Generation of a Mouse Model Lacking the Non-Homologous End-Joining Factor Mri/Cyren
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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]. -
Phosphatidylinositol-3-Kinase Related Kinases (Pikks) in Radiation-Induced Dna Damage
Mil. Med. Sci. Lett. (Voj. Zdrav. Listy) 2012, vol. 81(4), p. 177-187 ISSN 0372-7025 DOI: 10.31482/mmsl.2012.025 REVIEW ARTICLE PHOSPHATIDYLINOSITOL-3-KINASE RELATED KINASES (PIKKS) IN RADIATION-INDUCED DNA DAMAGE Ales Tichy 1, Kamila Durisova 1, Eva Novotna 1, Lenka Zarybnicka 1, Jirina Vavrova 1, Jaroslav Pejchal 2, Zuzana Sinkorova 1 1 Department of Radiobiology, Faculty of Health Sciences in Hradec Králové, University of Defence in Brno, Czech Republic 2 Centrum of Advanced Studies, Faculty of Health Sciences in Hradec Králové, University of Defence in Brno, Czech Republic. Received 5 th September 2012. Revised 27 th November 2012. Published 7 th December 2012. Summary This review describes a drug target for cancer therapy, family of phosphatidylinositol-3 kinase related kinases (PIKKs), and it gives a comprehensive review of recent information. Besides general information about phosphatidylinositol-3 kinase superfamily, it characterizes a DNA-damage response pathway since it is monitored by PIKKs. Key words: PIKKs; ATM; ATR; DNA-PK; Ionising radiation; DNA-repair ABBREVIATIONS therapy and radiation play a pivotal role. Since cancer is one of the leading causes of death worldwide, it is DSB - double stand breaks, reasonable to invest time and resources in the enligh - IR - ionising radiation, tening of mechanisms, which underlie radio-resis - p53 - TP53 tumour suppressors, tance. PI - phosphatidylinositol. The aim of this review is to describe the family INTRODUCTION of phosphatidyinositol 3-kinases (PI3K) and its func - tional subgroup - phosphatidylinositol-3-kinase rela - An efficient cancer treatment means to restore ted kinases (PIKKs) and their relation to repairing of controlled tissue growth via interfering with cell sig - radiation-induced DNA damage. -
A Process of Resection-Dependent Nonhomologous End Joining Involving the Goddess Artemis
A process of resection-dependent nonhomologous end joining involving the goddess Artemis Article (Published Version) Jeggo, Penny and Löbrich, Markus (2017) A process of resection-dependent nonhomologous end joining involving the goddess Artemis. Trends in Biochemical Sciences, 42 (9). pp. 690-701. ISSN 0968-0004 This version is available from Sussex Research Online: http://sro.sussex.ac.uk/id/eprint/77876/ This document is made available in accordance with publisher policies and may differ from the published version or from the version of record. If you wish to cite this item you are advised to consult the publisher’s version. Please see the URL above for details on accessing the published version. Copyright and reuse: Sussex Research Online is a digital repository of the research output of the University. Copyright and all moral rights to the version of the paper presented here belong to the individual author(s) and/or other copyright owners. To the extent reasonable and practicable, the material made available in SRO has been checked for eligibility before being made available. Copies of full text items generally can be reproduced, displayed or performed and given to third parties in any format or medium for personal research or study, educational, or not-for-profit purposes without prior permission or charge, provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way. http://sro.sussex.ac.uk [160_TD$IF]Opinion A Process of Resection- Dependent Nonhomologous End Joining Involving the Goddess Artemis Markus Löbrich1,* and Penny Jeggo2,* DNA double-strand breaks (DSBs) are a hazardous form of damage that can Trends potentially cause cell death or genomic rearrangements. -
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 ................................................................................................................. -
Radiation-Sensitive Severe Combined Immunodeficiency (RS-SCID)
