1
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Pavani R, Tripathi V, Vrtis KB, Zong D, Chari R, Callen E, Pankajam AV, Zhen G, Matos-Rodrigues G, Yang J, Wu S, Reginato G, Wu W, Cejka P, Walter JC, Nussenzweig A. Structure and repair of replication-coupled DNA breaks. Science 2024:eado3867. [PMID: 38900911 DOI: 10.1126/science.ado3867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 06/10/2024] [Indexed: 06/22/2024]
Abstract
Using CRISPR/Cas9 nicking enzymes, we examine the interaction between the replication machinery and single strand breaks, one of the most common forms of endogenous DNA damage. We show that replication fork collapse at leading strand nicks generates resected single-ended double-strand breaks (seDSBs) that are repaired by homologous recombination (HR). If these seDSBs are not promptly repaired, arrival of adjacent forks creates double ended DSBs (deDSBs), which could drive genomic scarring in HR-deficient cancers. deDSBs can also be generated directly when the replication fork bypasses lagging strand nicks. Unlike deDSBs produced independently of replication, end-resection at nick-induced se/deDSBs is BRCA1-independent. Nevertheless, BRCA1 antagonizes 53BP1 suppression of RAD51 filament formation. These results highlight unique mechanisms that maintain replication fork stability.
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Affiliation(s)
- Raphael Pavani
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Veenu Tripathi
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Kyle B Vrtis
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Blavatnik Institute, Boston, MA, USA
| | - Dali Zong
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Raj Chari
- Genome Modification Core, Frederick National Lab for Cancer Research, Frederick, MD, USA
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ajith V Pankajam
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Gang Zhen
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Jiajie Yang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Shuheng Wu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Giordano Reginato
- Institute for Research in Biomedicine, Universita della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, 6500, Switzerland
| | - Wei Wu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Petr Cejka
- Institute for Research in Biomedicine, Universita della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, 6500, Switzerland
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Blavatnik Institute, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard University, Boston, MA, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
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2
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Schreuder A, Wendel TJ, Dorresteijn CGV, Noordermeer SM. (Single-stranded DNA) gaps in understanding BRCAness. Trends Genet 2024:S0168-9525(24)00100-8. [PMID: 38789375 DOI: 10.1016/j.tig.2024.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024]
Abstract
The tumour-suppressive roles of BRCA1 and 2 have been attributed to three seemingly distinct functions - homologous recombination, replication fork protection, and single-stranded (ss)DNA gap suppression - and their relative importance is under debate. In this review, we examine the origin and resolution of ssDNA gaps and discuss the recent advances in understanding the role of BRCA1/2 in gap suppression. There are ample data showing that gap accumulation in BRCA1/2-deficient cells is linked to genomic instability and chemosensitivity. However, it remains unclear whether there is a causative role and the function of BRCA1/2 in gap suppression cannot unambiguously be dissected from their other functions. We therefore conclude that the three functions of BRCA1 and 2 are closely intertwined and not mutually exclusive.
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Affiliation(s)
- Anne Schreuder
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Tiemen J Wendel
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Carlo G V Dorresteijn
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands
| | - Sylvie M Noordermeer
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands; Oncode Institute, Utrecht, The Netherlands.
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3
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Nguyen DT, Mahajan U, Angappulige DH, Doshi A, Mahajan NP, Mahajan K. Amino Terminal Acetylation of HOXB13 Regulates the DNA Damage Response in Prostate Cancer. Cancers (Basel) 2024; 16:1622. [PMID: 38730575 PMCID: PMC11083449 DOI: 10.3390/cancers16091622] [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: 03/25/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 05/13/2024] Open
Abstract
Advanced localized prostate cancers (PC) recur despite chemotherapy, radiotherapy and/or androgen deprivation therapy. We recently reported HOXB13 lysine (K)13 acetylation as a gain-of-function modification that regulates interaction with the SWI/SNF chromatin remodeling complex and is critical for anti-androgen resistance. However, whether acetylated HOXB13 promotes PC cell survival following treatment with genotoxic agents is not known. Herein, we show that K13-acetylated HOXB13 is induced rapidly in PC cells in response to DNA damage induced by irradiation (IR). It colocalizes with the histone variant γH2AX at sites of double strand breaks (DSBs). Treatment of PCs with the Androgen Receptor (AR) antagonist Enzalutamide (ENZ) did not suppress DNA-damage-induced HOXB13 acetylation. In contrast, HOXB13 depletion or loss of acetylation overcame resistance of PC cells to ENZ and synergized with IR. HOXB13K13A mutants show diminished replication fork progression, impaired G2/M arrest with significant cell death following DNA damage. Mechanistically, we found that amino terminus regulates HOXB13 nuclear puncta formation that is essential for proper DNA damage response. Therefore, targeting HOXB13 acetylation with CBP/p300 inhibitors in combination with DNA damaging therapy may be an effective strategy to overcome anti-androgen resistance of PCs.
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Affiliation(s)
- Duy T. Nguyen
- Division of Urologic Surgery, Department of Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
- Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224, USA
| | - Urvashi Mahajan
- Division of Urologic Surgery, Department of Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
- A.T. Still University of Health Sciences, Kirksville, MO 63501, USA
| | - Duminduni Hewa Angappulige
- Division of Urologic Surgery, Department of Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Aashna Doshi
- Division of Urologic Surgery, Department of Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Nupam P. Mahajan
- Division of Urologic Surgery, Department of Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Kiran Mahajan
- Division of Urologic Surgery, Department of Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
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4
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Elango R, Nilavar N, Li AG, Duffey EE, Jiang Y, Nguyen D, Abakir A, Willis NA, Houseley J, Scully R. Two-ended recombination at a Flp-nickase-broken replication fork. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.10.588130. [PMID: 38645103 PMCID: PMC11030319 DOI: 10.1101/2024.04.10.588130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Collision of a replication fork with a DNA nick is thought to generate a one-ended break, fostering genomic instability. Collision of the opposing converging fork with the nick could, in principle, form a second DNA end, enabling conservative repair by homologous recombination (HR). To study mechanisms of nickase-induced HR, we developed the Flp recombinase "step arrest" nickase in mammalian cells. Flp-nickase-induced HR entails two-ended, BRCA2/RAD51-dependent short tract gene conversion (STGC), BRCA2/RAD51-independent long tract gene conversion, and discoordinated two-ended invasions. HR induced by a replication-independent break and by the Flp-nickase differ in their dependence on BRCA1 . To determine the origin of the second DNA end during Flp-nickase-induced STGC, we blocked the opposing fork using a site-specific Tus/ Ter replication fork barrier. Flp-nickase-induced STGC remained robust and two-ended. Thus, collision of a single replication fork with a Flp-nick can trigger two-ended HR, possibly reflecting replicative bypass of lagging strand nicks. This response may limit genomic instability during replication of a nicked DNA template.
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5
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Vontalge EJ, Kavlashvili T, Dahmen SN, Cranford MT, Dewar JM. Control of DNA replication in vitro using a reversible replication barrier. Nat Protoc 2024:10.1038/s41596-024-00977-1. [PMID: 38594502 DOI: 10.1038/s41596-024-00977-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 01/19/2024] [Indexed: 04/11/2024]
Abstract
A major obstacle to studying DNA replication is that it involves asynchronous and highly delocalized events. A reversible replication barrier overcomes this limitation and allows replication fork movement to be synchronized and localized, facilitating the study of replication fork function and replication coupled repair. Here we provide details on establishing a reversible replication barrier in vitro and using it to monitor different aspects of DNA replication. DNA template containing an array of lac operator (lacO) sequences is first bound to purified lac repressor (LacR). This substrate is then replicated in vitro using a biochemical replication system, which results in replication forks stalled on either side of the LacR array regardless of when or where they arise. Once replication forks are synchronized at the barrier, isopropyl-β-D-thiogalactopyranoside can be added to disrupt LacR binding so that replication forks synchronously resume synthesis. We describe how this approach can be employed to control replication fork elongation, termination, stalling and uncoupling, as well as assays that can be used to monitor these processes. We also explain how this approach can be adapted to control whether replication forks encounter a DNA lesion on the leading or lagging strand template and whether a converging fork is present. The required reagents can be prepared in 1-2 weeks and experiments using this approach are typically performed over 1-3 d. The main requirements for utilizing the LacR replication barrier are basic biochemical expertise and access to an in vitro system to study DNA replication. Investigators should also be trained in working with radioactive materials.
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Affiliation(s)
- Emma J Vontalge
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Tamar Kavlashvili
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Steven N Dahmen
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Matthew T Cranford
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - James M Dewar
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.
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6
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Cameron G, Gruszka D, Xie S, Kaya Ç, Nasmyth KA, Srinivasan M, Yardimci H. Sister chromatid cohesion establishment during DNA replication termination. Science 2024; 384:119-124. [PMID: 38484038 PMCID: PMC7615807 DOI: 10.1126/science.adf0224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 02/27/2024] [Indexed: 04/06/2024]
Abstract
Newly copied sister chromatids are tethered together by the cohesin complex, but how sister chromatid cohesion coordinates with DNA replication is poorly understood. Prevailing models suggest that cohesin complexes, bound to DNA before replication, remain behind the advancing replication fork to keep sister chromatids together. By visualizing single replication forks colliding with preloaded cohesin complexes, we find that the replisome instead pushes cohesin to where a converging replisome is met. Whereas the converging replisomes are removed during DNA replication termination, cohesin remains on nascent DNA and provides cohesion. Additionally, we show that CMG (CDC45-MCM2-7-GINS) helicase disassembly during replication termination is vital for proper cohesion in budding yeast. Together, our results support a model wherein sister chromatid cohesion is established during DNA replication termination.
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Affiliation(s)
| | | | - Sherry Xie
- The Francis Crick Institute; London, United Kingdom
| | - Çağla Kaya
- The Francis Crick Institute; London, United Kingdom
| | - Kim A Nasmyth
- Department of Biochemistry, University of Oxford; Oxford, United Kingdom
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7
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Piguet B, Houseley J. Transcription as source of genetic heterogeneity in budding yeast. Yeast 2024; 41:171-185. [PMID: 38196235 DOI: 10.1002/yea.3926] [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: 10/07/2023] [Revised: 12/10/2023] [Accepted: 12/20/2023] [Indexed: 01/11/2024] Open
Abstract
Transcription presents challenges to genome stability both directly, by altering genome topology and exposing single-stranded DNA to chemical insults and nucleases, and indirectly by introducing obstacles to the DNA replication machinery. Such obstacles include the RNA polymerase holoenzyme itself, DNA-bound regulatory factors, G-quadruplexes and RNA-DNA hybrid structures known as R-loops. Here, we review the detrimental impacts of transcription on genome stability in budding yeast, as well as the mitigating effects of transcription-coupled nucleotide excision repair and of systems that maintain DNA replication fork processivity and integrity. Interactions between DNA replication and transcription have particular potential to induce mutation and structural variation, but we conclude that such interactions must have only minor effects on DNA replication by the replisome with little if any direct mutagenic outcome. However, transcription can significantly impair the fidelity of replication fork rescue mechanisms, particularly Break Induced Replication, which is used to restart collapsed replication forks when other means fail. This leads to de novo mutations, structural variation and extrachromosomal circular DNA formation that contribute to genetic heterogeneity, but only under particular conditions and in particular genetic contexts, ensuring that the bulk of the genome remains extremely stable despite the seemingly frequent interactions between transcription and DNA replication.
