1
|
Jaiswal AS, Kim HS, Schärer OD, Sharma N, Williamson E, Srinivasan G, Phillips L, Kong K, Arya S, Misra A, Dutta A, Gupta Y, Walter C, Burma S, Narayan S, Sung P, Nickoloff J, Hromas R. EEPD1 promotes repair of oxidatively-stressed replication forks. NAR Cancer 2023; 5:zcac044. [PMID: 36683914 PMCID: PMC9846428 DOI: 10.1093/narcan/zcac044] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/22/2022] [Accepted: 12/14/2022] [Indexed: 01/19/2023] Open
Abstract
Unrepaired oxidatively-stressed replication forks can lead to chromosomal instability and neoplastic transformation or cell death. To meet these challenges cells have evolved a robust mechanism to repair oxidative genomic DNA damage through the base excision repair (BER) pathway, but less is known about repair of oxidative damage at replication forks. We found that depletion or genetic deletion of EEPD1 decreases clonogenic cell survival after oxidative DNA damage. We demonstrate that EEPD1 is recruited to replication forks stressed by oxidative damage induced by H2O2 and that EEPD1 promotes replication fork repair and restart and decreases chromosomal abnormalities after such damage. EEPD1 binds to abasic DNA structures and promotes resolution of genomic abasic sites after oxidative stress. We further observed that restoration of expression of EEPD1 via expression vector transfection restores cell survival and suppresses chromosomal abnormalities induced by oxidative stress in EEPD1-depleted cells. Consistent with this, we found that EEPD1 preserves replication fork integrity by preventing oxidatively-stressed unrepaired fork fusion, thereby decreasing chromosome instability and mitotic abnormalities. Our results indicate a novel role for EEPD1 in replication fork preservation and maintenance of chromosomal stability during oxidative stress.
Collapse
Affiliation(s)
- Aruna S Jaiswal
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Hyun-Suk Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Neelam Sharma
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Elizabeth A Williamson
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Gayathri Srinivasan
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Linda Phillips
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Kimi Kong
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Shailee Arya
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Anurag Misra
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Arijit Dutta
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Yogesh Gupta
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Christi A Walter
- Department of Cell Systems and Anatomy, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Sandeep Burma
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229, USA
- Department of Neurosurgery, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Satya Narayan
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL 32610, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Jac A Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Robert Hromas
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX 78229, USA
| |
Collapse
|
2
|
Muraszko J, Kramarz K, Argunhan B, Ito K, Baranowska G, Kurokawa Y, Murayama Y, Tsubouchi H, Lambert S, Iwasaki H, Dziadkowiec D. Rrp1 translocase and ubiquitin ligase activities restrict the genome destabilising effects of Rad51 in fission yeast. Nucleic Acids Res 2021; 49:6832-6848. [PMID: 34157114 PMCID: PMC8266636 DOI: 10.1093/nar/gkab511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 05/27/2021] [Accepted: 06/06/2021] [Indexed: 11/20/2022] Open
Abstract
Rad51 is the key protein in homologous recombination that plays important roles during DNA replication and repair. Auxiliary factors regulate Rad51 activity to facilitate productive recombination, and prevent inappropriate, untimely or excessive events, which could lead to genome instability. Previous genetic analyses identified a function for Rrp1 (a member of the Rad5/16-like group of SWI2/SNF2 translocases) in modulating Rad51 function, shared with the Rad51 mediator Swi5-Sfr1 and the Srs2 anti-recombinase. Here, we show that Rrp1 overproduction alleviates the toxicity associated with excessive Rad51 levels in a manner dependent on Rrp1 ATPase domain. Purified Rrp1 binds to DNA and has a DNA-dependent ATPase activity. Importantly, Rrp1 directly interacts with Rad51 and removes it from double-stranded DNA, confirming that Rrp1 is a translocase capable of modulating Rad51 function. Rrp1 affects Rad51 binding at centromeres. Additionally, we demonstrate in vivo and in vitro that Rrp1 possesses E3 ubiquitin ligase activity with Rad51 as a substrate, suggesting that Rrp1 regulates Rad51 in a multi-tiered fashion.
Collapse
Affiliation(s)
| | - Karol Kramarz
- Institut Curie, Université PSL, CNRS UMR3348, 91400 Orsay, France.,Université Paris-Saclay, CNRS UMR3348, 91400 Orsay, France
| | - Bilge Argunhan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Kentaro Ito
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | | | - Yumiko Kurokawa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Yasuto Murayama
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Hideo Tsubouchi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Sarah Lambert
- Institut Curie, Université PSL, CNRS UMR3348, 91400 Orsay, France.,Université Paris-Saclay, CNRS UMR3348, 91400 Orsay, France
| | - Hiroshi Iwasaki
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | | |
Collapse
|
3
|
Liu Y, Wang L, Xu X, Yuan Y, Zhang B, Li Z, Xie Y, Yan R, Zheng Z, Ji J, Murray JM, Carr AM, Kong D. The intra-S phase checkpoint directly regulates replication elongation to preserve the integrity of stalled replisomes. Proc Natl Acad Sci U S A 2021; 118:e2019183118. [PMID: 34108240 PMCID: PMC8214678 DOI: 10.1073/pnas.2019183118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
DNA replication is dramatically slowed down under replication stress. The regulation of replication speed is a conserved response in eukaryotes and, in fission yeast, requires the checkpoint kinases Rad3ATR and Cds1Chk2 However, the underlying mechanism of this checkpoint regulation remains unresolved. Here, we report that the Rad3ATR-Cds1Chk2 checkpoint directly targets the Cdc45-MCM-GINS (CMG) replicative helicase under replication stress. When replication forks stall, the Cds1Chk2 kinase directly phosphorylates Cdc45 on the S275, S322, and S397 residues, which significantly reduces CMG helicase activity. Furthermore, in cds1Chk2 -mutated cells, the CMG helicase and DNA polymerases are physically separated, potentially disrupting replisomes and collapsing replication forks. This study demonstrates that the intra-S phase checkpoint directly regulates replication elongation, reduces CMG helicase processivity, prevents CMG helicase delinking from DNA polymerases, and therefore helps preserve the integrity of stalled replisomes and replication forks.
