Structural Mechanism of DNA-End Synapsis in the Non- Homologous End Joining Pathway for Repairing Double-Strand Breaks: Bridge Over Troubled Ends
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RB Localizes to DNA Double-Strand Breaks and Promotes DNA End Resection and Homologous Recombination Through the Recruitment of BRG1
Downloaded from genesdev.cshlp.org on October 9, 2021 - Published by Cold Spring Harbor Laboratory Press RB localizes to DNA double-strand breaks and promotes DNA end resection and homologous recombination through the recruitment of BRG1 Renier Vélez-Cruz,1 Swarnalatha Manickavinayaham,1 Anup K. Biswas,1,3 Regina Weaks Clary,1,2 Tolkappiyan Premkumar,1,2 Francesca Cole,1,2 and David G. Johnson1,2 1Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville Texas 78957, USA; 2The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas 77225, USA The retinoblastoma (RB) tumor suppressor is recognized as a master regulator that controls entry into the S phase of the cell cycle. Its loss leads to uncontrolled cell proliferation and is a hallmark of cancer. RB works by binding to members of the E2F family of transcription factors and recruiting chromatin modifiers to the promoters of E2F target genes. Here we show that RB also localizes to DNA double-strand breaks (DSBs) dependent on E2F1 and ATM kinase activity and promotes DSB repair through homologous recombination (HR), and its loss results in genome insta- bility. RB is necessary for the recruitment of the BRG1 ATPase to DSBs, which stimulates DNA end resection and HR. A knock-in mutation of the ATM phosphorylation site on E2F1 (S29A) prevents the interaction between E2F1 and TopBP1 and recruitment of RB, E2F1, and BRG1 to DSBs. This knock-in mutation also impairs DNA repair, increases genomic instability, and renders mice hypersensitive to IR. Importantly, depletion of RB in osteosarcoma and breast cancer cell lines results in sensitivity to DNA-damaging drugs, which is further exacerbated by poly-ADP ribose polymerase (PARP) inhibitors. -
DNA Damage Response
biomolecules Editorial DNA Damage Response Valentyn Oksenych 1,2,3,4,* and Denis E. Kainov 1,5,* 1 Department for Cancer Research and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway 2 Department of Biosciences and Nutrition (BioNuT), Karolinska Institutet, 14183 Huddinge, Sweden 3 KG Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, 0316 Oslo, Norway 4 Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway 5 Institute of Technology, University of Tartu, 50090 Tartu, Estonia * Correspondence: [email protected] (V.O.); [email protected] (D.E.K.) DNA in our cells is constantly modified by internal and external factors. For exam- ple, metabolic byproducts, ionizing radiation (IR), ultraviolet (UV) light, and medicines can induce spontaneous DNA lesions [1–3]. However, DNA modifications can also be programmed. In particular, the recombination activating gene (RAG) can induce breaks generated during the V(D)J recombination in developing B and T lymphocytes [1,2]. In addition, activation-induced cytidine deaminase (AID) makes DNA break during the class-switch recombination (CSR) and somatic hypermutation (SHM) in B cells [1,2]. One focus of this Special Issue is on the non-homologous end-joining (NHEJ) DNA repair pathway and DNA repair and DNA damage response (DDR) factors. Oksenych et al. and others found the functional redundancy of these factors in mammalian cells. In particu- lar, a genetic interaction was found between the X-ray repair cross-complementing protein 4 (XRCC4)-like factor (XLF, also known as Cernunnos) and the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) [4,5], the paralog of XRCC4 and XLF (PAXX) [6–9], and the modulator of retrovirus infection (MRI, also known as Cyren) [10]. -
DNA Damage Induced During Mitosis Undergoes DNA Repair
bioRxiv preprint doi: https://doi.org/10.1101/2020.01.03.893784; this version posted January 3, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 DNA damage induced during mitosis 2 undergoes DNA repair synthesis 3 4 5 Veronica Gomez Godinez1 ,Sami Kabbara2,3,1a, Adria Sherman1,3, Tao Wu3,4, 6 Shirli Cohen1, Xiangduo Kong5, Jose Luis Maravillas-Montero6,1b, Zhixia Shi1, 7 Daryl Preece,4,3, Kyoko Yokomori5, Michael W. Berns1,2,3,4* 8 9 1Institute of Engineering in Medicine, University of Ca-San Diego, San Diego, California, United 10 States of America 11 12 2Department of Developmental and Cell Biology, University of Ca-Irvine, Irvine, California, United 13 States of America 14 15 3Beckman Laser Institute, University of Ca-Irvine, Irvine, California, United States of America 16 17 4Department of Biomedical Engineering, University of Ca-Irvine, Irvine, California, United States of 18 America 19 20 5Department of Biological Chemistry, University of Ca-Irvine, Irvine, California, United States of 21 America 22 23 6Department of Physiology, University of Ca-Irvine, Irvine, California, United States of America 24 25 1aCurrent Address: Tulane Department of Opthalmology, New Orleans, Louisiana, United States of 26 America 27 28 1bCurrent Address: Universidad Nacional Autonoma de Mexico, Mexico CDMX, Mexico 29 30 31 32 *Corresponding Author 33 34 [email protected](M.W.B) 35 36 37 38 39 40 41 42 43 44 45 46 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.01.03.893784; this version posted January 3, 2020. -