Radiation-sensitive severe combined immunodeficiency (RS-SCID) Contact details Introduction Molecular Genetics Service Severe combined immunodeficiency (SCID) is a group of genetically and Level 6, York House phenotypically heterogeneous disorders that can be immunologically classified by the 37 Queen Square absence or presence of T, B, and natural killer (NK) cells. The most severe form of - - + London, WC1N 3BH SCID has the T B NK phenotype, accounting for ~20% of all cases in which patients T +44 (0) 20 7762 6888 present with a virtual absence of both circulating T and B cells, while maintaining a F +44 (0) 20 7813 8578 normal level and function of NK cells. This form of SCID is caused by autosomal recessive mutations in at least three primary genes necessary for V(D)J recombination, RAG1, RAG2, and DCLRE1C (ARTEMIS). DCLRE1C mutations Samples required cause a T and B cell deficient form of SCID that is clinically indistinguishable from a • 5ml venous blood in plastic EDTA RAG1/RAG2 disorder. Infants present with severe recurrent viral, bacterial or fungal bottles (>1ml from neonates) infections and failure-to-thrive. Defects in DCLRE1C can be distinguished from RAG • Prenatal testing must be arranged defects because the former has the additional feature of increased sensitivity to in advance, through a Clinical ionising radiation in bone marrow and fibroblast cells. Genetics department if possible. The DNA crosslink repair 1C gene (DCLRE1C; MIM 605988) encodes ARTEMIS • Amniotic fluid or CV samples which is an essential factor of V(D)J recombination during lymphocyte development should be sent to Cytogenetics for and in the repair of DNA double-strand breaks (DSB) by the non-homologous end dissecting and culturing, with joining (NHEJ) pathway. -
DOE Systems Biology Knowledgebase Implementation Plan
DOE Systems Biology Knowledgebase Implementation Plan As part of the U.S. Department of Energy’s (DOE) Office of Science, the Office of Biological and Environmental Research (BER) supports fundamental research and technology development aimed at achieving predictive, systems-level understand- ing of complex biological and environmental systems to advance DOE missions in energy, climate, and environment. DOE Contact Susan Gregurick 301.903.7672, [email protected] Office of Biological and Environmental Research U.S. Department of Energy Office of Science www.science.doe.gov/Program_Offices/BER.htm Acknowledgements The DOE Office of Biological and Environmental Research appreciates the vision and leadership exhibited by Bob Cottingham and Brian Davison (both from Oak Ridge National Laboratory) over the past year to conceptualize and guide the effort to create the DOE Systems Biology Knowledgebase Implementation Plan. Furthermore, we are grateful for the valuable contributions from about 300 members of the scientific community to organize, participate in, and provide the intellectual output of 5 work- shops, which culminated with the implementation plan. The plan was rendered into its current form by the efforts of the Biological and Environmental Research Information System (Oak Ridge National Laboratory). The report is available via • www.genomicscience.energy.gov/compbio/ • www.science.doe.gov/ober/BER_workshops.html • www.systemsbiologyknowledgebase.org Suggested citation for entire report: U.S. DOE. 2010. DOE Systems Biology Knowledgebase Implementation Plan. U.S. Department of Energy Office of Science (www.genomicscience.energy.gov/compbio/). DOE Systems Biology Knowledgebase Implementation Plan September 30, 2010 Office of Biological and Environmental Research The document is available via genomicscience.energy.gov/compbio/. -
Structural Mechanism of DNA-End Synapsis in the Non- Homologous End Joining Pathway for Repairing Double-Strand Breaks: Bridge Over Troubled Ends
This is a repository copy of Structural mechanism of DNA-end synapsis in the non- homologous end joining pathway for repairing double-strand breaks: bridge over troubled ends. White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/154931/ Version: Accepted Version Article: Wu, Q orcid.org/0000-0002-6948-7043 (2019) Structural mechanism of DNA-end synapsis in the non-homologous end joining pathway for repairing double-strand breaks: bridge over troubled ends. Biochemical Society Transactions, 47 (6). pp. 1609-1619. ISSN 0300-5127 https://doi.org/10.1042/bst20180518 © 2019 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society. This is an author produced version of a paper published in Biochemical Society Transactions. Uploaded in accordance with the publisher's self-archiving policy. Reuse Items deposited in White Rose Research Online are protected by copyright, with all rights reserved unless indicated otherwise. They may be downloaded and/or printed for private study, or other acts as permitted by national copyright laws. The publisher or other rights holders may allow further reproduction and re-use of the full text version. This is indicated by the licence information on the White Rose Research Online record for the item. Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ -
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. -
Diagnostic Interpretation of Genetic Studies in Patients with Primary