Collapse
Affiliation(s)
- Yang Liu
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Lu Wang
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Xin Xu
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Yue Yuan
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Bo Zhang
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Zeyang Li
- National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Yuchen Xie
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Rui Yan
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Zeqi Zheng
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Jianguo Ji
- National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Johanne M Murray
- Genome Damage and Stability Center, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, United Kingdom
| | - Antony M Carr
- Genome Damage and Stability Center, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, United Kingdom
| | - Daochun Kong
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China;
- National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
4
|
Waraky A, Lin Y, Warsito D, Haglund F, Aleem E, Larsson O. Nuclear insulin-like growth factor 1 receptor phosphorylates proliferating cell nuclear antigen and rescues stalled replication forks after DNA damage. J Biol Chem 2017; 292:18227-18239. [PMID: 28924044 DOI: 10.1074/jbc.m117.781492] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/15/2017] [Indexed: 12/20/2022] Open
Abstract
We have previously shown that the insulin-like growth factor 1 receptor (IGF-1R) translocates to the cell nucleus, where it binds to enhancer-like regions and increases gene transcription. Further studies have demonstrated that nuclear IGF-1R (nIGF-1R) physically and functionally interacts with some nuclear proteins, i.e. the lymphoid enhancer-binding factor 1 (Lef1), histone H3, and Brahma-related gene-1 proteins. In this study, we identified the proliferating cell nuclear antigen (PCNA) as a nIGF-1R-binding partner. PCNA is a pivotal component of the replication fork machinery and a main regulator of the DNA damage tolerance (DDT) pathway. We found that IGF-1R interacts with and phosphorylates PCNA in human embryonic stem cells and other cell lines. In vitro MS analysis of PCNA co-incubated with the IGF-1R kinase indicated tyrosine residues 60, 133, and 250 in PCNA as IGF-1R targets, and PCNA phosphorylation was followed by mono- and polyubiquitination. Co-immunoprecipitation experiments suggested that these ubiquitination events may be mediated by DDT-dependent E2/E3 ligases (e.g. RAD18 and SHPRH/HLTF). Absence of IGF-1R or mutation of Tyr-60, Tyr-133, or Tyr-250 in PCNA abrogated its ubiquitination. Unlike in cells expressing IGF-1R, externally induced DNA damage in IGF-1R-negative cells caused G1 cell cycle arrest and S phase fork stalling. Taken together, our results suggest a role of IGF-1R in DDT.
Collapse
Affiliation(s)
- Ahmed Waraky
- From the Department of Oncology-Pathology, Cancer Center Karolinska, Karolinska Institutet, Stockholm SE-171 76, Sweden
| | - Yingbo Lin
- From the Department of Oncology-Pathology, Cancer Center Karolinska, Karolinska Institutet, Stockholm SE-171 76, Sweden
| | - Dudi Warsito
- From the Department of Oncology-Pathology, Cancer Center Karolinska, Karolinska Institutet, Stockholm SE-171 76, Sweden
| | - Felix Haglund
- From the Department of Oncology-Pathology, Cancer Center Karolinska, Karolinska Institutet, Stockholm SE-171 76, Sweden
| | - Eiman Aleem
- From the Department of Oncology-Pathology, Cancer Center Karolinska, Karolinska Institutet, Stockholm SE-171 76, Sweden
| | - Olle Larsson
- From the Department of Oncology-Pathology, Cancer Center Karolinska, Karolinska Institutet, Stockholm SE-171 76, Sweden
| |
Collapse
|
5
|
Morrow CA, Nguyen MO, Fower A, Wong IN, Osman F, Bryer C, Whitby MC. Inter-Fork Strand Annealing causes genomic deletions during the termination of DNA replication. eLife 2017; 6. [PMID: 28586299 PMCID: PMC5461108 DOI: 10.7554/elife.25490] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 05/22/2017] [Indexed: 11/29/2022] Open
Abstract
Problems that arise during DNA replication can drive genomic alterations that are instrumental in the development of cancers and many human genetic disorders. Replication fork barriers are a commonly encountered problem, which can cause fork collapse and act as hotspots for replication termination. Collapsed forks can be rescued by homologous recombination, which restarts replication. However, replication restart is relatively slow and, therefore, replication termination may frequently occur by an active fork converging on a collapsed fork. We find that this type of non-canonical fork convergence in fission yeast is prone to trigger deletions between repetitive DNA sequences via a mechanism we call Inter-Fork Strand Annealing (IFSA) that depends on the recombination proteins Rad52, Exo1 and Mus81, and is countered by the FANCM-related DNA helicase Fml1. Based on our findings, we propose that IFSA is a potential threat to genomic stability in eukaryotes. DOI:http://dx.doi.org/10.7554/eLife.25490.001
Collapse
Affiliation(s)
- Carl A Morrow
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Michael O Nguyen
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Andrew Fower
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Io Nam Wong
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Fekret Osman
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Claire Bryer
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Matthew C Whitby
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
6
|
Singh S, Vaughan CA, Frum RA, Grossman SR, Deb S, Palit Deb S. Mutant p53 establishes targetable tumor dependency by promoting unscheduled replication. J Clin Invest 2017; 127:1839-1855. [PMID: 28394262 DOI: 10.1172/jci87724] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 02/16/2017] [Indexed: 01/09/2023] Open
Abstract
Gain-of-function (GOF) p53 mutations are observed frequently in most intractable human cancers and establish dependency for tumor maintenance and progression. While some of the genes induced by GOF p53 have been implicated in more rapid cell proliferation compared with p53-null cancer cells, the mechanism for dependency of tumor growth on mutant p53 is unknown. This report reveals a therapeutically targetable mechanism for GOF p53 dependency. We have shown that GOF p53 increases DNA replication origin firing, stabilizes replication forks, and promotes micronuclei formation, thus facilitating the proliferation of cells with genomic abnormalities. In contrast, absence or depletion of GOF p53 leads to decreased origin firing and a higher frequency of fork collapse in isogenic cells, explaining their poorer proliferation rate. Following genome-wide analyses utilizing ChIP-Seq and RNA-Seq, GOF p53-induced origin firing, micronuclei formation, and fork protection were traced to the ability of GOF p53 to transactivate cyclin A and CHK1. Highlighting the therapeutic potential of CHK1's role in GOF p53 dependency, experiments in cell culture and mouse xenografts demonstrated that inhibition of CHK1 selectively blocked proliferation of cells and tumors expressing GOF p53. Our data suggest the possibility that checkpoint inhibitors could efficiently and selectively target cancers expressing GOF p53 alleles.