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8
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Jones RM, Reynolds-Winczura A, Gambus A. A Decade of Discovery-Eukaryotic Replisome Disassembly at Replication Termination. BIOLOGY 2024; 13:233. [PMID: 38666845 PMCID: PMC11048390 DOI: 10.3390/biology13040233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024]
Abstract
The eukaryotic replicative helicase (CMG complex) is assembled during DNA replication initiation in a highly regulated manner, which is described in depth by other manuscripts in this Issue. During DNA replication, the replicative helicase moves through the chromatin, unwinding DNA and facilitating nascent DNA synthesis by polymerases. Once the duplication of a replicon is complete, the CMG helicase and the remaining components of the replisome need to be removed from the chromatin. Research carried out over the last ten years has produced a breakthrough in our understanding, revealing that replication termination, and more specifically replisome disassembly, is indeed a highly regulated process. This review brings together our current understanding of these processes and highlights elements of the mechanism that are conserved or have undergone divergence throughout evolution. Finally, we discuss events beyond the classic termination of DNA replication in S-phase and go over the known mechanisms of replicative helicase removal from chromatin in these particular situations.
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Affiliation(s)
- Rebecca M. Jones
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham B15 2TT, UK; (R.M.J.); (A.R.-W.)
- School of Biosciences, Aston University, Birmingham B4 7ET, UK
| | - Alicja Reynolds-Winczura
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham B15 2TT, UK; (R.M.J.); (A.R.-W.)
| | - Agnieszka Gambus
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham B15 2TT, UK; (R.M.J.); (A.R.-W.)
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9
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Peng Y, Bryan C, Yang K. Mass Spectrometry Evidence for Forming Schiff Base 3'-DNA-Histone Cross-Links from Abasic Sites in Vitro and in Human Cells. Chem Res Toxicol 2024; 37:216-219. [PMID: 38232149 DOI: 10.1021/acs.chemrestox.3c00377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Histones catalyze DNA strand incision at apurinic/apyrimidinic (AP) sites accompanied by the formation of reversible but long-lived DNA-protein cross-links at 3'-termini (3'-histone-DPCs). However, the chemical structures of 3'-histone-DPCs are not well characterized, and whether they are formed in cells is uncertain. In this study, we developed a liquid chromatography with tandem mass spectrometry workflow to characterize DPCs produced from the reaction of histones with AP sites and wish to report evidence that histones cross-link to incised AP sites via Schiff bases. We also demonstrated for the first time that 3'-histone-DPCs are produced endogenously in human embryonic kidney 293T cells.
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Affiliation(s)
- Ying Peng
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Cameron Bryan
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Kun Yang
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
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10
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van de Kooij B, Schreuder A, Pavani R, Garzero V, Uruci S, Wendel TJ, van Hoeck A, San Martin Alonso M, Everts M, Koerse D, Callen E, Boom J, Mei H, Cuppen E, Luijsterburg MS, van Vugt MATM, Nussenzweig A, van Attikum H, Noordermeer SM. EXO1 protects BRCA1-deficient cells against toxic DNA lesions. Mol Cell 2024; 84:659-674.e7. [PMID: 38266640 DOI: 10.1016/j.molcel.2023.12.039] [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: 03/16/2023] [Revised: 10/14/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
Inactivating mutations in the BRCA1 and BRCA2 genes impair DNA double-strand break (DSB) repair by homologous recombination (HR), leading to chromosomal instability and cancer. Importantly, BRCA1/2 deficiency also causes therapeutically targetable vulnerabilities. Here, we identify the dependency on the end resection factor EXO1 as a key vulnerability of BRCA1-deficient cells. EXO1 deficiency generates poly(ADP-ribose)-decorated DNA lesions during S phase that associate with unresolved DSBs and genomic instability in BRCA1-deficient but not in wild-type or BRCA2-deficient cells. Our data indicate that BRCA1/EXO1 double-deficient cells accumulate DSBs due to impaired repair by single-strand annealing (SSA) on top of their HR defect. In contrast, BRCA2-deficient cells retain SSA activity in the absence of EXO1 and hence tolerate EXO1 loss. Consistent with a dependency on EXO1-mediated SSA, we find that BRCA1-mutated tumors show elevated EXO1 expression and increased SSA-associated genomic scars compared with BRCA1-proficient tumors. Overall, our findings uncover EXO1 as a promising therapeutic target for BRCA1-deficient tumors.
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Affiliation(s)
- Bert van de Kooij
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands; Department of Medical Oncology, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Anne Schreuder
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands; Oncode Institute, Utrecht 3521 AL, the Netherlands
| | - Raphael Pavani
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Veronica Garzero
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands; Oncode Institute, Utrecht 3521 AL, the Netherlands
| | - Sidrit Uruci
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands
| | - Tiemen J Wendel
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands; Oncode Institute, Utrecht 3521 AL, the Netherlands
| | - Arne van Hoeck
- Oncode Institute, Utrecht 3521 AL, the Netherlands; Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht 3584 CG, the Netherlands
| | - Marta San Martin Alonso
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands; Oncode Institute, Utrecht 3521 AL, the Netherlands
| | - Marieke Everts
- Department of Medical Oncology, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Dana Koerse
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jasper Boom
- Sequencing Analysis Support Core, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands
| | - Edwin Cuppen
- Oncode Institute, Utrecht 3521 AL, the Netherlands; Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht 3584 CG, the Netherlands; Hartwig Medical Foundation, Amsterdam 1098 XH, the Netherlands
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands.
| | - Sylvie M Noordermeer
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands; Oncode Institute, Utrecht 3521 AL, the Netherlands.
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11
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Ramírez Montero D, Liu Z, Dekker NH. De novo fabrication of custom-sequence plasmids for the synthesis of long DNA constructs with extrahelical features. Biophys J 2024; 123:31-41. [PMID: 37968907 PMCID: PMC10808024 DOI: 10.1016/j.bpj.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/06/2023] [Accepted: 11/13/2023] [Indexed: 11/17/2023] Open
Abstract
DNA constructs for single-molecule experiments often require specific sequences and/or extrahelical/noncanonical structures to study DNA-processing mechanisms. The precise introduction of such structures requires extensive control of the sequence of the initial DNA substrate. A commonly used substrate in the synthesis of DNA constructs is plasmid DNA. Nevertheless, the controlled introduction of specific sequences and extrahelical/noncanonical structures into plasmids often requires several rounds of cloning on pre-existing plasmids whose sequence one cannot fully control. Here, we describe a simple and efficient way to synthesize 10.1-kb plasmids de novo using synthetic gBlocks that provides full control of the sequence. Using these plasmids, we developed a 1.5-day protocol to assemble 10.1-kb linear DNA constructs with end and internal modifications. As a proof of principle, we synthesize two different DNA constructs with biotinylated ends and one or two internal 3' single-stranded DNA flaps, characterize them using single-molecule force and fluorescence spectroscopy, and functionally validate them by showing that the eukaryotic replicative helicase Cdc45/Mcm2-7/GINS (CMG) binds the 3' single-stranded DNA flap and translocates in the expected direction. We anticipate that our approach can be used to synthesize custom-sequence DNA constructs for a variety of force and fluorescence single-molecule spectroscopy experiments to interrogate DNA replication, DNA repair, and transcription.
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Affiliation(s)
- Daniel Ramírez Montero
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Zhaowei Liu
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
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12
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Caldecott KW. Causes and consequences of DNA single-strand breaks. Trends Biochem Sci 2024; 49:68-78. [PMID: 38040599 DOI: 10.1016/j.tibs.2023.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/20/2023] [Accepted: 11/03/2023] [Indexed: 12/03/2023]
Abstract
DNA single-strand breaks (SSBs) are among the most common lesions arising in human cells, with tens to hundreds of thousands arising in each cell, each day. Cells have efficient mechanisms for the sensing and repair of these ubiquitous DNA lesions, but the failure of these processes to rapidly remove SSBs can lead to a variety of pathogenic outcomes. The threat posed by unrepaired SSBs is illustrated by the existence of at least six genetic diseases in which SSB repair (SSBR) is defective, all of which are characterised by neurodevelopmental and/or neurodegenerative pathology. Here, I review current understanding of how SSBs arise and impact on critical molecular processes, such as DNA replication and gene transcription, and their links to human disease.
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Affiliation(s)
- Keith W Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK.
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13
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Golfier S, Quail T, Brugués J. Single-Molecule Approaches to Study DNA Condensation. Methods Mol Biol 2024; 2740:1-19. [PMID: 38393466 DOI: 10.1007/978-1-0716-3557-5_1] [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: 02/25/2024]
Abstract
Proteins drive genome compartmentalization across different length scales. While the identities of these proteins have been well-studied, the physical mechanisms that drive genome organization have remained largely elusive. Studying these mechanisms is challenging owing to a lack of methodologies to parametrize physical models in cellular contexts. Furthermore, because of the complex, entangled, and dense nature of chromatin, conventional live imaging approaches often lack the spatial resolution to dissect these principles. In this chapter, we will describe how to image the interactions of λ-DNA with proteins under purified and cytoplasmic conditions. First, we will outline how to prepare biotinylated DNA, functionalize coverslips with biotin-conjugated poly-ethylene glycol (PEG), and assemble DNA microchannels compatible for the imaging of protein-DNA interactions using total internal fluorescence microscopy. Then we will describe experimental methods to image protein-DNA interactions in vitro and DNA loop extrusion using Xenopus laevis egg extracts.
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Affiliation(s)
- Stefan Golfier
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
- B CUBE, Center for Molecular Bioengineering, TU Dresden, Dresden, Germany
| | - Thomas Quail
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
- EMBL Heidelberg, Cell Biology and Biophysics Unit, Heidelberg, Germany
| | - Jan Brugués
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.
- Center for Systems Biology Dresden, Dresden, Germany.
- Physics of Life, TU Dresden, Dresden, Germany.