Generation of a Mouse Model Lacking the Non-Homologous End-Joining Factor Mri/Cyren
biomolecules Article Generation of a Mouse Model Lacking the Non-Homologous End-Joining Factor Mri/Cyren 1,2, 1,2, 1,2, 1,2 Sergio Castañeda-Zegarra y , Camilla Huse y, Øystein Røsand y, Antonio Sarno , Mengtan Xing 1,2, Raquel Gago-Fuentes 1,2, Qindong Zhang 1,2, Amin Alirezaylavasani 1,2, Julia Werner 1,2,3, Ping Ji 1, Nina-Beate Liabakk 1, Wei Wang 1, Magnar Bjørås 1,2 and Valentyn Oksenych 1,2,4,* 1 Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway; [email protected] (S.C.-Z.); [email protected] (C.H.); [email protected] (Ø.R.); [email protected] (A.S.); [email protected] (M.X.); [email protected] (R.G.-F.); [email protected] (Q.Z.); [email protected] (A.A.); [email protected] (J.W.); [email protected] (P.J.); [email protected] (N.-B.L.); [email protected] (W.W.); [email protected] (M.B.) 2 St. Olavs Hospital, Trondheim University Hospital, Clinic of Medicine, Postboks 3250, Sluppen, 7006 Trondheim, Norway 3 Molecular Biotechnology MS programme, Heidelberg University, 69120 Heidelberg, Germany 4 Department of Biosciences and Nutrition (BioNut), Karolinska Institutet, 14183 Huddinge, Sweden * Correspondence: [email protected]; Tel.: +47-913-43-084 These authors contributed equally to this work. y Received: 7 November 2019; Accepted: 26 November 2019; Published: 28 November 2019 Abstract: Classical non-homologous end joining (NHEJ) is a molecular pathway that detects, processes, and ligates DNA double-strand breaks (DSBs) throughout the cell cycle. -
Insights Into Regulation of Human RAD51 Nucleoprotein Filament Activity During
Insights into Regulation of Human RAD51 Nucleoprotein Filament Activity During Homologous Recombination Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Ravindra Bandara Amunugama, B.S. Biophysics Graduate Program The Ohio State University 2011 Dissertation Committee: Richard Fishel PhD, Advisor Jeffrey Parvin MD PhD Charles Bell PhD Michael Poirier PhD Copyright by Ravindra Bandara Amunugama 2011 ABSTRACT Homologous recombination (HR) is a mechanistically conserved pathway that occurs during meiosis and following the formation of DNA double strand breaks (DSBs) induced by exogenous stresses such as ionization radiation. HR is also involved in restoring replication when replication forks have stalled or collapsed. Defective recombination machinery leads to chromosomal instability and predisposition to tumorigenesis. However, unregulated HR repair system also leads to similar outcomes. Fortunately, eukaryotes have evolved elegant HR repair machinery with multiple mediators and regulatory inputs that largely ensures an appropriate outcome. A fundamental step in HR is the homology search and strand exchange catalyzed by the RAD51 recombinase. This process requires the formation of a nucleoprotein filament (NPF) on single-strand DNA (ssDNA). In Chapter 2 of this dissertation I describe work on identification of two residues of human RAD51 (HsRAD51) subunit interface, F129 in the Walker A box and H294 of the L2 ssDNA binding region that are essential residues for salt-induced recombinase activity. Mutation of F129 or H294 leads to loss or reduced DNA induced ATPase activity and formation of a non-functional NPF that eliminates recombinase activity. DNA binding studies indicate that these residues may be essential for sensing the ATP nucleotide for a functional NPF formation. -
Error-Prone DNA Repair As Cancer's Achilles' Heel
cancers Review Alternative Non-Homologous End-Joining: Error-Prone DNA Repair as Cancer’s Achilles’ Heel Daniele Caracciolo, Caterina Riillo , Maria Teresa Di Martino , Pierosandro Tagliaferri and Pierfrancesco Tassone * Department of Experimental and Clinical Medicine, Magna Græcia University, Campus Salvatore Venuta, 88100 Catanzaro, Italy; [email protected] (D.C.); [email protected] (C.R.); [email protected] (M.T.D.M.); [email protected] (P.T.) * Correspondence: [email protected] Simple Summary: Cancer onset and progression lead to a high rate of DNA damage, due to replicative and metabolic stress. To survive in this dangerous condition, cancer cells switch the DNA repair machinery from faithful systems to error-prone pathways, strongly increasing the mutational rate that, in turn, supports the disease progression and drug resistance. Although DNA repair de-regulation boosts genomic instability, it represents, at the same time, a critical cancer vulnerability that can be exploited for synthetic lethality-based therapeutic intervention. We here discuss the role of the error-prone DNA repair, named Alternative Non-Homologous End Joining (Alt-NHEJ), as inducer of genomic instability and as a potential therapeutic target. We portray different strategies to drug Alt-NHEJ and discuss future challenges for selecting patients who could benefit from Alt-NHEJ inhibition, with the aim of precision oncology. Abstract: Error-prone DNA repair pathways promote genomic instability which leads to the onset of cancer hallmarks by progressive genetic aberrations in tumor cells. The molecular mechanisms which Citation: Caracciolo, D.; Riillo, C.; Di foster this process remain mostly undefined, and breakthrough advancements are eagerly awaited. Martino, M.T.; Tagliaferri, P.; Tassone, In this context, the alternative non-homologous end joining (Alt-NHEJ) pathway is considered P. -