Collapse
|
7
|
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: 98] [Impact Index Per Article: 14.0] [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
|
8
|
Beyer T, Weinert T. Ontogeny of Unstable Chromosomes Generated by Telomere Error in Budding Yeast. PLoS Genet 2016; 12:e1006345. [PMID: 27716774 PMCID: PMC5065131 DOI: 10.1371/journal.pgen.1006345] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 09/07/2016] [Indexed: 11/19/2022] Open
Abstract
DNA replication errors at certain sites in the genome initiate chromosome instability that ultimately leads to stable genomic rearrangements. Where instability begins is often unclear. And, early instability may form unstable chromosome intermediates whose transient nature also hinders mechanistic understanding. We report here a budding yeast model that reveals the genetic ontogeny of genome rearrangements, from initial replication error to unstable chromosome formation to their resolution. Remarkably, the initial error often arises in or near the telomere, and frequently forms unstable chromosomes. Early unstable chromosomes may then resolve to an internal "collection site" where a dicentric forms and resolves to an isochromosome (other outcomes are possible at each step). The initial telomere-proximal unstable chromosome is increased in mutants in telomerase subunits, Tel1, and even Rad9, with no known telomere-specific function. Defects in Tel1 and in Rrm3, a checkpoint protein kinase with a role in telomere maintenance and a DNA helicase, respectively, synergize dramatically to generate unstable chromosomes, further illustrating the consequence of replication error in the telomere. Collectively, our results suggest telomeric replication errors may be a common cause of seemingly unrelated genomic rearrangements located hundreds of kilobases away.
Collapse
Affiliation(s)
- Tracey Beyer
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Ted Weinert
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, United States of America
- * E-mail:
| |
Collapse
|
9
|
Son MY, Deng CX, Hoeijmarkers JH, Rebel VI, Hasty P. A mechanism for 1,4-Benzoquinone-induced genotoxicity. Oncotarget 2016; 7:46433-46447. [PMID: 27340773 PMCID: PMC5216808 DOI: 10.18632/oncotarget.10184] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 05/22/2016] [Indexed: 12/30/2022] Open
Abstract
Benzene is a common environmental toxin and its metabolite, 1-4-Benzoquinone (BQ) causes hematopoietic cancers like myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). BQ has not been comprehensively assessed for its impact on genome maintenance, limiting our understanding of the true health risks associated with benzene exposure and our ability to identify people with increased sensitivity to this genotoxin. Here we analyze the impact BQ exposure has on wild type and DNA repair-defective mouse embryonic stem (ES) cells and wild type human cells. We find that double strand break (DSB) repair and replication fork maintenance pathways including homologous recombination (HR) and Fanconi anemia (FA) suppress BQ toxicity. BQ-induced damage efficiently stalls replication forks, yet poorly induces ATR/DNA-PKCS responses. Furthermore, the pattern of BQ-induced γH2AX and 53BP1foci is consistent with the formation of poly(ADP-ribose) polymerase 1 (PARP1)-stabilized regressed replication forks. At a biochemical level, BQ inhibited topoisomerase 1 (topo1)-mediated DNA ligation and nicking in vitro; thus providing mechanism for the cellular phenotype. These data are consistent with a model that proposes BQ interferes with type I topoisomerase's ability to maintain replication fork restart and progression leading to chromosomal instability that has the potential to cause hematopoietic cancers like MDS and AML.
Collapse
Affiliation(s)
- Mi Young Son
- Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Chu-Xia Deng
- Faculty of Health Sciences, University of Macau, Macau SAR China
| | - Jan H. Hoeijmarkers
- Department of Genetics, Cancer Genomics Netherlands, Erasmus MC, The Netherlands
| | - Vivienne I. Rebel
- Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
- The Cancer Therapy Research Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
- The Barshop Center of Aging, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
- Greehey Children's Cancer Research Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
- Current address: BioAffinity, San Antonio, Texas, USA
| | - Paul Hasty
- Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
- The Cancer Therapy Research Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
- The Barshop Center of Aging, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| |
Collapse
|
10
|
Dungrawala H, Rose KL, Bhat KP, Mohni KN, Glick GG, Couch FB, Cortez D. The Replication Checkpoint Prevents Two Types of Fork Collapse without Regulating Replisome Stability. Mol Cell 2015; 59:998-1010. [PMID: 26365379 DOI: 10.1016/j.molcel.2015.07.030] [Citation(s) in RCA: 270] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 06/17/2015] [Accepted: 07/28/2015] [Indexed: 02/06/2023]
Abstract
The ATR replication checkpoint ensures that stalled forks remain stable when replisome movement is impeded. Using an improved iPOND protocol combined with SILAC mass spectrometry, we characterized human replisome dynamics in response to fork stalling. Our data provide a quantitative picture of the replisome and replication stress response proteomes in 32 experimental conditions. Importantly, rather than stabilize the replisome, the checkpoint prevents two distinct types of fork collapse. Unsupervised hierarchical clustering of protein abundance on nascent DNA is sufficient to identify protein complexes and place newly identified replisome-associated proteins into functional pathways. As an example, we demonstrate that ZNF644 complexes with the G9a/GLP methyltransferase at replication forks and is needed to prevent replication-associated DNA damage. Our data reveal how the replication checkpoint preserves genome integrity, provide insights into the mechanism of action of ATR inhibitors, and will be a useful resource for replication, DNA repair, and chromatin investigators.