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14
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Lewis JS, van Oijen AM, Spenkelink LM. Embracing Heterogeneity: Challenging the Paradigm of Replisomes as Deterministic Machines. Chem Rev 2023; 123:13419-13440. [PMID: 37971892 PMCID: PMC10790245 DOI: 10.1021/acs.chemrev.3c00436] [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: 06/25/2023] [Revised: 10/15/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023]
Abstract
The paradigm of cellular systems as deterministic machines has long guided our understanding of biology. Advancements in technology and methodology, however, have revealed a world of stochasticity, challenging the notion of determinism. Here, we explore the stochastic behavior of multi-protein complexes, using the DNA replication system (replisome) as a prime example. The faithful and timely copying of DNA depends on the simultaneous action of a large set of enzymes and scaffolding factors. This fundamental cellular process is underpinned by dynamic protein-nucleic acid assemblies that must transition between distinct conformations and compositional states. Traditionally viewed as a well-orchestrated molecular machine, recent experimental evidence has unveiled significant variability and heterogeneity in the replication process. In this review, we discuss recent advances in single-molecule approaches and single-particle cryo-EM, which have provided insights into the dynamic processes of DNA replication. We comment on the new challenges faced by structural biologists and biophysicists as they attempt to describe the dynamic cascade of events leading to replisome assembly, activation, and progression. The fundamental principles uncovered and yet to be discovered through the study of DNA replication will inform on similar operating principles for other multi-protein complexes.
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Affiliation(s)
- Jacob S. Lewis
- Macromolecular
Machines Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Antoine M. van Oijen
- Molecular
Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Lisanne M. Spenkelink
- Molecular
Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
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15
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Draxler A, Blaschke A, Binar J, Weber M, Haslacher M, Bartak V, Bragagna L, Mare G, Maqboul L, Klapp R, Herzog T, Széll M, Petrera A, Laky B, Wagner KH, Thell R. Age-related influence on DNA damage, proteomic inflammatory markers and oxidative stress in hospitalized COVID-19 patients compared to healthy controls. Redox Biol 2023; 67:102914. [PMID: 37832397 PMCID: PMC10585323 DOI: 10.1016/j.redox.2023.102914] [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: 07/06/2023] [Revised: 09/29/2023] [Accepted: 10/01/2023] [Indexed: 10/15/2023] Open
Abstract
COVID-19 infections are accompanied by adverse changes in inflammatory pathways that are also partly influenced by increased oxidative stress and might result in elevated DNA damage. The aim of this case-control study was to examine whether COVID-19 patients show differences in oxidative stress-related markers, unconjugated bilirubin (UCB), an inflammation panel and DNA damage compared to healthy, age-and sex-matched controls. The Comet assay with and without the treatment of formamidopyrimidine DNA glycosylase (FPG) and H2O2 challenge was used to detect DNA damage in whole blood. qPCR was applied for gene expression, UCB was analyzed via HPLC, targeted proteomics were applied using Olink® inflammation panel and various oxidative stress as well as clinical biochemistry markers were analyzed in plasma. Hospitalized COVID-19 patients (n = 48) demonstrated higher serum levels of 55 inflammatory proteins (p < 0.001), including hs-C-reactive protein levels (p < 0.05), compared to healthy controls (n = 48). Interestingly, significantly increased age-related DNA damage (%-DNA in tail) after formamidopyrimidine DNA glycosylase (FPG) treatment was measured in younger (n = 24, average age 55.7 years; p < 0.05) but not in older COVID-19 patients (n = 24, average age 83.5 years; p > 0.05). Although various oxidative stress markers were not altered (e.g., FRAP, malondialdehyde, p > 0.05), a significant increased ratio of oxidized to reduced glutathione was detected in COVID-19 patients compared to healthy controls (p < 0.05). UCB levels were significantly lower in individuals with COVID-19, especially in younger COVID-19 patients (p < 0.05). These results suggest that COVID-19 infections exert effects on DNA damage related to age in hospitalized COVID-19 patients that might be driven by changes in inflammatory pathways but are not altered by oxidative stress parameters.
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Affiliation(s)
- Agnes Draxler
- Department of Nutritional Sciences, University of Vienna, Austria; Vienna Doctoral School for Pharmaceutical, Nutritional and Sport Sciences (PhaNuSpo), University of Vienna, Josef Holaubek-Platz 2, 1090, Vienna, Austria.
| | | | - Jessica Binar
- Department of Nutritional Sciences, University of Vienna, Austria.
| | - Maria Weber
- Department of Nutritional Sciences, University of Vienna, Austria; Research Platform Active Ageing, University of Vienna, Austria.
| | | | - Viktoria Bartak
- Department of Nutritional Sciences, University of Vienna, Austria.
| | - Laura Bragagna
- Department of Nutritional Sciences, University of Vienna, Austria; Vienna Doctoral School for Pharmaceutical, Nutritional and Sport Sciences (PhaNuSpo), University of Vienna, Josef Holaubek-Platz 2, 1090, Vienna, Austria.
| | - George Mare
- Department of Nutritional Sciences, University of Vienna, Austria.
| | - Lina Maqboul
- Department of Nutritional Sciences, University of Vienna, Austria; Research Platform Active Ageing, University of Vienna, Austria.
| | - Rebecca Klapp
- Department of Nutritional Sciences, University of Vienna, Austria.
| | - Theresa Herzog
- Klinik Donaustadt, Emergency Department, Langobardenstraße 122, 1220, Vienna, Austria.
| | - Marton Széll
- Klinik Donaustadt, Emergency Department, Langobardenstraße 122, 1220, Vienna, Austria.
| | - Agnese Petrera
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Brenda Laky
- Medical University of Vienna, Austria; Austrian Society of Regenerative Medicine, Vienna, Austria.
| | - Karl-Heinz Wagner
- Department of Nutritional Sciences, University of Vienna, Austria; Research Platform Active Ageing, University of Vienna, Austria.
| | - Rainer Thell
- Medical University of Vienna, Austria; Klinik Donaustadt, Emergency Department, Langobardenstraße 122, 1220, Vienna, Austria.
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16
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Serrano‐Benitez A, Wells SE, Drummond‐Clarke L, Russo LC, Thomas JC, Leal GA, Farrow M, Edgerton JM, Balasubramanian S, Yang M, Frezza C, Gautam A, Brazina J, Burdova K, Hoch NC, Jackson SP, Caldecott KW. Unrepaired base excision repair intermediates in template DNA strands trigger replication fork collapse and PARP inhibitor sensitivity. EMBO J 2023; 42:e113190. [PMID: 37492888 PMCID: PMC10505916 DOI: 10.15252/embj.2022113190] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 05/17/2023] [Accepted: 07/07/2023] [Indexed: 07/27/2023] Open
Abstract
DNA single-strand breaks (SSBs) disrupt DNA replication and induce chromosome breakage. However, whether SSBs induce chromosome breakage when present behind replication forks or ahead of replication forks is unclear. To address this question, we exploited an exquisite sensitivity of SSB repair-defective human cells lacking PARP activity or XRCC1 to the thymidine analogue 5-chloro-2'-deoxyuridine (CldU). We show that incubation with CldU in these cells results in chromosome breakage, sister chromatid exchange, and cytotoxicity by a mechanism that depends on the S phase activity of uracil DNA glycosylase (UNG). Importantly, we show that CldU incorporation in one cell cycle is cytotoxic only during the following cell cycle, when it is present in template DNA. In agreement with this, while UNG induces SSBs both in nascent strands behind replication forks and in template strands ahead of replication forks, only the latter trigger fork collapse and chromosome breakage. Finally, we show that BRCA-defective cells are hypersensitive to CldU, either alone and/or in combination with PARP inhibitor, suggesting that CldU may have clinical utility.
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Affiliation(s)
- Almudena Serrano‐Benitez
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- The Wellcome and Cancer Research UK Gurdon Institute and Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Sophie E Wells
- Genome Damage and Stability Centre, School of Life SciencesUniversity of SussexFalmerUK
| | - Lylah Drummond‐Clarke
- Genome Damage and Stability Centre, School of Life SciencesUniversity of SussexFalmerUK
| | - Lilian C Russo
- Departament of Biochemistry, Chemistry InstituteUniversity of São PauloSão PauloBrazil
| | - John Christopher Thomas
- The Wellcome and Cancer Research UK Gurdon Institute and Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Giovanna A Leal
- Departament of Biochemistry, Chemistry InstituteUniversity of São PauloSão PauloBrazil
| | - Mark Farrow
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
| | | | - Shankar Balasubramanian
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Ming Yang
- CECAD Research Center, Faculty of MedicineUniversity Hospital CologneCologneGermany
| | - Christian Frezza
- CECAD Research Center, Faculty of MedicineUniversity Hospital CologneCologneGermany
| | - Amit Gautam
- Genome Damage and Stability Centre, School of Life SciencesUniversity of SussexFalmerUK
| | - Jan Brazina
- Genome Damage and Stability Centre, School of Life SciencesUniversity of SussexFalmerUK
| | - Kamila Burdova
- Genome Damage and Stability Centre, School of Life SciencesUniversity of SussexFalmerUK
| | - Nicolas C Hoch
- Departament of Biochemistry, Chemistry InstituteUniversity of São PauloSão PauloBrazil
| | - Stephen P Jackson
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- The Wellcome and Cancer Research UK Gurdon Institute and Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Keith W Caldecott
- Genome Damage and Stability Centre, School of Life SciencesUniversity of SussexFalmerUK
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17
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Ramírez Montero D, Sánchez H, van Veen E, van Laar T, Solano B, Diffley JFX, Dekker NH. Nucleotide binding halts diffusion of the eukaryotic replicative helicase during activation. Nat Commun 2023; 14:2082. [PMID: 37059705 PMCID: PMC10104875 DOI: 10.1038/s41467-023-37093-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/02/2023] [Indexed: 04/16/2023] Open
Abstract
The eukaryotic replicative helicase CMG centrally orchestrates the replisome and leads the way at the front of replication forks. Understanding the motion of CMG on the DNA is therefore key to our understanding of DNA replication. In vivo, CMG is assembled and activated through a cell-cycle-regulated mechanism involving 36 polypeptides that has been reconstituted from purified proteins in ensemble biochemical studies. Conversely, single-molecule studies of CMG motion have thus far relied on pre-formed CMG assembled through an unknown mechanism upon overexpression of individual constituents. Here, we report the activation of CMG fully reconstituted from purified yeast proteins and the quantification of its motion at the single-molecule level. We observe that CMG can move on DNA in two ways: by unidirectional translocation and by diffusion. We demonstrate that CMG preferentially exhibits unidirectional translocation in the presence of ATP, whereas it preferentially exhibits diffusive motion in the absence of ATP. We also demonstrate that nucleotide binding halts diffusive CMG independently of DNA melting. Taken together, our findings support a mechanism by which nucleotide binding allows newly assembled CMG to engage with the DNA within its central channel, halting its diffusion and facilitating the initial DNA melting required to initiate DNA replication.
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Affiliation(s)
- Daniel Ramírez Montero
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Humberto Sánchez
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Edo van Veen
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Theo van Laar
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Belén Solano
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - John F X Diffley
- Chromosome Replication Laboratory, Francis Crick Institute, London, UK.
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands.