The Response to DNA Damage at Telomeric Repeats and Its Consequences for Telomere Function
Review The Response to DNA Damage at Telomeric Repeats and Its Consequences for Telomere Function Ylli Doksani IFOM, The FIRC Institute of Molecular Oncology, via Adamello 16, 20139 Milan, Italy; [email protected]; Tel.: +39-02-574303258 Received: 26 March 2019; Accepted: 18 April 2019; Published: 24 April 2019 Abstract: Telomeric repeats, coated by the shelterin complex, prevent inappropriate activation of the DNA damage response at the ends of linear chromosomes. Shelterin has evolved distinct solutions to protect telomeres from different aspects of the DNA damage response. These solutions include formation of t-loops, which can sequester the chromosome terminus from DNA-end sensors and inhibition of key steps in the DNA damage response. While blocking the DNA damage response at chromosome ends, telomeres make wide use of many of its players to deal with exogenous damage and replication stress. This review focuses on the interplay between the end-protection functions and the response to DNA damage occurring inside the telomeric repeats, as well as on the consequences that telomere damage has on telomere structure and function. Keywords: telomere maintenance; shelterin complex; end-protection problem; telomere damage; telomeric double strand breaks; telomere replication; alternative lengthening of telomeres 1. Telomere Structure and End-Protection Functions Mammalian telomeres are made of tandem TTAGGG repeats that extend several kilobases and terminate with a 3′ single-stranded overhang about 50–400 nucleotides long. Telomeric repeats are coated in a sequence-specific fashion by a 6-protein complex named shelterin that prevents the activation of the Double Strand Break (DSB) response at chromosome ends [1-3]. -
UC San Diego UC San Diego Electronic Theses and Dissertations
UC San Diego UC San Diego Electronic Theses and Dissertations Title Methods and Characterization of smORF-Encoded Microproteins Permalink https://escholarship.org/uc/item/25k5d8z0 Author Rathore, Annie Publication Date 2018 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA SAN DIEGO Methods and Characterization of smORF-Encoded Microproteins A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Biology by Annie Rathore Committee in charge: Professor Alan Saghatelian, Chair Professor Christopher Benner Professor Christopher Glass Professor Randolph Hampton Professor Martin Hetzer Professor Jens Lykke-Anderson 2018 © Annie Rathore, 2018 All rights reserved. The Dissertation of Annie Rathore is approved, and is acceptable in quality and form for publication on microfilm and electronically: Chair University of California San Diego 2018 iii TABLE OF CONTENTS Signature Page .......................................................................................................................... iii Table of Contents ....................................................................................................................... iv List of Figures ............................................................................................................................ vi Acknowledgements ................................................................................................................. -
Microhomology-Mediated End Joining: a Back-Up Survival Mechanism Or Dedicated Pathway? Agnel Sfeir1,* and Lorraine S
TIBS 1174 No. of Pages 14 Review Microhomology-Mediated End Joining: A Back-up Survival Mechanism or Dedicated Pathway? Agnel Sfeir1,* and Lorraine S. Symington2,* DNA double-strand breaks (DSBs) disrupt the continuity of chromosomes and Trends their repair by error-free mechanisms is essential to preserve genome integrity. MMEJ is a mutagenic DSB repair Microhomology-mediated end joining (MMEJ) is an error-prone repair mecha- mechanism that uses 1–16 nt of fl nism that involves alignment of microhomologous sequences internal to the homology anking the initiating DSB to align the ends for repair. broken ends before joining, and is associated with deletions and insertions that mark the original break site, as well as chromosome translocations. Whether MMEJ is associated with deletions and insertions that mark the original MMEJ has a physiological role or is simply a back-up repair mechanism is a break site, as well as chromosome matter of debate. Here we review recent findings pertaining to the mechanism of translocations. MMEJ and discuss its role in normal and cancer cells. RPA prevents MMEJ by inhibiting annealing between MHs exposed by Introduction end resection. Our cells are constantly exposed to extrinsic and intrinsic insults that cause several types of DNA Recent studies implicate DNA Polu fl lesions, including highly toxic breaks in icted on both strands of the double helix. To counteract (encoded by PolQ) in a subset of MMEJ the harmful effects of these double-strand breaks (DSBs), cells evolved specialized mechanisms events, particularly those associated to sense and repair DNA damage. The repair of DSBs is required to preserve genetic material, but with insertions at the break site. -