Collapse
Affiliation(s)
- Huzefa Dungrawala
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kristie L Rose
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kamakoti P Bhat
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kareem N Mohni
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Gloria G Glick
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Frank B Couch
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
| |
Collapse
|
11
|
Abstract
The Breakage Fusion Bridge (BFB) process is a key marker for genomic instability, producing highly rearranged genomes in relatively small numbers of cell cycles. While the process itself was observed during the late 1930s, little is known about the extent of BFB in tumor genome evolution. Moreover, BFB can dramatically increase copy numbers of chromosomal segments, which in turn hardens the tasks of both reference-assisted and ab initio genome assembly. Based on available data such as Next Generation Sequencing (NGS) and Array Comparative Genomic Hybridization (aCGH) data, we show here how BFB evidence may be identified, and how to enumerate all possible evolutions of the process with respect to observed data. Specifically, we describe practical algorithms that, given a chromosomal arm segmentation and noisy segment copy number estimates, produce all segment count vectors supported by the data that can be produced by BFB, and all corresponding BFB architectures. This extends the scope of analyses described in our previous work, which produced a single count vector and architecture per instance. We apply these analyses to a comprehensive human cancer dataset, demonstrate the effectiveness and efficiency of the computation, and suggest methods for further assertions of candidate BFB samples. Source code of our tool can be found online.
Collapse
Affiliation(s)
- Shay Zakov
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California
| |
Collapse
|
12
|
Abstract
Billions of base pairs of DNA must be replicated trillions of times in a human lifetime. Complete and accurate replication once and only once per cell division cycle is essential to maintain genome integrity and prevent disease. Impediments to replication fork progression including difficult to replicate DNA sequences, conflicts with transcription, and DNA damage further add to the genome maintenance challenge. These obstacles frequently cause fork stalling, but only rarely cause a failure to complete replication. Robust mechanisms ensure that stalled forks remain stable and capable of either resuming DNA synthesis or being rescued by converging forks. However, when failures do happen the fork collapses leading to genome rearrangements, cell death and disease. Despite intense interest, the mechanisms to repair damaged replication forks, stabilize them, and ensure successful replication remain only partly understood. Different models of fork collapse have been proposed with varying descriptions of what happens to the DNA and replisome. Here, I will define fork collapse and describe what is known about how the replication checkpoint prevents it to maintain genome stability.
Collapse
|
13
|
Pietrobon V, Fréon K, Hardy J, Costes A, Iraqui I, Ochsenbein F, Lambert SA. The chromatin assembly factor 1 promotes Rad51-dependent template switches at replication forks by counteracting D-loop disassembly by the RecQ-type helicase Rqh1. PLoS Biol 2014; 12:e1001968. [PMID: 25313826 PMCID: PMC4196752 DOI: 10.1371/journal.pbio.1001968] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 09/04/2014] [Indexed: 11/25/2022] Open
Abstract
A molecular switch for times of replication stress - Chromatin Assembly Factor 1 helps to protect DNA during recombination-mediated template-switching, favoring the rescue of stalled replication forks by both beneficial and detrimental homologous recombination events. At blocked replication forks, homologous recombination mediates the nascent strands to switch template in order to ensure replication restart, but faulty template switches underlie genome rearrangements in cancer cells and genomic disorders. Recombination occurs within DNA packaged into chromatin that must first be relaxed and then restored when recombination is completed. The chromatin assembly factor 1, CAF-1, is a histone H3-H4 chaperone involved in DNA synthesis-coupled chromatin assembly during DNA replication and DNA repair. We reveal a novel chromatin factor-dependent step during replication-coupled DNA repair: Fission yeast CAF-1 promotes Rad51-dependent template switches at replication forks, independently of the postreplication repair pathway. We used a physical assay that allows the analysis of the individual steps of template switch, from the recruitment of recombination factors to the formation of joint molecules, combined with a quantitative measure of the resulting rearrangements. We reveal functional and physical interplays between CAF-1 and the RecQ-helicase Rqh1, the BLM homologue, mutations in which cause Bloom's syndrome, a human disease associating genome instability with cancer predisposition. We establish that CAF-1 promotes template switch by counteracting D-loop disassembly by Rqh1. Consequently, the likelihood of faulty template switches is controlled by antagonistic activities of CAF-1 and Rqh1 in the stability of the D-loop. D-loop stabilization requires the ability of CAF-1 to interact with PCNA and is thus linked to the DNA synthesis step. We propose that CAF-1 plays a regulatory role during template switch by assembling chromatin on the D-loop and thereby impacting the resolution of the D-loop. Obstacles to the progression of DNA replication forks can result in genome rearrangements that are often observed in cancer cells and genomic disorders. Homologous recombination is a mechanism of restarting stalled replication fork that involves synthesis of the new DNA strands switching templates to a second (allelic) copy of the DNA sequence. However, the new strands can also occasionally recombine with nonallelic repeats (distinct regions of the genome that resemble the correct one) and thereby cause the inappropriate fusion of normally distant DNA segments; this is known as faulty template switching. The chromatin assembly factor 1 (CAF-1) is already known to be involved in depositing nucleosomes on DNA during DNA replication and repair. We have found that CAF-1 is also involved in the recombination-mediated template switch pathway in response to replication stress. Using both genetic and physical assays that allow the different steps of template switch to be analyzed, we reveal that CAF-1 protects recombination intermediates from disassembly by the RecQ-type helicase Rqh1, the homologue of BLM (people with mutations that affect BLM have Bloom's syndrome, an inherited predisposition to genome instability and cancer). Consequently, the likelihood of faulty template switch is controlled by the antagonistic activities of CAF-1 and Rqh1. We thus identified an evolutionarily conserved interplay between CAF-1 and RecQ-type helicases that helps to maintain genome stability in the face of replication stress.