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18
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Schindler N, Tonn M, Kellner V, Fung JJ, Lockhart A, Vydzhak O, Juretschke T, Möckel S, Beli P, Khmelinskii A, Luke B. Genetic requirements for repair of lesions caused by single genomic ribonucleotides in S phase. Nat Commun 2023; 14:1227. [PMID: 36869098 PMCID: PMC9984532 DOI: 10.1038/s41467-023-36866-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 02/21/2023] [Indexed: 03/05/2023] Open
Abstract
Single ribonucleoside monophosphates (rNMPs) are transiently present in eukaryotic genomes. The RNase H2-dependent ribonucleotide excision repair (RER) pathway ensures error-free rNMP removal. In some pathological conditions, rNMP removal is impaired. If these rNMPs hydrolyze during, or prior to, S phase, toxic single-ended double-strand breaks (seDSBs) can occur upon an encounter with replication forks. How such rNMP-derived seDSB lesions are repaired is unclear. We expressed a cell cycle phase restricted allele of RNase H2 to nick at rNMPs in S phase and study their repair. Although Top1 is dispensable, the RAD52 epistasis group and Rtt101Mms1-Mms22 dependent ubiquitylation of histone H3 become essential for rNMP-derived lesion tolerance. Consistently, loss of Rtt101Mms1-Mms22 combined with RNase H2 dysfunction leads to compromised cellular fitness. We refer to this repair pathway as nick lesion repair (NLR). The NLR genetic network may have important implications in the context of human pathologies.
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Affiliation(s)
- Natalie Schindler
- Johannes Gutenberg University Mainz, Institute for Developmental Neurology (IDN), Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany.
| | - Matthias Tonn
- Johannes Gutenberg University Mainz, Institute for Developmental Neurology (IDN), Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany
| | - Vanessa Kellner
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.,Department of Biology, New York University, New York, NY, USA
| | - Jia Jun Fung
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Arianna Lockhart
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Olga Vydzhak
- Johannes Gutenberg University Mainz, Institute for Developmental Neurology (IDN), Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany
| | - Thomas Juretschke
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Stefanie Möckel
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Anton Khmelinskii
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Brian Luke
- Johannes Gutenberg University Mainz, Institute for Developmental Neurology (IDN), Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany. .,Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
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19
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van de Kooij B, Schreuder A, Pavani RS, Garzero V, Van Hoeck A, San Martin Alonso M, Koerse D, Wendel TJ, Callen E, Boom J, Mei H, Cuppen E, Nussenzweig A, van Attikum H, Noordermeer SM. EXO1-mediated DNA repair by single-strand annealing is essential for BRCA1-deficient cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529205. [PMID: 37720033 PMCID: PMC10503826 DOI: 10.1101/2023.02.24.529205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Deficiency for the repair of DNA double-strand breaks (DSBs) via homologous recombination (HR) leads to chromosomal instability and diseases such as cancer. Yet, defective HR also results in vulnerabilities that can be exploited for targeted therapy. Here, we identify such a vulnerability and show that BRCA1-deficient cells are dependent on the long-range end-resection factor EXO1 for survival. EXO1 loss results in DNA replication-induced lesions decorated by poly(ADP-ribose)-chains. In cells that lack both BRCA1 and EXO1, this is accompanied by unresolved DSBs due to impaired single-strand annealing (SSA), a DSB repair process that requires the activity of both proteins. In contrast, BRCA2-deficient cells have increased SSA, also in the absence of EXO1, and hence are not dependent on EXO1 for survival. In agreement with our mechanistic data, BRCA1-mutated tumours have elevated EXO1 expression and contain more genomic signatures of SSA compared to BRCA1-proficient tumours. Collectively, our data indicate that EXO1 is a promising novel target for treatment of BRCA1-deficient tumours.
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20
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Kavlashvili T, Liu W, Mohamed TM, Cortez D, Dewar JM. Replication fork uncoupling causes nascent strand degradation and fork reversal. Nat Struct Mol Biol 2023; 30:115-124. [PMID: 36593312 PMCID: PMC9868089 DOI: 10.1038/s41594-022-00871-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 10/14/2022] [Indexed: 01/03/2023]
Abstract
Genotoxins cause nascent strand degradation (NSD) and fork reversal during DNA replication. NSD and fork reversal are crucial for genome stability and are exploited by chemotherapeutic approaches. However, it is unclear how NSD and fork reversal are triggered. Additionally, the fate of the replicative helicase during these processes is unknown. We developed a biochemical approach to study synchronous, localized NSD and fork reversal using Xenopus egg extracts and validated this approach with experiments in human cells. We show that replication fork uncoupling stimulates NSD of both nascent strands and progressive conversion of uncoupled forks to reversed forks. Notably, the replicative helicase remains bound during NSD and fork reversal. Unexpectedly, NSD occurs before and after fork reversal, indicating that multiple degradation steps take place. Overall, our data show that uncoupling causes NSD and fork reversal and elucidate key events that precede fork reversal.
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Affiliation(s)
- Tamar Kavlashvili
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Wenpeng Liu
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Taha M Mohamed
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - James M Dewar
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.
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21
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Liu SC, Feng YL, Sun XN, Chen RD, Liu Q, Xiao JJ, Zhang JN, Huang ZC, Xiang JF, Chen GQ, Yang Y, Lou C, Li HD, Cai Z, Xu SM, Lin H, Xie AY. Target residence of Cas9-sgRNA influences DNA double-strand break repair pathway choices in CRISPR/Cas9 genome editing. Genome Biol 2022; 23:165. [PMID: 35915475 PMCID: PMC9341079 DOI: 10.1186/s13059-022-02736-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 07/22/2022] [Indexed: 12/05/2022] Open
Abstract
Background Due to post-cleavage residence of the Cas9-sgRNA complex at its target, Cas9-induced DNA double-strand breaks (DSBs) have to be exposed to engage DSB repair pathways. Target interaction of Cas9-sgRNA determines its target binding affinity and modulates its post-cleavage target residence duration and exposure of Cas9-induced DSBs. This exposure, via different mechanisms, may initiate variable DNA damage responses, influencing DSB repair pathway choices and contributing to mutational heterogeneity in genome editing. However, this regulation of DSB repair pathway choices is poorly understood. Results In repair of Cas9-induced DSBs, repair pathway choices vary widely at different target sites and classical nonhomologous end joining (c-NHEJ) is not even engaged at some sites. In mouse embryonic stem cells, weakening the target interaction of Cas9-sgRNA promotes bias towards c-NHEJ and increases target dissociation and reduces target residence of Cas9-sgRNAs in vitro. As an important strategy for enhancing homology-directed repair, inactivation of c-NHEJ aggravates off-target activities of Cas9-sgRNA due to its weak interaction with off-target sites. By dislodging Cas9-sgRNA from its cleaved targets, DNA replication alters DSB end configurations and suppresses c-NHEJ in favor of other repair pathways, whereas transcription has little effect on c-NHEJ engagement. Dissociation of Cas9-sgRNA from its cleaved target by DNA replication may generate three-ended DSBs, resulting in palindromic fusion of sister chromatids, a potential source for CRISPR/Cas9-induced on-target chromosomal rearrangements. Conclusions Target residence of Cas9-sgRNA modulates DSB repair pathway choices likely through varying dissociation of Cas9-sgRNA from cleaved DNA, thus widening on-target and off-target mutational spectra in CRISPR/Cas9 genome editing. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02736-5.
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22
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Reusswig KU, Bittmann J, Peritore M, Courtes M, Pardo B, Wierer M, Mann M, Pfander B. Unscheduled DNA replication in G1 causes genome instability and damage signatures indicative of replication collisions. Nat Commun 2022; 13:7014. [PMID: 36400763 PMCID: PMC9674678 DOI: 10.1038/s41467-022-34379-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/24/2022] [Indexed: 11/19/2022] Open
Abstract
DNA replicates once per cell cycle. Interfering with the regulation of DNA replication initiation generates genome instability through over-replication and has been linked to early stages of cancer development. Here, we engineer genetic systems in budding yeast to induce unscheduled replication in a G1-like cell cycle state. Unscheduled G1 replication initiates at canonical S-phase origins. We quantifiy the composition of replisomes in G1- and S-phase and identified firing factors, polymerase α, and histone supply as factors that limit replication outside S-phase. G1 replication per se does not trigger cellular checkpoints. Subsequent replication during S-phase, however, results in over-replication and leads to chromosome breaks and chromosome-wide, strand-biased occurrence of RPA-bound single-stranded DNA, indicating head-to-tail replication collisions as a key mechanism generating genome instability upon G1 replication. Low-level, sporadic induction of G1 replication induces an identical response, indicating findings from synthetic systems are applicable to naturally occurring scenarios of unscheduled replication initiation.
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Affiliation(s)
- Karl-Uwe Reusswig
- grid.418615.f0000 0004 0491 845XDNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany ,grid.38142.3c000000041936754XPresent Address: Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA ,grid.65499.370000 0001 2106 9910Present Address: Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215 USA
| | - Julia Bittmann
- grid.418615.f0000 0004 0491 845XDNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Martina Peritore
- grid.418615.f0000 0004 0491 845XDNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany ,grid.7551.60000 0000 8983 7915Present Address: Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), 51147 Cologne, Germany
| | - Mathilde Courtes
- grid.433120.7Institut de Génétique Humaine (IGH), Université de Montpellier – Centre National de la Recherche Scientifique, 34396 Montpellier, France
| | - Benjamin Pardo
- grid.433120.7Institut de Génétique Humaine (IGH), Université de Montpellier – Centre National de la Recherche Scientifique, 34396 Montpellier, France
| | - Michael Wierer
- grid.418615.f0000 0004 0491 845XProteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany ,grid.5254.60000 0001 0674 042XPresent Address: Proteomics Research Infrastructure, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Matthias Mann
- grid.418615.f0000 0004 0491 845XProteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Boris Pfander
- grid.418615.f0000 0004 0491 845XDNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany ,grid.7551.60000 0000 8983 7915Present Address: Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), 51147 Cologne, Germany ,grid.6190.e0000 0000 8580 3777Present Address: Genome Maintenance Mechanisms in Health and Disease, Institute of Genome Stability in Ageing and Disease, CECAD Research Center, University of Cologne, 50931 Cologne, Germany
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23
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Li K, Liu Y, Ding Y, Zhang Z, Feng J, Hu J, Chen J, Lian Z, Chen Y, Hu K, Chen Z, Cai Z, Liu M, Pang X. BCL6 is regulated by the MAPK/ELK1 axis and promotes KRAS-driven lung cancer. J Clin Invest 2022; 132:161308. [PMID: 36377663 PMCID: PMC9663163 DOI: 10.1172/jci161308] [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: 04/25/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Mutational activation of KRAS is a common oncogenic event in lung cancer, yet effective therapies are still lacking. Here, we identify B cell lymphoma 6 (BCL6) as a lynchpin in KRAS-driven lung cancer. BCL6 expression was increased upon KRAS activation in lung tumor tissue in mice and was positively correlated with the expression of KRAS-GTP, the active form of KRAS, in various human cancer cell lines. Moreover, BCL6 was highly expressed in human KRAS-mutant lung adenocarcinomas and was associated with poor patient survival. Mechanistically, the MAPK/ERK/ELK1 signaling axis downstream of mutant KRAS directly regulated BCL6 expression. BCL6 maintained the global expression of prereplication complex components; therefore, BCL6 inhibition induced stalling of the replication fork, leading to DNA damage and growth arrest in KRAS-mutant lung cancer cells. Importantly, BCL6-specific knockout in lungs significantly reduced the tumor burden and mortality in the LSL-KrasG12D/+ lung cancer mouse model. Likewise, pharmacological inhibition of BCL6 significantly impeded the growth of KRAS-mutant lung cancer cells both in vitro and in vivo. In summary, our findings reveal a crucial role of BCL6 in promoting KRAS-addicted lung cancer and suggest BCL6 as a therapeutic target for the treatment of this intractable disease.
