Proteins/metabolism
- Protein Binding
- Protein Interaction Domains and Motifs
- S Phase
- Saccharomyces cerevisiae/enzymology
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/growth & development
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Saccharomyces cerevisiae Proteins/ultrastructure
- Structure-Activity Relationship
- Time Factors
- Cohesins
Collapse
Affiliation(s)
- Catarina P Samora
- Chromosome Segregation Laboratory, Francis Crick Institute, London WC2A 3LY, UK
| | - Julie Saksouk
- Institute of Human Genetics (IGH), CNRS, 34396 Montpellier, France
| | - Panchali Goswami
- Macromolecular Machines Laboratory, Francis Crick Institute, South Mimms EN6 3LD, UK
| | - Ben O Wade
- Structural Biology of Chromosome Segregation Laboratory, Francis Crick Institute, London WC2A 3LY, UK
| | - Martin R Singleton
- Structural Biology of Chromosome Segregation Laboratory, Francis Crick Institute, London WC2A 3LY, UK
| | - Paul A Bates
- Biomolecular Modelling Laboratory, Francis Crick Institute, London WC2A 3LY, UK
| | | | - Alessandro Costa
- Macromolecular Machines Laboratory, Francis Crick Institute, South Mimms EN6 3LD, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, Francis Crick Institute, London WC2A 3LY, UK.
| |
Collapse
|
48
|
Marchese FP, Grossi E, Marín-Béjar O, Bharti SK, Raimondi I, González J, Martínez-Herrera DJ, Athie A, Amadoz A, Brosh RM, Huarte M. A Long Noncoding RNA Regulates Sister Chromatid Cohesion. Mol Cell 2016; 63:397-407. [PMID: 27477908 DOI: 10.1016/j.molcel.2016.06.031] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/18/2016] [Accepted: 06/21/2016] [Indexed: 01/01/2023]
Abstract
Long noncoding RNAs (lncRNAs) are involved in diverse cellular processes through multiple mechanisms. Here, we describe a previously uncharacterized human lncRNA, CONCR (cohesion regulator noncoding RNA), that is transcriptionally activated by MYC and is upregulated in multiple cancer types. The expression of CONCR is cell cycle regulated, and it is required for cell-cycle progression and DNA replication. Moreover, cells depleted of CONCR show severe defects in sister chromatid cohesion, suggesting an essential role for CONCR in cohesion establishment during cell division. CONCR interacts with and regulates the activity of DDX11, a DNA-dependent ATPase and helicase involved in DNA replication and sister chromatid cohesion. These findings unveil a direct role for an lncRNA in the establishment of sister chromatid cohesion by modulating DDX11 enzymatic activity.
Collapse
Affiliation(s)
- Francesco P Marchese
- Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, University of Navarra, 55 Pio XII Avenue, 31008 Pamplona, Spain; Institute of Health Research of Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Elena Grossi
- Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, University of Navarra, 55 Pio XII Avenue, 31008 Pamplona, Spain; Institute of Health Research of Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Oskar Marín-Béjar
- Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, University of Navarra, 55 Pio XII Avenue, 31008 Pamplona, Spain; Institute of Health Research of Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Sanjay Kumar Bharti
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Ivan Raimondi
- Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, University of Navarra, 55 Pio XII Avenue, 31008 Pamplona, Spain; Institute of Health Research of Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Jovanna González
- Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, University of Navarra, 55 Pio XII Avenue, 31008 Pamplona, Spain; Institute of Health Research of Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Dannys Jorge Martínez-Herrera
- Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, University of Navarra, 55 Pio XII Avenue, 31008 Pamplona, Spain; Institute of Health Research of Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Alejandro Athie
- Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, University of Navarra, 55 Pio XII Avenue, 31008 Pamplona, Spain; Institute of Health Research of Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Alicia Amadoz
- Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, University of Navarra, 55 Pio XII Avenue, 31008 Pamplona, Spain; Institute of Health Research of Navarra (IdiSNA), 31008 Pamplona, Spain
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Maite Huarte
- Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, University of Navarra, 55 Pio XII Avenue, 31008 Pamplona, Spain; Institute of Health Research of Navarra (IdiSNA), 31008 Pamplona, Spain.
| |
Collapse
|
49
|
Cucco F, Musio A. Genome stability: What we have learned from cohesinopathies. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2016; 172:171-8. [PMID: 27091086 DOI: 10.1002/ajmg.c.31492] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Cohesin is a multiprotein complex involved in many DNA-related processes such as proper chromosome segregation, replication, transcription, and repair. Mutations in cohesin gene pathways are responsible for human diseases, collectively referred to as cohesinopathies. In addition, both cohesin gene expression dysregulation and mutations have been identified in cancer. Cohesinopathy cells are characterized by genome instability (GIN) visualized by a constellation of markers such as chromosome aneuploidies, chromosome aberrations, precocious sister chromatid separation, premature centromere separation, micronuclei formation, and sensitivity to genotoxic drugs. The emerging picture suggests that GIN observed in cohesinopathies may result from the synergistic effects of the multiple cohesin dysfunctions. © 2016 Wiley Periodicals, Inc.
Collapse
|
50
|
Mendoza O, Bourdoncle A, Boulé JB, Brosh RM, Mergny JL. G-quadruplexes and helicases. Nucleic Acids Res 2016; 44:1989-2006. [PMID: 26883636 PMCID: PMC4797304 DOI: 10.1093/nar/gkw079] [Citation(s) in RCA: 311] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/01/2016] [Indexed: 12/16/2022] Open
Abstract
Guanine-rich DNA strands can fold in vitro into non-canonical DNA structures called G-quadruplexes. These structures may be very stable under physiological conditions. Evidence suggests that G-quadruplex structures may act as ‘knots’ within genomic DNA, and it has been hypothesized that proteins may have evolved to remove these structures. The first indication of how G-quadruplex structures could be unfolded enzymatically came in the late 1990s with reports that some well-known duplex DNA helicases resolved these structures in vitro. Since then, the number of studies reporting G-quadruplex DNA unfolding by helicase enzymes has rapidly increased. The present review aims to present a general overview of the helicase/G-quadruplex field.
Collapse
Affiliation(s)
- Oscar Mendoza
- University of Bordeaux, ARNA Laboratory F-33000 Bordeaux, France INSERM U1212,CNRS UMR 5320, IECB, F-33600 Pessac, France
| | - Anne Bourdoncle
- University of Bordeaux, ARNA Laboratory F-33000 Bordeaux, France INSERM U1212,CNRS UMR 5320, IECB, F-33600 Pessac, France
| | - Jean-Baptiste Boulé
- CNRS UMR 7196, INSERM U1154, MNHN, F-75005 Paris, France Sorbonne Universités, F-75005 Paris, France
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Jean-Louis Mergny
- University of Bordeaux, ARNA Laboratory F-33000 Bordeaux, France INSERM U1212,CNRS UMR 5320, IECB, F-33600 Pessac, France
| |
Collapse
|