Collapse
Affiliation(s)
- Violena Pietrobon
- Institut Curie, Centre de Recherche, Orsay, France
- Centre national de la Recherche Scientifique, UMR3348, Centre Universitaire, Orsay, France
| | - Karine Fréon
- Institut Curie, Centre de Recherche, Orsay, France
- Centre national de la Recherche Scientifique, UMR3348, Centre Universitaire, Orsay, France
| | - Julien Hardy
- Institut Curie, Centre de Recherche, Orsay, France
- Centre national de la Recherche Scientifique, UMR3348, Centre Universitaire, Orsay, France
| | - Audrey Costes
- Institut Curie, Centre de Recherche, Orsay, France
- Centre national de la Recherche Scientifique, UMR3348, Centre Universitaire, Orsay, France
| | - Ismail Iraqui
- Institut Curie, Centre de Recherche, Orsay, France
- Centre national de la Recherche Scientifique, UMR3348, Centre Universitaire, Orsay, France
| | - Françoise Ochsenbein
- Commissariat à l'Energie Atomique, iBiTec-S, Service de Biologie Intégrative et de Génétique Moléculaire, Gif-sur-Yvette, France
| | - Sarah A.E. Lambert
- Institut Curie, Centre de Recherche, Orsay, France
- Centre national de la Recherche Scientifique, UMR3348, Centre Universitaire, Orsay, France
- * E-mail:
| |
Collapse
|
14
|
Yoon SW, Kim DK, Kim KP, Park KS. Rad51 regulates cell cycle progression by preserving G2/M transition in mouse embryonic stem cells. Stem Cells Dev 2014; 23:2700-11. [PMID: 24991985 DOI: 10.1089/scd.2014.0129] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Homologous recombination (HR) maintains genomic integrity against DNA replication stress and deleterious lesions, such as double-strand breaks (DSBs). Rad51 recombinase is critical for HR events that mediate the exchange of genetic information between parental chromosomes in eukaryotes. Additionally, Rad51 and HR accessory factors may facilitate replication fork progression by preventing replication fork collapse and repair DSBs that spontaneously arise during the normal cell cycle. In this study, we demonstrated a novel role for Rad51 during the cell cycle in mouse embryonic stem cells (mESCs). In mESCs, Rad51 was constitutively expressed throughout the cell cycle, and the formation of Rad51 foci increased as the cells entered S phase. Suppression of Rad51 expression caused cells to accumulate at G2/M phase and activated the DNA damage checkpoint, but it did not affect the self-renewal or differentiation capacity of mESCs. Even though Rad51 suppression significantly inhibited the proliferation rate of mESCs, Rad51 suppression did not affect the replication fork progression and speed, indicating that Rad51 repaired DNA damage and promoted DNA replication in S phase through an independent mechanism. In conclusion, Rad51 may contribute to G2/M transition in mESCs, while preserving genomic integrity in global organization of DNA replication fork.
Collapse
Affiliation(s)
- Sang-Wook Yoon
- 1 Department of Life Science, Chung-Ang University , Seoul, Korea
| | | | | | | |
Collapse
|
15
|
Hasty P, Montagna C. Chromosomal Rearrangements in Cancer: Detection and potential causal mechanisms. Mol Cell Oncol 2014; 1:e29904. [PMID: 26203462 PMCID: PMC4507279 DOI: 10.4161/mco.29904] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 06/20/2014] [Accepted: 06/23/2014] [Indexed: 12/13/2022]
Abstract
Many cancers exhibit chromosomal rearrangements. These rearrangements can be simple with a single balanced fusion preserving the proper complement of genetic information or they can be complex with one or more fusions that distort this balance. A range of technological advances has improved our ability to detect and understand these rearrangements leading to speculation of causal mechanisms including defective DNA double strand break (DSB) repair and faulty DNA replication. A better understanding of these potential cancer-causing mechanisms will lead to novel therapeutic regimes to fight cancer. This review describes the technological advances used to detect simple and complex chromosomal rearrangements, cancers that exhibit these rearrangements, potential mechanisms that rearrange chromosomes and intervention strategies designed to specifically attack fusion gene products and causal DNA repair/synthesis pathways.
Collapse
Affiliation(s)
- Paul Hasty
- Department of Molecular Medicine/Institute of Biotechnology; The University of Texas Health Science Center at San Antonio; San Antonio, TX USA
| | - Cristina Montagna
- Department of Genetics and Pathology; Albert Einstein College of Medicine of Yeshiva University; Michael F. Price Center; Bronx, NY USA
| |
Collapse
|
16
|
Zhang Y, Baranovskiy AG, Tahirov TH, Pavlov YI. The C-terminal domain of the DNA polymerase catalytic subunit regulates the primase and polymerase activities of the human DNA polymerase α-primase complex. J Biol Chem 2014; 289:22021-34. [PMID: 24962573 DOI: 10.1074/jbc.m114.570333] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The initiation of DNA synthesis during replication of the human genome is accomplished primarily by the DNA polymerase α-primase complex, which makes the RNA-DNA primers accessible to processive DNA pols. The structural information needed to understand the mechanism of regulation of this complex biochemical reaction is incomplete. The presence of two enzymes in one complex poses the question of how these two enzymes cooperate during priming of DNA synthesis. Yeast two-hybrid and direct pulldown assays revealed that the N-terminal domain of the large subunit of primase (p58N) directly interacts with the C-terminal domain of the catalytic subunit of polα (p180C). We found that a complex of the C-terminal domain of the catalytic subunit of polα with the second subunit (p180C-p70) stimulated primase activity, whereas the whole catalytically active heterodimer of polα (p180ΔN-p70) inhibited RNA synthesis by primase. Conversely, the polα catalytic domain without the C-terminal part (p180ΔN-core) possessed a much higher propensity to extend the RNA primer than the two-subunit polα (p180ΔN-p70), suggesting that p180C and/or p70 are involved in the negative regulation of DNA pol activity. We conclude that the interaction between p180C, p70, and p58 regulates the proper primase and polymerase function. The composition of the template DNA is another important factor determining the activity of the complex. We have found that polα activity strongly depends on the sequence of the template and that homopyrimidine runs create a strong barrier for DNA synthesis by polα.