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Affiliation(s)
- Kun Li
- Changning Maternity and Infant Health Hospital and Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences and
- Joint Translational Science and Technology Research Institute, East China Normal University, Shanghai, China
- Cancer Institute, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yanan Liu
- Changning Maternity and Infant Health Hospital and Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences and
| | - Yi Ding
- Changning Maternity and Infant Health Hospital and Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences and
| | - Zhengwei Zhang
- Changning Maternity and Infant Health Hospital and Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences and
| | - Juanjuan Feng
- Changning Maternity and Infant Health Hospital and Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences and
| | - Jiaxin Hu
- Changning Maternity and Infant Health Hospital and Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences and
| | - Jiwei Chen
- Changning Maternity and Infant Health Hospital and Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences and
| | - Zhengke Lian
- Changning Maternity and Infant Health Hospital and Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences and
| | - Yiliang Chen
- Department of Biochemistry and Molecular Biology, School of Medicine, Tongji University, Shanghai, China
| | - Kewen Hu
- Cancer Institute, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhi Chen
- Medical Research Institute, Wuhan University, Wuhan, China
| | - Zhenyu Cai
- Department of Biochemistry and Molecular Biology, School of Medicine, Tongji University, Shanghai, China
| | - Mingyao Liu
- Changning Maternity and Infant Health Hospital and Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences and
| | - Xiufeng Pang
- Changning Maternity and Infant Health Hospital and Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences and
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24
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Kochenova OV, Mukkavalli S, Raman M, Walter JC. Cooperative assembly of p97 complexes involved in replication termination. Nat Commun 2022; 13:6591. [PMID: 36329031 PMCID: PMC9633789 DOI: 10.1038/s41467-022-34210-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
The p97 ATPase extracts polyubiquitylated proteins from diverse cellular structures in preparation for destruction by the proteasome. p97 functions with Ufd1-Npl4 and a variety of UBA-UBX co-factors, but how p97 complexes assemble on ubiquitylated substrates is unclear. To address this, we investigated how p97 disassembles the CMG helicase after it is ubiquitylated during replication termination. We show that p97Ufd1-Npl4 recruitment to CMG requires the UBA-UBX protein Ubxn7, and conversely, stable Ubxn7 binding to CMG requires p97Ufd1-Npl4. This cooperative assembly involves interactions between Ubxn7, p97, Ufd1-Npl4, and ubiquitin. Another p97 co-factor, Faf1, partially compensates for the loss of Ubxn7. Surprisingly, p97Ufd1-Npl4-Ubxn7 and p97Ufd1-Npl4-Faf1 also assemble cooperatively on unanchored ubiquitin chains. We propose that cooperative and substrate-independent recognition of ubiquitin chains allows p97 to recognize an unlimited number of polyubiquitylated proteins while avoiding the formation of partial, inactive complexes.
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Affiliation(s)
- Olga V Kochenova
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Sirisha Mukkavalli
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Malavika Raman
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA, 02115, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
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25
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Jiang Y. Contribution of Microhomology to Genome Instability: Connection between DNA Repair and Replication Stress. Int J Mol Sci 2022; 23:12937. [PMID: 36361724 PMCID: PMC9657218 DOI: 10.3390/ijms232112937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/23/2022] [Accepted: 10/23/2022] [Indexed: 11/23/2023] Open
Abstract
Microhomology-mediated end joining (MMEJ) is a highly mutagenic pathway to repair double-strand breaks (DSBs). MMEJ was thought to be a backup pathway of homologous recombination (HR) and canonical nonhomologous end joining (C-NHEJ). However, it attracts more attention in cancer research due to its special function of microhomology in many different aspects of cancer. In particular, it is initiated with DNA end resection and upregulated in homologous recombination-deficient cancers. In this review, I summarize the following: (1) the recent findings and contributions of MMEJ to genome instability, including phenotypes relevant to MMEJ; (2) the interaction between MMEJ and other DNA repair pathways; (3) the proposed mechanistic model of MMEJ in DNA DSB repair and a new connection with microhomology-mediated break-induced replication (MMBIR); and (4) the potential clinical application by targeting MMEJ based on synthetic lethality for cancer therapy.
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Affiliation(s)
- Yuning Jiang
- Department of Radiation Oncology, University of Virginia, Charlottesville, VA 22903, USA
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26
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Quaas CE, Lin B, Long DT. Transcription suppression is mediated by the HDAC1-Sin3 complex in Xenopus nucleoplasmic extract. J Biol Chem 2022; 298:102578. [PMID: 36220390 PMCID: PMC9650048 DOI: 10.1016/j.jbc.2022.102578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 09/24/2022] [Accepted: 10/05/2022] [Indexed: 11/09/2022] Open
Abstract
Modification of histones provides a dynamic mechanism to regulate chromatin structure and access to DNA. Histone acetylation, in particular, plays a prominent role in controlling the interaction between DNA, histones, and other chromatin-associated proteins. Defects in histone acetylation patterns interfere with normal gene expression and underlie a wide range of human diseases. Here, we utilize Xenopus egg extracts to investigate how changes in histone acetylation influence transcription of a defined gene construct. We show that inhibition of histone deacetylase 1 and 2 (HDAC1/2) specifically counteracts transcription suppression by preventing chromatin compaction and deacetylation of histone residues H4K5 and H4K8. Acetylation of these sites supports binding of the chromatin reader and transcription regulator BRD4. We also identify HDAC1 as the primary driver of transcription suppression and show that this activity is mediated through the Sin3 histone deacetylase complex. These findings highlight functional differences between HDAC1 and HDAC2, which are often considered to be functionally redundant, and provide additional molecular context for their activity.
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27
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Li J, Zhao H, McMahon A, Yan S. APE1 assembles biomolecular condensates to promote the ATR-Chk1 DNA damage response in nucleolus. Nucleic Acids Res 2022; 50:10503-10525. [PMID: 36200829 PMCID: PMC9561277 DOI: 10.1093/nar/gkac853] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/14/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
Multifunctional protein APE1/APEX1/HAP1/Ref-1 (designated as APE1) plays important roles in nuclease-mediated DNA repair and redox regulation in transcription. However, it is unclear how APE1 regulates the DNA damage response (DDR) pathways. Here we show that siRNA-mediated APE1-knockdown or APE1 inhibitor treatment attenuates the ATR–Chk1 DDR under stress conditions in multiple immortalized cell lines. Congruently, APE1 overexpression (APE1-OE) activates the ATR DDR under unperturbed conditions, which is independent of APE1 nuclease and redox functions. Structural and functional analysis reveals a direct requirement of the extreme N-terminal motif within APE1 in the assembly of distinct biomolecular condensates in vitro and DNA/RNA-independent activation of the ATR DDR. Overexpressed APE1 co-localizes with nucleolar NPM1 and assembles biomolecular condensates in nucleoli in cancer but not non-malignant cells, which recruits ATR and activator molecules TopBP1 and ETAA1. APE1 protein can directly activate ATR to phosphorylate its substrate Chk1 in in vitro kinase assays. W119R mutant of APE1 is deficient in nucleolar condensation, and is incapable of activating nucleolar ATR DDR in cells and ATR kinase in vitro. APE1-OE-induced nucleolar ATR DDR activation leads to compromised ribosomal RNA transcription and reduced cell viability. Taken together, we propose distinct mechanisms by which APE1 regulates ATR DDR pathways.
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Affiliation(s)
- Jia Li
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Haichao Zhao
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Anne McMahon
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Shan Yan
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.,School of Data Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.,Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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28
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Feng YL, Liu Q, Chen RD, Liu SC, Huang ZC, Liu KM, Yang XY, Xie AY. DNA nicks induce mutational signatures associated with BRCA1 deficiency. Nat Commun 2022; 13:4285. [PMID: 35879372 PMCID: PMC9314409 DOI: 10.1038/s41467-022-32011-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
Analysis of human cancer genome sequences has revealed specific mutational signatures associated with BRCA1-deficient tumors, but the underlying mechanisms remain poorly understood. Here, we show that one-ended DNA double strand breaks (DSBs) converted from CRISPR/Cas9-induced nicks by DNA replication, not two-ended DSBs, cause more characteristic chromosomal aberrations and micronuclei in Brca1-deficient cells than in wild-type cells. BRCA1 is required for efficient homologous recombination of these nick-converted DSBs and suppresses bias towards long tract gene conversion and tandem duplication (TD) mediated by two-round strand invasion in a replication strand asymmetry. However, aberrant repair of these nick-converted one-ended DSBs, not that of two-ended DSBs in Brca1-deficient cells, generates mutational signatures such as small indels with microhomology (MH) at the junctions, translocations and small MH-mediated TDs, resembling those in BRCA1-deficient tumors. These results suggest a major contribution of DNA nicks to mutational signatures associated with BRCA1 deficiency in cancer and the underlying mechanisms.
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Affiliation(s)
- Yi-Li Feng
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310019, Hangzhou, Zhejiang, P. R. China. .,Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 310029, Hangzhou, Zhejiang, P. R. China.
| | - Qian Liu
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310019, Hangzhou, Zhejiang, P. R. China.,Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 310029, Hangzhou, Zhejiang, P. R. China
| | - Ruo-Dan Chen
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310019, Hangzhou, Zhejiang, P. R. China.,Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 310029, Hangzhou, Zhejiang, P. R. China
| | - Si-Cheng Liu
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310019, Hangzhou, Zhejiang, P. R. China.,Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 310029, Hangzhou, Zhejiang, P. R. China
| | - Zhi-Cheng Huang
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310019, Hangzhou, Zhejiang, P. R. China.,Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 310029, Hangzhou, Zhejiang, P. R. China
| | - Kun-Ming Liu
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310019, Hangzhou, Zhejiang, P. R. China.,Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 310029, Hangzhou, Zhejiang, P. R. China
| | - Xiao-Ying Yang
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310019, Hangzhou, Zhejiang, P. R. China.,Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 310029, Hangzhou, Zhejiang, P. R. China
| | - An-Yong Xie
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310019, Hangzhou, Zhejiang, P. R. China. .,Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 310029, Hangzhou, Zhejiang, P. R. China.