A Novel Role of the Dna2 Translocase Function in DNA Break Resection
Downloaded from genesdev.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press A novel role of the Dna2 translocase function in DNA break resection Adam S. Miller,1,4 James M. Daley,1,4 Nhung Tuyet Pham,2 Hengyao Niu,3 Xiaoyu Xue,1 Grzegorz Ira,2 and Patrick Sung1 1Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA; 2Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; 3Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana 47405, USA DNA double-strand break repair by homologous recombination entails nucleolytic resection of the 5′ strand at break ends. Dna2, a flap endonuclease with 5′–3′ helicase activity, is involved in the resection process. The Dna2 helicase activity has been implicated in Okazaki fragment processing during DNA replication but is thought to be dispen- sable for DNA end resection. Unexpectedly, we found a requirement for the helicase function of Dna2 in end re- section in budding yeast cells lacking exonuclease 1. Biochemical analysis reveals that ATP hydrolysis-fueled translocation of Dna2 on ssDNA facilitates 5′ flap cleavage near a single-strand–double strand junction while at- tenuating 3′ flap incision. Accordingly, the ATP hydrolysis-defective dna2-K1080E mutant is less able to generate long products in a reconstituted resection system. Our study thus reveals a previously unrecognized role of the Dna2 translocase activity in DNA break end resection and in the imposition of the 5′ strand specificity of end resection. [Keywords: DNA repair; double-strand break; end resection; homologous recombination] Supplemental material is available for this article. -
Beyond Gene Expression
Beyond gene expression Citation for published version (APA): Gupta, R. (2021). Beyond gene expression: novel methods and applications of transcript expression analyses in RNA-Seq. Maastricht University. https://doi.org/10.26481/dis.20210304rg Document status and date: Published: 01/01/2021 DOI: 10.26481/dis.20210304rg Document Version: Publisher's PDF, also known as Version of record Please check the document version of this publication: • A submitted manuscript is the version of the article upon submission and before peer-review. There can be important differences between the submitted version and the official published version of record. People interested in the research are advised to contact the author for the final version of the publication, or visit the DOI to the publisher's website. • The final author version and the galley proof are versions of the publication after peer review. • The final published version features the final layout of the paper including the volume, issue and page numbers. Link to publication General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal. -
HELB Is a Feedback Inhibitor of DNA End Resection
HELB Is a Feedback Inhibitor of DNA End Resection by Ján Tkáč A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Graduate Department of Molecular Genetics University of Toronto © Copyright by Ján Tkáč (2016) ABSTRACT HELB Is a Feedback Inhibitor of DNA End Resection Ján Tkáč Doctor of Philosophy Department of Molecular Genetics University of Toronto 2016 DNA double-strand breaks are toxic lesions, which jeopardize the genomic integrity and survival of all cells and organisms. Repair of these lesions by homologous recombination requires the formation of 3′ single-stranded DNA (ssDNA) overhangs by a nucleolytic process known as DNA end resection. Recent studies have significantly expanded our understanding of the initiation of resection, the molecular machinery involved in its execution, and its regulation throughout the cell cycle. However, the mechanisms that control and limit DNA end resection once the process has begun are unknown. I hypothesized that such activities may be coordinated by the ssDNA-binding complex Replication Protein A (RPA), which rapidly coats the 3′ ssDNA overhangs produced by resection. A proteomic analysis of RPA interactions following DNA damage identified the superfamily 1B translocase, DNA helicase B (HELB). Using cellular and biochemical approaches, I found that following RPA-dependent recruitment of HELB to the sites of DNA double-strand breaks, HELB inhibits EXO1 and BLM-DNA2 nucleases, which catalyze long-range resection. This function requires HELB’s catalytic activity and ssDNA binding, suggesting a mechanism where HELB translocates along ssDNA to displace the nucleases. HELB acts independently of 53BP1 and is exported from the nucleus as cells approach S phase, concomitant with the upregulation of resection.