Collapse
Affiliation(s)
- Yinbo Zhang
- From the Eppley Institute for Research in Cancer and Allied Diseases, Department of Biochemistry and Molecular Biology, and
| | | | - Tahir H Tahirov
- From the Eppley Institute for Research in Cancer and Allied Diseases,
| | - Youri I Pavlov
- From the Eppley Institute for Research in Cancer and Allied Diseases, Department of Biochemistry and Molecular Biology, and Department of Pathology and Microbiology, University of Nebraska Medical Center, Nebraska Medical Center, Omaha, Nebraska 68198-6805
| |
Collapse
|
17
|
Abstract
The MYC oncogene is a multifunctional protein that is aberrantly expressed in a significant fraction of tumors from diverse tissue origins. Because of its multifunctional nature, it has been difficult to delineate the exact contributions of MYC's diverse roles to tumorigenesis. Here, we review the normal role of MYC in regulating DNA replication as well as its ability to generate DNA replication stress when overexpressed. Finally, we discuss the possible mechanisms by which replication stress induced by aberrant MYC expression could contribute to genomic instability and cancer.
Collapse
Affiliation(s)
| | - Jean Gautier
- Institute for Cancer Genetics, Columbia University, New York, New York 10032 Department of Genetics and Development, Columbia University, New York, New York 10032
| |
Collapse
|
18
|
Beuzer P, Quivy JP, Almouzni G. Establishment of a replication fork barrier following induction of DNA binding in mammalian cells. Cell Cycle 2014; 13:1607-16. [PMID: 24675882 PMCID: PMC4050166 DOI: 10.4161/cc.28627] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Understanding the mechanisms that lead to replication fork blocks (RFB) and the means to bypass them is important given the threat that they represent for genome stability if inappropriately handled. Here, to study this issue in mammals, we use integrated arrays of the LacO and/or TetO as a tractable system to follow in time a process in an individual cell and at a single locus. Importantly, we show that induction of the binding by LacI and TetR proteins, and not the presence of the repeats, is key to form the RFB. We find that the binding of the proteins to the arrays during replication causes a prolonged persistence of replication foci at the site. This, in turn, induces a local DNA damage repair (DDR) response, with the recruitment of proteins involved in double-strand break (DSB) repair such as TOPBP1 and 53BP1, and the phosphorylation of H2AX. Furthermore, the appearance of micronuclei and DNA bridges after mitosis is consistent with an incomplete replication. We discuss how the many DNA binding proteins encountered during replication can be dealt with and the consequences of incomplete replication. Future studies exploiting this type of system should help analyze how an RFB, along with bypass mechanisms, are controlled in order to maintain genome integrity.
Collapse
Affiliation(s)
- Paolo Beuzer
- Institut Curie; Centre de Recherche; Paris, France; CNRS; UMR3664; Paris, France; Equipe Labellisée Ligue contre le Cancer; UMR3664; Paris, France; UPMC; UMR3664; Paris, France; Sorbonne University; PSL; Paris, France
| | - Jean-Pierre Quivy
- Institut Curie; Centre de Recherche; Paris, France; CNRS; UMR3664; Paris, France; Equipe Labellisée Ligue contre le Cancer; UMR3664; Paris, France; UPMC; UMR3664; Paris, France; Sorbonne University; PSL; Paris, France
| | - Geneviève Almouzni
- Institut Curie; Centre de Recherche; Paris, France; CNRS; UMR3664; Paris, France; Equipe Labellisée Ligue contre le Cancer; UMR3664; Paris, France; UPMC; UMR3664; Paris, France; Sorbonne University; PSL; Paris, France
| |
Collapse
|
19
|
Deb SP, Singh S, Deb S. MDM2 overexpression, activation of signaling networks, and cell proliferation. Subcell Biochem 2014; 85:215-34. [PMID: 25201197 DOI: 10.1007/978-94-017-9211-0_12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Frequent overexpression of MDM2 in human cancers suggests that the protein confers a survival advantage to cancer cells. However, overexpression of MDM2 in normal cells seems to restrict cell proliferation. This review discusses the cell growth regulatory functions of MDM2 in normal and genetically defective cells to assess how cancer cells evade the growth-restricting consequence of MDM2 overexpression. Similar to oncoproteins that induce a DNA damage response and oncogene induced senescence in non-transformed cells, MDM2 induces G1-arrest and intra-S phase checkpoint responses that control untimely DNA replication in the face of genetic challenges.
Collapse
Affiliation(s)
- Swati Palit Deb
- Department of Biochemistry and Molecular Biology, and the Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23298, USA,
| | | | | |
Collapse
|
20
|
Cauwood JD, Johnson AL, Widger A, Cha RS. Recombinogenic conditions influence partner choice in spontaneous mitotic recombination. PLoS Genet 2013; 9:e1003931. [PMID: 24244194 PMCID: PMC3820797 DOI: 10.1371/journal.pgen.1003931] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 09/16/2013] [Indexed: 11/18/2022] Open
Abstract
Mammalian common fragile sites are loci of frequent chromosome breakage and putative recombination hotspots. Here, we utilized Replication Slow Zones (RSZs), a budding yeast homolog of the mammalian common fragile sites, to examine recombination activities at these loci. We found that rates of URA3 inactivation of a hisG-URA3-hisG reporter at RSZ and non-RSZ loci were comparable under all conditions tested, including those that specifically promote chromosome breakage at RSZs (hydroxyurea [HU], mec1Δ sml1Δ, and high temperature), and those that suppress it (sml1Δ and rrm3Δ). These observations indicate that RSZs are not recombination hotspots and that chromosome fragility and recombination activity can be uncoupled. Results confirmed recombinogenic effects of HU, mec1Δ sml1Δ, and rrm3Δ and identified temperature as a regulator of mitotic recombination. We also found that these conditions altered the nature of recombination outcomes, leading to a significant increase in the frequency of URA3 inactivation via loss of heterozygosity (LOH), the type of genetic alteration involved in cancer development. Further analyses revealed that the increase was likely due to down regulation of intrachromatid and intersister (IC/IS) bias in mitotic recombination, and that RSZs exhibited greater sensitivity to HU dependent loss of IC/IS bias than non RSZ loci. These observations suggest that recombinogenic conditions contribute to genome rearrangements not only by increasing the overall recombination activity, but also by altering the nature of recombination outcomes by their effects on recombination partner choice. Similarly, fragile sites may contribute to cancer more frequently than non-fragile loci due their enhanced sensitivity to certain conditions that down-regulate the IC/IS bias rather than intrinsically higher rates of recombination. Chromosome rearrangements are frequently associated with human cancers. Such rearrangement can result from a DNA break followed by an erroneous repair. Mammalian common fragile sites are one of the most extensively studied naturally occurring breakage prone regions of the genome. It has been proposed that fragile sites are recombination hotspots and that increased recombination activity at these loci contribute to cancer. We examined this hypothesis using a model organism, budding yeast Saccharomyces cerevisiae, where a homolog of the mammalian common fragile sites has been identified. Unexpectedly, our results showed that the rate of recombination at the fragile sites was not any higher than non fragile sites, even under the conditions that promoted chromosome breakage at the fragile sites. However, we found that the frequency of loss of heterozygosity (LOH) and translocation, the type of recombination outcomes known to contribute to cancer, to be significantly elevated at fragile sites under certain conditions. These findings suggest that the fragile sites might indeed contribute to cancer more frequently than non-fragile loci, but the reason for this is likely to be due the nature of the recombination outcome(s) rather than higher rates of recombination.