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29
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Saxena S, Zou L. Hallmarks of DNA replication stress. Mol Cell 2022; 82:2298-2314. [PMID: 35714587 DOI: 10.1016/j.molcel.2022.05.004] [Citation(s) in RCA: 101] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/15/2022] [Accepted: 05/04/2022] [Indexed: 12/12/2022]
Abstract
Faithful DNA replication is critical for the maintenance of genomic integrity. Although DNA replication machinery is highly accurate, the process of DNA replication is constantly challenged by DNA damage and other intrinsic and extrinsic stresses throughout the genome. A variety of cellular stresses interfering with DNA replication, which are collectively termed replication stress, pose a threat to genomic stability in both normal and cancer cells. To cope with replication stress and maintain genomic stability, cells have evolved a complex network of cellular responses to alleviate and tolerate replication problems. This review will focus on the major sources of replication stress, the impacts of replication stress in cells, and the assays to detect replication stress, offering an overview of the hallmarks of DNA replication stress.
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Affiliation(s)
- Sneha Saxena
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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30
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Van Ravenstein SX, Mehta KP, Kavlashvili T, Byl JAW, Zhao R, Osheroff N, Cortez D, Dewar JM. Topoisomerase II poisons inhibit vertebrate DNA replication through distinct mechanisms. EMBO J 2022; 41:e110632. [PMID: 35578785 PMCID: PMC9194788 DOI: 10.15252/embj.2022110632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 11/09/2022] Open
Abstract
Topoisomerase II (TOP2) unlinks chromosomes during vertebrate DNA replication. TOP2 "poisons" are widely used chemotherapeutics that stabilize TOP2 complexes on DNA, leading to cytotoxic DNA breaks. However, it is unclear how these drugs affect DNA replication, which is a major target of TOP2 poisons. Using Xenopus egg extracts, we show that the TOP2 poisons etoposide and doxorubicin both inhibit DNA replication through different mechanisms. Etoposide induces TOP2-dependent DNA breaks and TOP2-dependent fork stalling by trapping TOP2 behind replication forks. In contrast, doxorubicin does not lead to appreciable break formation and instead intercalates into parental DNA to stall replication forks independently of TOP2. In human cells, etoposide stalls forks in a TOP2-dependent manner, while doxorubicin stalls forks independently of TOP2. However, both drugs exhibit TOP2-dependent cytotoxicity. Thus, etoposide and doxorubicin inhibit DNA replication through distinct mechanisms despite shared genetic requirements for cytotoxicity.
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Affiliation(s)
| | - Kavi P Mehta
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Tamar Kavlashvili
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jo Ann W Byl
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Runxiang Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.,Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, TN, USA
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - James M Dewar
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
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31
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Dahiya R, Hu Q, Ly P. Mechanistic origins of diverse genome rearrangements in cancer. Semin Cell Dev Biol 2022; 123:100-109. [PMID: 33824062 PMCID: PMC8487437 DOI: 10.1016/j.semcdb.2021.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/08/2021] [Indexed: 12/14/2022]
Abstract
Cancer genomes frequently harbor structural chromosomal rearrangements that disrupt the linear DNA sequence order and copy number. To date, diverse classes of structural variants have been identified across multiple cancer types. These aberrations span a wide spectrum of complexity, ranging from simple translocations to intricate patterns of rearrangements involving multiple chromosomes. Although most somatic rearrangements are acquired gradually throughout tumorigenesis, recent interrogation of cancer genomes have uncovered novel categories of complex rearrangements that arises rapidly through a one-off catastrophic event, including chromothripsis and chromoplexy. Here we review the cellular and molecular mechanisms contributing to the formation of diverse structural rearrangement classes during cancer development. Genotoxic stress from a myriad of extrinsic and intrinsic sources can trigger DNA double-strand breaks that are subjected to DNA repair with potentially mutagenic outcomes. We also highlight how aberrant nuclear structures generated through mitotic cell division errors, such as rupture-prone micronuclei and chromosome bridges, can instigate massive DNA damage and the formation of complex rearrangements in cancer genomes.
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Affiliation(s)
- Rashmi Dahiya
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Qing Hu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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32
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Claussin C, Vazquez J, Whitehouse I. Single-molecule mapping of replisome progression. Mol Cell 2022; 82:1372-1382.e4. [PMID: 35240057 PMCID: PMC8995386 DOI: 10.1016/j.molcel.2022.02.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/22/2021] [Accepted: 02/02/2022] [Indexed: 10/19/2022]
Abstract
Fundamental aspects of DNA replication, such as the anatomy of replication stall sites, how replisomes are influenced by gene transcription, and whether the progression of sister replisomes is coordinated, are poorly understood. Available techniques do not allow the precise mapping of the positions of individual replisomes on chromatin. We have developed a method called Replicon-seq that entails the excision of full-length replicons by controlled nuclease cleavage at replication forks. Replicons are sequenced using Nanopore, which provides a single-molecule readout of long DNA. Using Replicon-seq, we found that sister replisomes function autonomously and yet progress through chromatin with remarkable consistency. Replication forks that encounter obstacles pause for a short duration but rapidly resume synthesis. The helicase Rrm3 plays a critical role both in mitigating the effect of protein barriers and with facilitating efficient termination. Replicon-seq provides a high-resolution means of defining how individual replisomes move across the genome.
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Affiliation(s)
- Clémence Claussin
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Jacob Vazquez
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Iestyn Whitehouse
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
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33
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Tingler M, Philipp M, Burkhalter MD. DNA Replication proteins in primary microcephaly syndromes. Biol Cell 2022; 114:143-159. [PMID: 35182397 DOI: 10.1111/boc.202100061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 11/30/2022]
Abstract
SCOPE Improper expansion of neural stem and progenitor cells during brain development manifests in primary microcephaly. It is characterized by a reduced head circumference, which correlates with a reduction in brain size. This often corresponds to a general underdevelopment of the brain and entails cognitive, behavioral and motoric retardation. In the past decade significant research efforts have been undertaken to identify genes and the molecular mechanisms underlying microcephaly. One such gene set encompasses factors required for DNA replication. Intriguingly, a growing body of evidence indicates that a substantial number of these genes mediate faithful centrosome and cilium function in addition to their canonical function in genome duplication. Here, we summarize, which DNA replication factors are associated with microcephaly syndromes and to which extent they impact on centrosomes and cilia. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Melanie Tingler
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University Tübingen, Tübingen, 72074, Germany
| | - Melanie Philipp
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University Tübingen, Tübingen, 72074, Germany
| | - Martin D Burkhalter
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University Tübingen, Tübingen, 72074, Germany
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34
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LeGault KN, Barth ZK, DePaola P, Seed KD. A phage parasite deploys a nicking nuclease effector to inhibit viral host replication. Nucleic Acids Res 2022; 50:8401-8417. [PMID: 35066583 PMCID: PMC9410903 DOI: 10.1093/nar/gkac002] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 12/17/2021] [Accepted: 01/12/2022] [Indexed: 12/11/2022] Open
Abstract
PLEs (phage-inducible chromosomal island-like elements) are phage parasites integrated into the chromosome of epidemic Vibrio cholerae. In response to infection by its viral host ICP1, PLE excises, replicates and hijacks ICP1 structural components for transduction. Through an unknown mechanism, PLE prevents ICP1 from transitioning to rolling circle replication (RCR), a prerequisite for efficient packaging of the viral genome. Here, we characterize a PLE-encoded nuclease, NixI, that blocks phage development likely by nicking ICP1’s genome as it transitions to RCR. NixI-dependent cleavage sites appear in ICP1’s genome during infection of PLE(+) V. cholerae. Purified NixI demonstrates in vitro nuclease activity specifically for sites in ICP1’s genome and we identify a motif that is necessary for NixI-mediated cleavage. Importantly, NixI is sufficient to limit ICP1 genome replication and eliminate progeny production, representing the most inhibitory PLE-encoded mechanism revealed to date. We identify distant NixI homologs in an expanded family of putative phage parasites in vibrios that lack nucleotide homology to PLEs but nonetheless share genomic synteny with PLEs. More generally, our results reveal a previously unknown mechanism deployed by phage parasites to limit packaging of their viral hosts’ genome and highlight the prominent role of nuclease effectors as weapons in the arms race between antagonizing genomes.
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Affiliation(s)
- Kristen N LeGault
- Department of Plant and Microbial Biology, University of California, Berkeley, 271 Koshland Hall, Berkeley, CA 94720, USA
| | - Zachary K Barth
- Department of Plant and Microbial Biology, University of California, Berkeley, 271 Koshland Hall, Berkeley, CA 94720, USA
| | - Peter DePaola
- Department of Plant and Microbial Biology, University of California, Berkeley, 271 Koshland Hall, Berkeley, CA 94720, USA
| | - Kimberley D Seed
- Department of Plant and Microbial Biology, University of California, Berkeley, 271 Koshland Hall, Berkeley, CA 94720, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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35
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Kavlashvili T, Dewar JM. Approaches to Monitor Termination of DNA Replication Using Xenopus Egg Extracts. Methods Mol Biol 2022; 2444:105-123. [PMID: 35290634 DOI: 10.1007/978-1-0716-2063-2_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
DNA replication is crucial for cell viability and genome integrity. Despite its crucial role in genome duplication, the final stage of DNA replication, which is termed termination, is relatively unexplored. Our knowledge of termination is limited by cellular approaches to study DNA replication, which cannot readily detect termination. In contrast, the Xenopus laevis egg extract system allows for all of DNA replication to be readily detected. Here we describe the use of this system and assays to monitor replication termination.
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Affiliation(s)
- Tamar Kavlashvili
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - James M Dewar
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.
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36
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Conwell SC, Cranford MT, Kavlashvili T, Dewar JM. Replication fork collapse in vitro using Xenopus egg extracts. Methods Enzymol 2022; 672:317-338. [DOI: 10.1016/bs.mie.2022.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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37
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Zhou H, Zaher MS, Walter JC, Brown A. Structure of CRL2Lrr1, the E3 ubiquitin ligase that promotes DNA replication termination in vertebrates. Nucleic Acids Res 2021; 49:13194-13206. [PMID: 34850944 PMCID: PMC8682755 DOI: 10.1093/nar/gkab1174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 11/17/2022] Open
Abstract
When vertebrate replisomes from neighboring origins converge, the Mcm7 subunit of the replicative helicase, CMG, is ubiquitylated by the E3 ubiquitin ligase, CRL2Lrr1. Polyubiquitylated CMG is then disassembled by the p97 ATPase, leading to replication termination. To avoid premature replisome disassembly, CRL2Lrr1 is only recruited to CMGs after they converge, but the underlying mechanism is unclear. Here, we use cryogenic electron microscopy to determine structures of recombinant Xenopus laevis CRL2Lrr1 with and without neddylation. The structures reveal that CRL2Lrr1 adopts an unusually open architecture, in which the putative substrate-recognition subunit, Lrr1, is located far from the catalytic module that catalyzes ubiquitin transfer. We further demonstrate that a predicted, flexible pleckstrin homology domain at the N-terminus of Lrr1 is essential to target CRL2Lrr1 to terminated CMGs. We propose a hypothetical model that explains how CRL2Lrr1’s catalytic module is positioned next to the ubiquitylation site on Mcm7, and why CRL2Lrr1 binds CMG only after replisomes converge.