AAAAI Work Group Report Diagnostic interpretation of genetic studies in patients with primary immunodeficiency diseases: A working group report of the Primary Immunodeficiency Diseases Committee of the American Academy of Allergy, Asthma & Immunology Ivan K. Chinn, MD,a,b Alice Y. Chan, MD, PhD,c Karin Chen, MD,d Janet Chou, MD,e,f Morna J. Dorsey, MD, MMSc,c Joud Hajjar, MD, MS,a,b Artemio M. Jongco III, MPH, MD, PhD,g,h,i Michael D. Keller, MD,j Lisa J. Kobrynski, MD, MPH,k Attila Kumanovics, MD,l Monica G. Lawrence, MD,m Jennifer W. Leiding, MD,n,o,p Patricia L. Lugar, MD,q Jordan S. Orange, MD, PhD,r,s Kiran Patel, MD,k Craig D. Platt, MD, PhD,e,f Jennifer M. Puck, MD,c Nikita Raje, MD,t,u Neil Romberg, MD,v,w Maria A. Slack, MD,x,y Kathleen E. Sullivan, MD, PhD,v,w Teresa K. Tarrant, MD,z Troy R. Torgerson, MD, PhD,aa,bb and Jolan E. Walter, MD, PhDn,o,cc Houston, Tex; San Francisco, Calif; Salt Lake City, Utah; Boston, Mass; Great Neck and Rochester, NY; Washington, DC; Atlanta, Ga; Rochester, Minn; Charlottesville, Va; St Petersburg, Fla; Durham, NC; Kansas City, Mo; Philadelphia, Pa; and Seattle, Wash AAAAI Position Statements,Work Group Reports, and Systematic Reviews are not to be considered to reflect current AAAAI standards or policy after five years from the date of publication. The statement below is not to be construed as dictating an exclusive course of action nor is it intended to replace the medical judgment of healthcare professionals. -
Artemis, a Novel DNA Double-Strand Break Repair/V(D)J Recombination Protein, Is Mutated in Human Severe Combined Immune Deficiency
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Cell, Vol. 105, 177±186, April 20, 2001, Copyright 2001 by Cell Press Artemis, a Novel DNA Double-Strand Break Repair/V(D)J Recombination Protein, Is Mutated in Human Severe Combined Immune Deficiency Despina Moshous,* Isabelle Callebaut,² is flanked by recombination signal sequences (RSSs) Re gina de Chasseval,* Barbara Corneo,* composed of conserved heptamers and nonamers sep- Marina Cavazzana-Calvo,* FrancË oise Le Deist,* arated by random sequences of either 12 or 23 nucleo- Ilhan Tezcan,³ Ozden Sanal,³ Yves Bertrand,§ tides. V(D)J recombination can be roughly divided into Noel Philippe,§ Alain Fischer,* three steps. First, the RAG1 and RAG2 proteins initiate and Jean-Pierre de Villartay* the rearrangement process through the recognition of *De veloppement Normal et Pathologique the RSS and the introduction of a DNA double-strand du SysteÁ me Immunitaire break (dsb) at the border of the heptamer (Schatz et INSERM U429 al., 1989; Oettinger et al., 1990). The subsequent step Hoà pital Necker Enfants Malades consists of recognition and signaling of the DNA damage 149 rue de SeÁ vres to the ubiquitously expressed DNA repair machinery. 75015 Paris The description of the murine scid anomaly, character- France ized by a lack of circulating mature B and T lymphocytes ² LMCP, CNRS UMR C7590 (Bosma et al., 1983), as a general DNA repair defect Universite s Paris 6 et Paris 7 accompanied by an increased sensitivity to ionizing ra- Paris 75005 diation or other agents causing DNA dsb, provided the France link between V(D)J recombination and DNA dsb repair ³ Immunology Division (Fulop and Phillips, 1990; Biedermann et al., 1991; Hen- Hacettepe University drickson et al., 1991). -
Anti-Artemis (DCLRE1C) Produced in Rabbit, Affinity Isolated Antibody
Anti-Artemis (DCLRE1C) Produced in rabbit, Affinity Isolated Antibody Product Number A 1605 Product Description Precautions and Disclaimer Anti-Artemis (DCLRE1C) is produced in rabbit using as Due to the sodium azide content a material safety sheet immunogen a peptide corresponding to the human (MSDS) for this product has been sent to the attention Artemis protein (amino acids 677-692). The antibody is of the safety officer of your institution. Consult the affinity-purified using the immunizing peptide MSDS for information regarding hazardous and safe immobilized on agarose. handling practices. Anti-Artemis (DCLRE1C) reacts with residues 677-692 Storage/Stability (GESIAKKRKCSLLDT) of human artemis. The antibody Store at -20 °C. The antibody may be stored at 2-8 °C may be used in immunoblotting (~78 kDa). A weak for up to three months. For prolonged storage, freeze in signal is often seen due to low expression levels. working aliquots at -20 °C. Avoid repeated freezing and thawing. Do not store in a “frost-free” freezer. Artemis is a novel protein that is involved in V(D)J recombination/DNA repair. Mutations cause human T- Product Profile B-severe combined immunodeficiency associated with For immunoblotting, a working antibody dilution of increased cellular radiosenstivity (RS-SCID). 1:250-1:1,000 is recommended using human testis lysate. Reagent The antibody is supplied as a solution of ~1 mg/mL in Note: In order to obtain the best results in various phosphate buffered saline containing 0.02% sodium techniques and preparations, we recommend deter- azide. mining optimal working dilutions by titration. References 1.