Collapse
Affiliation(s)
- James D. Cauwood
- Stem Cell Biology and Developmental Genetics, National Institute for Medical Research, MRC, The Ridgeway, London, United Kingdom
| | - Anthony L. Johnson
- Stem Cell Biology and Developmental Genetics, National Institute for Medical Research, MRC, The Ridgeway, London, United Kingdom
| | - Alexander Widger
- Stem Cell Biology and Developmental Genetics, National Institute for Medical Research, MRC, The Ridgeway, London, United Kingdom
| | - Rita S. Cha
- Stem Cell Biology and Developmental Genetics, National Institute for Medical Research, MRC, The Ridgeway, London, United Kingdom
- * E-mail:
| |
Collapse
|
21
|
Two replication fork maintenance pathways fuse inverted repeats to rearrange chromosomes. Nature 2013; 501:569-72. [PMID: 24013173 PMCID: PMC3805358 DOI: 10.1038/nature12500] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 07/22/2013] [Indexed: 12/27/2022]
Abstract
Replication fork (RF) maintenance pathways preserve chromosomes, but their faulty application at nonallelic repeats could generate rearrangements causing cancer, genomic disorders and speciation1-3. Potential causal mechanisms are homologous recombination (HR) and error-free postreplication repair (EF-PRR). HR repairs damage induced DNA double strand breaks (DSBs) and single-ended DSBs within replication. To facilitate HR, the recombinase RAD51 and mediator BRCA2 form a filament on the 3’ DNA strand at a break to enable annealing to the complementary sister chromatid4 while the RecQ helicase, BLM (Bloom syndrome mutated) suppresses crossing over to prevent recombination5. HR also stabilizes6,7 and restarts8,9 RFs without a DSB10,11. EF-PRR bypasses DNA incongruities that impede replication by ubiquitinating PCNA (proliferating cell nuclear antigen) using the RAD6/RAD18 and UBC13/MMS2/RAD5 ubiquitin ligase complexes12. Some components are common to both HR and EF-PRR like RAD51 and RAD1813,14. Here we delineate two pathways that spontaneously fuse inverted repeats to generate unstable chromosomal rearrangements in wild type mouse embryonic stem (ES) cells. Gamma-radiation induced a BLM-regulated pathway that selectively fused identical, but not mismatched repeats. By contrast, UV light induced a RAD18-dependent pathway that efficiently fused mismatched repeats. Furthermore, TREX2 (a 3’→5’ exonuclease) suppressed identical repeat fusion but enhanced mismatched repeat fusion, clearly separating these pathways. TREX2 associated with UBC13 and enhanced PCNA ubiquitination in response to UV light, consistent with it being a novel member of EF-PRR. RAD18 and TREX2 also suppressed RF stalling in response to nucleotide depletion. Interestingly, RF stalling induced fusion for identical and mismatched repeats implicating faulty replication as a causal mechanism for both pathways.
Collapse
|
22
|
Evertts AG, Coller HA. Back to the origin: reconsidering replication, transcription, epigenetics, and cell cycle control. Genes Cancer 2013; 3:678-96. [PMID: 23634256 DOI: 10.1177/1947601912474891] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In bacteria, replication is a carefully orchestrated event that unfolds the same way for each bacterium and each cell division. The process of DNA replication in bacteria optimizes cell growth and coordinates high levels of simultaneous replication and transcription. In metazoans, the organization of replication is more enigmatic. The lack of a specific sequence that defines origins of replication has, until recently, severely limited our ability to define the organizing principles of DNA replication. This question is of particular importance as emerging data suggest that replication stress is an important contributor to inherited genetic damage and the genomic instability in tumors. We consider here the replication program in several different organisms including recent genome-wide analyses of replication origins in humans. We review recent studies on the role of cytosine methylation in replication origins, the role of transcriptional looping and gene gating in DNA replication, and the role of chromatin's 3-dimensional structure in DNA replication. We use these new findings to consider several questions surrounding DNA replication in metazoans: How are origins selected? What is the relationship between replication and transcription? How do checkpoints inhibit origin firing? Why are there early and late firing origins? We then discuss whether oncogenes promote cancer through a role in DNA replication and whether errors in DNA replication are important contributors to the genomic alterations and gene fusion events observed in cancer. We conclude with some important areas for future experimentation.