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Affiliation(s)
- Haixia Zhou
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Manal S Zaher
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Alan Brown
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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Homologous Recombination as a Fundamental Genome Surveillance Mechanism during DNA Replication. Genes (Basel) 2021; 12:genes12121960. [PMID: 34946909 PMCID: PMC8701046 DOI: 10.3390/genes12121960] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/28/2022] Open
Abstract
Accurate and complete genome replication is a fundamental cellular process for the proper transfer of genetic material to cell progenies, normal cell growth, and genome stability. However, a plethora of extrinsic and intrinsic factors challenge individual DNA replication forks and cause replication stress (RS), a hallmark of cancer. When challenged by RS, cells deploy an extensive range of mechanisms to safeguard replicating genomes and limit the burden of DNA damage. Prominent among those is homologous recombination (HR). Although fundamental to cell division, evidence suggests that cancer cells exploit and manipulate these RS responses to fuel their evolution and gain resistance to therapeutic interventions. In this review, we focused on recent insights into HR-mediated protection of stress-induced DNA replication intermediates, particularly the repair and protection of daughter strand gaps (DSGs) that arise from discontinuous replication across a damaged DNA template. Besides mechanistic underpinnings of this process, which markedly differ depending on the extent and duration of RS, we highlight the pathophysiological scenarios where DSG repair is naturally silenced. Finally, we discuss how such pathophysiological events fuel rampant mutagenesis, promoting cancer evolution, but also manifest in adaptative responses that can be targeted for cancer therapy.
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Jones ML, Baris Y, Taylor MRG, Yeeles JTP. Structure of a human replisome shows the organisation and interactions of a DNA replication machine. EMBO J 2021; 40:e108819. [PMID: 34694004 PMCID: PMC8634136 DOI: 10.15252/embj.2021108819] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 02/01/2023] Open
Abstract
The human replisome is an elaborate arrangement of molecular machines responsible for accurate chromosome replication. At its heart is the CDC45-MCM-GINS (CMG) helicase, which, in addition to unwinding the parental DNA duplex, arranges many proteins including the leading-strand polymerase Pol ε, together with TIMELESS-TIPIN, CLASPIN and AND-1 that have key and varied roles in maintaining smooth replisome progression. How these proteins are coordinated in the human replisome is poorly understood. We have determined a 3.2 Å cryo-EM structure of a human replisome comprising CMG, Pol ε, TIMELESS-TIPIN, CLASPIN and AND-1 bound to replication fork DNA. The structure permits a detailed understanding of how AND-1, TIMELESS-TIPIN and Pol ε engage CMG, reveals how CLASPIN binds to multiple replisome components and identifies the position of the Pol ε catalytic domain. Furthermore, the intricate network of contacts contributed by MCM subunits and TIMELESS-TIPIN with replication fork DNA suggests a mechanism for strand separation.
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40
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Jenkyn-Bedford M, Jones ML, Baris Y, Labib KPM, Cannone G, Yeeles JTP, Deegan TD. A conserved mechanism for regulating replisome disassembly in eukaryotes. Nature 2021; 600:743-747. [PMID: 34700328 PMCID: PMC8695382 DOI: 10.1038/s41586-021-04145-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/14/2021] [Indexed: 11/28/2022]
Abstract
Replisome disassembly is the final step of eukaryotic DNA replication and is triggered by ubiquitylation of the CDC45-MCM-GINS (CMG) replicative helicase1-3. Despite being driven by evolutionarily diverse E3 ubiquitin ligases in different eukaryotes (SCFDia2 in budding yeast1, CUL2LRR1 in metazoa4-7), replisome disassembly is governed by a common regulatory principle, in which ubiquitylation of CMG is suppressed before replication termination, to prevent replication fork collapse. Recent evidence suggests that this suppression is mediated by replication fork DNA8-10. However, it is unknown how SCFDia2 and CUL2LRR1 discriminate terminated from elongating replisomes, to selectively ubiquitylate CMG only after termination. Here we used cryo-electron microscopy to solve high-resolution structures of budding yeast and human replisome-E3 ligase assemblies. Our structures show that the leucine-rich repeat domains of Dia2 and LRR1 are structurally distinct, but bind to a common site on CMG, including the MCM3 and MCM5 zinc-finger domains. The LRR-MCM interaction is essential for replisome disassembly and, crucially, is occluded by the excluded DNA strand at replication forks, establishing the structural basis for the suppression of CMG ubiquitylation before termination. Our results elucidate a conserved mechanism for the regulation of replisome disassembly in eukaryotes, and reveal a previously unanticipated role for DNA in preserving replisome integrity.
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Affiliation(s)
| | | | | | - Karim P M Labib
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, UK
| | | | | | - Tom D Deegan
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.
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41
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Kumar C, Batra S, Griffith JD, Remus D. The interplay of RNA:DNA hybrid structure and G-quadruplexes determines the outcome of R-loop-replisome collisions. eLife 2021; 10:72286. [PMID: 34494544 PMCID: PMC8479836 DOI: 10.7554/elife.72286] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 09/07/2021] [Indexed: 12/11/2022] Open
Abstract
R-loops are a major source of genome instability associated with transcription-induced replication stress. However, how R-loops inherently impact replication fork progression is not understood. Here, we characterize R-loop-replisome collisions using a fully reconstituted eukaryotic DNA replication system. We find that RNA:DNA hybrids and G-quadruplexes at both co-directional and head-on R-loops can impact fork progression by inducing fork stalling, uncoupling of leading strand synthesis from replisome progression, and nascent strand gaps. RNase H1 and Pif1 suppress replication defects by resolving RNA:DNA hybrids and G-quadruplexes, respectively. We also identify an intrinsic capacity of replisomes to maintain fork progression at certain R-loops by unwinding RNA:DNA hybrids, repriming leading strand synthesis downstream of G-quadruplexes, or utilizing R-loop transcripts to prime leading strand restart during co-directional R-loop-replisome collisions. Collectively, the data demonstrates that the outcome of R-loop-replisome collisions is modulated by R-loop structure, providing a mechanistic basis for the distinction of deleterious from non-deleterious R-loops.
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Affiliation(s)
- Charanya Kumar
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Sahil Batra
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center and Departments of Microbiology and Immunology, and Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Dirk Remus
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
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Xia Y, Fujisawa R, Deegan TD, Sonneville R, Labib KPM. TIMELESS-TIPIN and UBXN-3 promote replisome disassembly during DNA replication termination in Caenorhabditis elegans. EMBO J 2021; 40:e108053. [PMID: 34269473 PMCID: PMC8408604 DOI: 10.15252/embj.2021108053] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/30/2022] Open
Abstract
The eukaryotic replisome is rapidly disassembled during DNA replication termination. In metazoa, the cullin-RING ubiquitin ligase CUL-2LRR-1 drives ubiquitylation of the CMG helicase, leading to replisome disassembly by the p97/CDC-48 "unfoldase". Here, we combine in vitro reconstitution with in vivo studies in Caenorhabditis elegans embryos, to show that the replisome-associated TIMELESS-TIPIN complex is required for CUL-2LRR-1 recruitment and efficient CMG helicase ubiquitylation. Aided by TIMELESS-TIPIN, CUL-2LRR-1 directs a suite of ubiquitylation enzymes to ubiquitylate the MCM-7 subunit of CMG. Subsequently, the UBXN-3 adaptor protein directly stimulates the disassembly of ubiquitylated CMG by CDC-48_UFD-1_NPL-4. We show that UBXN-3 is important in vivo for replisome disassembly in the absence of TIMELESS-TIPIN. Correspondingly, co-depletion of UBXN-3 and TIMELESS causes profound synthetic lethality. Since the human orthologue of UBXN-3, FAF1, is a candidate tumour suppressor, these findings suggest that manipulation of CMG disassembly might be applicable to future strategies for treating human cancer.
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Affiliation(s)
- Yisui Xia
- The MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
| | - Ryo Fujisawa
- The MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
| | - Tom D Deegan
- The MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
| | - Remi Sonneville
- The MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
| | - Karim P M Labib
- The MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
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43
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Scully R, Elango R, Panday A, Willis NA. Recombination and restart at blocked replication forks. Curr Opin Genet Dev 2021; 71:154-162. [PMID: 34464818 DOI: 10.1016/j.gde.2021.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/28/2021] [Accepted: 08/06/2021] [Indexed: 01/07/2023]
Abstract
Replication fork stalling occurs when the replisome encounters a barrier to normal fork progression. Replisome stalling events are common during scheduled DNA synthesis, but vary in their severity. At one extreme, a lesion may induce only temporary pausing of a DNA polymerase; at the other, it may present a near-absolute barrier to the replicative helicase and effectively block fork progression. Many alternative pathways have evolved to respond to these different types of replication stress. Among these, the homologous recombination (HR) pathway plays an important role, protecting the stalled fork and processing it for repair. Here, we review recent advances in our understanding of how blocked replication forks in vertebrate cells can be processed for recombination and for replication restart.
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Affiliation(s)
- Ralph Scully
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA.
| | - Rajula Elango
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Arvind Panday
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Nicholas A Willis
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
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44
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Revisiting the BRCA-pathway through the lens of replication gap suppression: "Gaps determine therapy response in BRCA mutant cancer". DNA Repair (Amst) 2021; 107:103209. [PMID: 34419699 DOI: 10.1016/j.dnarep.2021.103209] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 12/12/2022]
Abstract
The toxic lesion emanating from chemotherapy that targets the DNA was initially debated, but eventually the DNA double strand break (DSB) ultimately prevailed. The reasoning was in part based on the perception that repairing a fractured chromosome necessitated intricate processing or condemned the cell to death. Genetic evidence for the DSB model was also provided by the extreme sensitivity of cells that were deficient in DSB repair. In particular, sensitivity characterized cells harboring mutations in the hereditary breast/ovarian cancer genes, BRCA1 or BRCA2, that function in the repair of DSBs by homologous recombination (HR). Along with functions in HR, BRCA proteins were found to prevent DSBs by protecting stalled replication forks from nuclease degradation. Coming full-circle, BRCA mutant cancer cells that gained resistance to genotoxic chemotherapy often displayed restored DNA repair by HR and/or restored fork protection (FP) implicating that the therapy was tolerated when DSB repair was intact or DSBs were prevented. Despite this well-supported paradigm that has been the impetus for targeted cancer therapy, here we argue that the toxic DNA lesion conferring response is instead single stranded DNA (ssDNA) gaps. We discuss the evidence that persistent ssDNA gaps formed in the wake of DNA replication rather than DSBs are responsible for cell killing following treatment with genotoxic chemotherapeutic agents. We also highlight that proteins, such as BRCA1, BRCA2, and RAD51 known for canonical DSB repair also have critical roles in normal replication as well as replication gap suppression (RGS) and repair. We review the literature that supports the idea that widespread gap induction proximal to treatment triggers apoptosis in a process that does not need or stem from DSB induction. Lastly, we discuss the clinical evidence for gaps and how to exploit them to enhance genotoxic chemotherapy response.