Collapse
|
23
|
An algorithmic approach for breakage-fusion-bridge detection in tumor genomes. Proc Natl Acad Sci U S A 2013; 110:5546-51. [PMID: 23503850 DOI: 10.1073/pnas.1220977110] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Breakage-fusion-bridge (BFB) is a mechanism of genomic instability characterized by the joining and subsequent tearing apart of sister chromatids. When this process is repeated during multiple rounds of cell division, it leads to patterns of copy number increases of chromosomal segments as well as fold-back inversions where duplicated segments are arranged head-to-head. These structural variations can then drive tumorigenesis. BFB can be observed in progress using cytogenetic techniques, but generally BFB must be inferred from data such as microarrays or sequencing collected after BFB has ceased. Making correct inferences from this data is not straightforward, particularly given the complexity of some cancer genomes and BFB's ability to generate a wide range of rearrangement patterns. Here we present algorithms to aid the interpretation of evidence for BFB. We first pose the BFB count-vector problem: given a chromosome segmentation and segment copy numbers, decide whether BFB can yield a chromosome with the given segment counts. We present a linear time algorithm for the problem, in contrast to a previous exponential time algorithm. We then combine this algorithm with fold-back inversions to develop tests for BFB. We show that, contingent on assumptions about cancer genome evolution, count vectors and fold-back inversions are sufficient evidence for detecting BFB. We apply the presented techniques to paired-end sequencing data from pancreatic tumors and confirm a previous finding of BFB as well as identify a chromosomal region likely rearranged by BFB cycles, demonstrating the practicality of our approach.
Collapse
|
24
|
Li PC, Petreaca RC, Jensen A, Yuan JP, Green MD, Forsburg SL. Replication fork stability is essential for the maintenance of centromere integrity in the absence of heterochromatin. Cell Rep 2013; 3:638-45. [PMID: 23478021 DOI: 10.1016/j.celrep.2013.02.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 01/06/2013] [Accepted: 02/05/2013] [Indexed: 12/18/2022] Open
Abstract
The centromere of many eukaryotes contains highly repetitive sequences marked by methylation of histone H3K9 by Clr4(KMT1). This recruits multiple heterochromatin proteins, including Swi6 and Chp1, to form a rigid centromere and ensure accurate chromosome segregation. In the absence of heterochromatin, cells show an increased rate of recombination in the centromere, as well as chromosome loss. These defects are severely aggravated by loss of replication fork stability. Thus, heterochromatin proteins and replication fork protection mechanisms work in concert to prevent abnormal recombination, preserve centromere integrity, and ensure faithful chromosome segregation.
Collapse
Affiliation(s)
- Pao-Chen Li
- Molecular & Computational Biology Program, University of Southern California, Los Angeles, CA 90089-2910, USA
| | | | | | | | | | | |
Collapse
|
25
|
Single-stranded annealing induced by re-initiation of replication origins provides a novel and efficient mechanism for generating copy number expansion via non-allelic homologous recombination. PLoS Genet 2013; 9:e1003192. [PMID: 23300490 PMCID: PMC3536649 DOI: 10.1371/journal.pgen.1003192] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 11/08/2012] [Indexed: 11/24/2022] Open
Abstract
Copy number expansions such as amplifications and duplications contribute to human phenotypic variation, promote molecular diversification during evolution, and drive the initiation and/or progression of various cancers. The mechanisms underlying these copy number changes are still incompletely understood, however. We recently demonstrated that transient, limited re-replication from a single origin in Saccharomyces cerevisiae efficiently induces segmental amplification of the re-replicated region. Structural analyses of such re-replication induced gene amplifications (RRIGA) suggested that RRIGA could provide a new mechanism for generating copy number variation by non-allelic homologous recombination (NAHR). Here we elucidate this new mechanism and provide insight into why it is so efficient. We establish that sequence homology is both necessary and sufficient for repetitive elements to participate in RRIGA and show that their recombination occurs by a single-strand annealing (SSA) mechanism. We also find that re-replication forks are prone to breakage, accounting for the widespread DNA damage associated with deregulation of replication proteins. These breaks appear to stimulate NAHR between re-replicated repeat sequences flanking a re-initiating replication origin. Our results support a RRIGA model where the expansion of a re-replication bubble beyond flanking homologous sequences followed by breakage at both forks in trans provides an ideal structural context for SSA–mediated NAHR to form a head-to-tail duplication. Given the remarkable efficiency of RRIGA, we suggest it may be an unappreciated contributor to copy number expansions in both disease and evolution. Duplications and amplifications of chromosomal segments are frequently observed in eukaryotic genomes, including both normal and cancerous human genomes. These copy number variations contribute to the phenotypic variation upon which natural selection acts. For example, the amplification of genes whose excessive copy number facilitates uncontrolled cell division is often selected for during tumor development. Copy number variations can often arise when repetitive sequence elements, which are dispersed throughout eukaryotic genomes, undergo a rearrangement called non-allelic homologous recombination. Exactly how these rearrangements occur is poorly understood. Here, using budding yeast to model this class of copy number variation, we uncover a new and highly efficient mechanism by which these variations can be generated. The precipitating event is the aberrant re-initiation of DNA replication at a replication origin. Normally the hundreds to thousands of origins scattered throughout a eukaryotic genome are tightly controlled such that each is permitted to initiate only once per cell cycle. However, disruptions in these controls can allow origins to re-initiate, and we show how the resulting DNA re-replication structure can be readily converted into a tandem duplication via non-allelic homologous recombination. Hence, the re-initiation of DNA replication is a potential source of copy number variation both in disease and during evolution.
Collapse
|
26
|
Abstract
RAD51 is important for restarting stalled replication forks and for repairing DNA double-strand breaks (DSBs) through a pathway called homology-directed repair (HDR). However, analysis of the consequences of specific RAD51 mutants has been difficult since they are toxic. Here we report on the dominant effects of two human RAD51 mutants defective for ATP binding (K133A) or ATP hydrolysis (K133R) expressed in mouse embryonic stem (ES) cells that also expressed normal mouse RAD51 from the other chromosome. These cells were defective for restarting stalled replication forks and repairing breaks. They were also hypersensitive to camptothecin, a genotoxin that generates breaks specifically at the replication fork. In addition, these cells exhibited a wide range of structural chromosomal changes that included multiple breakpoints within the same chromosome. Thus, ATP binding and hydrolysis are essential for chromosomal maintenance. Fusion of RAD51 to a fluorescent tag (enhanced green fluorescent protein [eGFP]) allowed visualization of these proteins at sites of replication and repair. We found very low levels of mutant protein present at these sites compared to normal protein, suggesting that low levels of mutant protein were sufficient for disruption of RAD51 activity and generation of chromosomal rearrangements.
Collapse
|