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45
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Coordinating DNA Replication and Mitosis through Ubiquitin/SUMO and CDK1. Int J Mol Sci 2021; 22:ijms22168796. [PMID: 34445496 PMCID: PMC8395760 DOI: 10.3390/ijms22168796] [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: 07/20/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 12/30/2022] Open
Abstract
Post-translational modification of the DNA replication machinery by ubiquitin and SUMO plays key roles in the faithful duplication of the genetic information. Among other functions, ubiquitination and SUMOylation serve as signals for the extraction of factors from chromatin by the AAA ATPase VCP. In addition to the regulation of DNA replication initiation and elongation, we now know that ubiquitination mediates the disassembly of the replisome after DNA replication termination, a process that is essential to preserve genomic stability. Here, we review the recent evidence showing how active DNA replication restricts replisome ubiquitination to prevent the premature disassembly of the DNA replication machinery. Ubiquitination also mediates the removal of the replisome to allow DNA repair. Further, we discuss the interplay between ubiquitin-mediated replisome disassembly and the activation of CDK1 that is required to set up the transition from the S phase to mitosis. We propose the existence of a ubiquitin–CDK1 relay, where the disassembly of terminated replisomes increases CDK1 activity that, in turn, favors the ubiquitination and disassembly of more replisomes. This model has important implications for the mechanism of action of cancer therapies that induce the untimely activation of CDK1, thereby triggering premature replisome disassembly and DNA damage.
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46
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Le TT, Ainsworth J, Polo Rivera C, Macartney T, Labib KP. Reconstitution of human CMG helicase ubiquitylation by CUL2LRR1 and multiple E2 enzymes. Biochem J 2021; 478:2825-2842. [PMID: 34195792 PMCID: PMC8331092 DOI: 10.1042/bcj20210315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 11/17/2022]
Abstract
Cullin ubiquitin ligases drive replisome disassembly during DNA replication termination. In worm, frog and mouse cells, CUL2LRR1 is required to ubiquitylate the MCM7 subunit of the CMG helicase. Here, we show that cullin ligases also drive CMG-MCM7 ubiquitylation in human cells, thereby making the helicase into a substrate for the p97 unfoldase. Using purified human proteins, including a panel of E2 ubiquitin-conjugating enzymes, we have reconstituted CMG helicase ubiquitylation, dependent upon neddylated CUL2LRR1. The reaction is highly specific to CMG-MCM7 and requires the LRR1 substrate targeting subunit, since replacement of LRR1 with the alternative CUL2 adaptor VHL switches ubiquitylation from CMG-MCM7 to HIF1. CUL2LRR1 firstly drives monoubiquitylation of CMG-MCM7 by the UBE2D class of E2 enzymes. Subsequently, CUL2LRR1 activates UBE2R1/R2 or UBE2G1/G2 to extend a single K48-linked ubiquitin chain on CMG-MCM7. Thereby, CUL2LRR1 converts CMG into a substrate for p97, which disassembles the ubiquitylated helicase during DNA replication termination.
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Affiliation(s)
- Thanh Thi Le
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Johanna Ainsworth
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Cristian Polo Rivera
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Thomas Macartney
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Karim P.M. Labib
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
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47
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Guilliam TA. Mechanisms for Maintaining Eukaryotic Replisome Progression in the Presence of DNA Damage. Front Mol Biosci 2021; 8:712971. [PMID: 34295925 PMCID: PMC8290200 DOI: 10.3389/fmolb.2021.712971] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 06/25/2021] [Indexed: 12/04/2022] Open
Abstract
The eukaryotic replisome coordinates template unwinding and nascent-strand synthesis to drive DNA replication fork progression and complete efficient genome duplication. During its advancement along the parental template, each replisome may encounter an array of obstacles including damaged and structured DNA that impede its progression and threaten genome stability. A number of mechanisms exist to permit replisomes to overcome such obstacles, maintain their progression, and prevent fork collapse. A combination of recent advances in structural, biochemical, and single-molecule approaches have illuminated the architecture of the replisome during unperturbed replication, rationalised the impact of impediments to fork progression, and enhanced our understanding of DNA damage tolerance mechanisms and their regulation. This review focusses on these studies to provide an updated overview of the mechanisms that support replisomes to maintain their progression on an imperfect template.
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Affiliation(s)
- Thomas A. Guilliam
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
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48
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Fairlamb MS, Whitaker AM, Bain FE, Spies M, Freudenthal BD. Construction of a Three-Color Prism-Based TIRF Microscope to Study the Interactions and Dynamics of Macromolecules. BIOLOGY 2021; 10:biology10070571. [PMID: 34201434 PMCID: PMC8301196 DOI: 10.3390/biology10070571] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/08/2021] [Accepted: 06/15/2021] [Indexed: 02/05/2023]
Abstract
Simple Summary Prism-based single-molecule total internal reflection fluorescence (prismTIRF) microscopes are excellent tools for studying macromolecular dynamics and interactions. Here, we provide an easy-to-follow guide for the design, assembly, and operation of a three-color prismTIRF microscope using commercially available components with the hope of assisting those who aim to implement TIRF imaging techniques in their laboratory. Abstract Single-molecule total internal reflection fluorescence (TIRF) microscopy allows for the real-time visualization of macromolecular dynamics and complex assembly. Prism-based TIRF microscopes (prismTIRF) are relatively simple to operate and can be easily modulated to fit the needs of a wide variety of experimental applications. While building a prismTIRF microscope without expert assistance can pose a significant challenge, the components needed to build a prismTIRF microscope are relatively affordable and, with some guidance, the assembly can be completed by a determined novice. Here, we provide an easy-to-follow guide for the design, assembly, and operation of a three-color prismTIRF microscope which can be utilized for the study of macromolecular complexes, including the multi-component protein–DNA complexes responsible for DNA repair, replication, and transcription. Our hope is that this article can assist laboratories that aspire to implement single-molecule TIRF techniques, and consequently expand the application of this technology.
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Affiliation(s)
- Max S. Fairlamb
- Department of Biochemistry and Molecular Biology and Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA; (M.S.F.); (A.M.W.)
| | - Amy M. Whitaker
- Department of Biochemistry and Molecular Biology and Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA; (M.S.F.); (A.M.W.)
| | - Fletcher E. Bain
- Department of Biochemistry and Molecular Biology, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA; (F.E.B.); (M.S.)
| | - Maria Spies
- Department of Biochemistry and Molecular Biology, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA; (F.E.B.); (M.S.)
| | - Bret D. Freudenthal
- Department of Biochemistry and Molecular Biology and Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA; (M.S.F.); (A.M.W.)
- Correspondence:
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49
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Shyian M, Shore D. Approaching Protein Barriers: Emerging Mechanisms of Replication Pausing in Eukaryotes. Front Cell Dev Biol 2021; 9:672510. [PMID: 34124054 PMCID: PMC8194067 DOI: 10.3389/fcell.2021.672510] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/03/2021] [Indexed: 11/13/2022] Open
Abstract
During nuclear DNA replication multiprotein replisome machines have to jointly traverse and duplicate the total length of each chromosome during each cell cycle. At certain genomic locations replisomes encounter tight DNA-protein complexes and slow down. This fork pausing is an active process involving recognition of a protein barrier by the approaching replisome via an evolutionarily conserved Fork Pausing/Protection Complex (FPC). Action of the FPC protects forks from collapse at both programmed and accidental protein barriers, thus promoting genome integrity. In addition, FPC stimulates the DNA replication checkpoint and regulates topological transitions near the replication fork. Eukaryotic cells have been proposed to employ physiological programmed fork pausing for various purposes, such as maintaining copy number at repetitive loci, precluding replication-transcription encounters, regulating kinetochore assembly, or controlling gene conversion events during mating-type switching. Here we review the growing number of approaches used to study replication pausing in vivo and in vitro as well as the characterization of additional factors recently reported to modulate fork pausing in different systems. Specifically, we focus on the positive role of topoisomerases in fork pausing. We describe a model where replisome progression is inherently cautious, which ensures general preservation of fork stability and genome integrity but can also carry out specialized functions at certain loci. Furthermore, we highlight classical and novel outstanding questions in the field and propose venues for addressing them. Given how little is known about replisome pausing at protein barriers in human cells more studies are required to address how conserved these mechanisms are.
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Affiliation(s)
- Maksym Shyian
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - David Shore
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
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50
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Fan Y, Köberlin MS, Ratnayeke N, Liu C, Deshpande M, Gerhardt J, Meyer T. LRR1-mediated replisome disassembly promotes DNA replication by recycling replisome components. J Cell Biol 2021; 220:212186. [PMID: 34037657 PMCID: PMC8160578 DOI: 10.1083/jcb.202009147] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 03/30/2021] [Accepted: 05/04/2021] [Indexed: 11/22/2022] Open
Abstract
After two converging DNA replication forks meet, active replisomes are disassembled and unloaded from chromatin. A key process in replisome disassembly is the unloading of CMG helicases (CDC45–MCM–GINS), which is initiated in Caenorhabditis elegans and Xenopus laevis by the E3 ubiquitin ligase CRL2LRR1. Here, we show that human cells lacking LRR1 fail to unload CMG helicases and accumulate increasing amounts of chromatin-bound replisome components as cells progress through S phase. Markedly, we demonstrate that the failure to disassemble replisomes reduces the rate of DNA replication increasingly throughout S phase by sequestering rate-limiting replisome components on chromatin and blocking their recycling. Continued binding of CMG helicases to chromatin during G2 phase blocks mitosis by activating an ATR-mediated G2/M checkpoint. Finally, we provide evidence that LRR1 is an essential gene for human cell division, suggesting that CRL2LRR1 enzyme activity is required for the proliferation of cancer cells and is thus a potential target for cancer therapy.
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Affiliation(s)
- Yilin Fan
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA.,Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY
| | - Marielle S Köberlin
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA
| | - Nalin Ratnayeke
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA.,Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY
| | - Chad Liu
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA
| | - Madhura Deshpande
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
| | - Jeannine Gerhardt
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY.,Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY
| | - Tobias Meyer
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA.,Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY
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