Atrx Deficiency Induces Telomere Dysfunction, Endocrine Defects, and Reduced Life Span
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Structure and Function of the Human Recq DNA Helicases
Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2005 Structure and function of the human RecQ DNA helicases Garcia, P L Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-34420 Dissertation Published Version Originally published at: Garcia, P L. Structure and function of the human RecQ DNA helicases. 2005, University of Zurich, Faculty of Science. Structure and Function of the Human RecQ DNA Helicases Dissertation zur Erlangung der naturwissenschaftlichen Doktorw¨urde (Dr. sc. nat.) vorgelegt der Mathematisch-naturwissenschaftlichen Fakultat¨ der Universitat¨ Z ¨urich von Patrick L. Garcia aus Unterseen BE Promotionskomitee Prof. Dr. Josef Jiricny (Vorsitz) Prof. Dr. Ulrich H ¨ubscher Dr. Pavel Janscak (Leitung der Dissertation) Z ¨urich, 2005 For my parents ii Summary The RecQ DNA helicases are highly conserved from bacteria to man and are required for the maintenance of genomic stability. All unicellular organisms contain a single RecQ helicase, whereas the number of RecQ homologues in higher organisms can vary. Mu- tations in the genes encoding three of the five human members of the RecQ family give rise to autosomal recessive disorders called Bloom syndrome, Werner syndrome and Rothmund-Thomson syndrome. These diseases manifest commonly with genomic in- stability and a high predisposition to cancer. However, the genetic alterations vary as well as the types of tumours in these syndromes. Furthermore, distinct clinical features are observed, like short stature and immunodeficiency in Bloom syndrome patients or premature ageing in Werner Syndrome patients. Also, the biochemical features of the human RecQ-like DNA helicases are diverse, pointing to different roles in the mainte- nance of genomic stability. -
ATRX Protects Cells Against Replication-Induced Genomic Instability
ATRX Protects Cells Against Replication-Induced Genomic Instability Danton Ivanochko M.Sc. Thesis This thesis is submitted to the Faculty of Graduate and Postdoctoral Studies in partial fulfillment of the requirements for the degree of Master of Science in Biochemistry with a specialization in Human and Molecular Genetics Department of Biochemistry, Microbiology, and Immunology Faculty of Medicine University of Ottawa, Ontario, Ontario, Canada © Danton Ivanochko, Ottawa, Canada, 2016 Dedicated to my parents. ii Abstract Expansive proliferation of neural progenitor cells (NPCs) is a prerequisite to the temporal waves of neuronal differentiation that generate the six-layered cerebral cortex. NPC expansion places a heavy burden on proteins that regulate chromatin packaging and genome integrity, which is further reflected by the growing number of developmental disorders caused by mutations in chromatin regulators. Accordingly, mutations in ATRX, a chromatin remodelling protein required for heterochromatin maintenance at telomeres and simple repeats, cause the ATR-X syndrome. Here, we demonstrate that proliferating ATRX-null cells accumulate DNA damage, while also exhibiting sensitivity to hydroxyurea-induced replication fork stalling. Specifically, PARP1 hyperactivation and replication-dependent double strand DNA breakage indicated replication fork protection defects, while DNA fiber assays confirmed that ATRX was required to protect replication forks from degradation. Interestingly, inhibition of the exonuclease MRE11 by the small molecule mirin could prevent degradation. Thus, ATRX is required to limit replication stress during NPC expansion. iii Acknowledgements First and foremost, I would like to thank my supervisor, Dr. David Picketts, for his guidance and support during my undergraduate and graduate studies. Thanks to the members of my thesis advisory committee, Dr. -
Curriculum Vitae
CURRICULUM VITAE NAME: Patricia Lynn Opresko BUSINESS ADDRESS: University of Pittsburgh Graduate School of Public Health Department of Environmental and UPMC Hillman Cancer Center 5117 Centre Avenue, Suite 2.6a Pittsburgh, PA15213-1863 Phone: 412-623-7764 Fax: 412-623-7761 E-mail: [email protected] EDUCATION AND TRAINING Undergraduate 1990 - 1994 DeSales University B.S., 1994 Chemistry and Center Valley, PA Biology Graduate 1994 - 2000 Pennsylvania State Ph.D., 2000 Biochemistry and University, College of Molecular Biology Medicine, Hershey, PA Post-Graduate 3/2000 - 5/2000 Pennsylvania State Postdoctoral Dr. Kristin Eckert, University, College of Fellow Mutagenesis and Medicine, Jake Gittlen Cancer etiology Cancer Research Institute Hershey, PA 2000-2005 National Institute on IRTA Postdoctoral Dr. Vilhelm Bohr Aging, National Fellow Molecular Institutes of Health, Gerontology and Baltimore, MD DNA Repair 1 APPOINTMENTS AND POSITIONS Academic 8/1/2018 – Co-leader Genome Stability Program, UPMC present Hillman Cancer Center 5/1/2018- Tenured Professor Pharmacology and Chemical Biology, present School of Medicine, University of Pittsburgh, Pittsburgh, PA 2/1/2018- Tenured Professor Environmental and Occupational Health, present Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 2014 – Tenured Associate Environmental and Occupational Health, 1/31/2018 Professor Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 2005 - 2014 Assistant Professor Environmental and Occupational Health, Graduate School -
Neurodegeneration in Accelerated Aging
DOCTOR OF MEDICAL SCIENCE DANISH MEDICAL JOURNAL Neurodegeneration in Accelerated Aging Morten Scheibye-Knudsen This review has been accepted as a thesis together with 7 previously published pa- pers by the University of Copenhagen, October 16, 2014 and defended on January 14, 2016 Official opponents: Alexander Bürkle, University of Konstanz Lars Eide, University of Oslo Correspondence: Center for Healthy Aging, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen E-mail: [email protected] Dan Med J 2016;63(11):B5308 INTRODUCTION The global elderly population has been progressively increasing throughout the 20th century and this growth is projected to per- sist into the late 21st century resulting in 20% of the total world population being aged 65 or more by the year 2100 (Figure 1). 80% of the total cost of health care is accrued after 40 years of Figure 2. The phenotype of human aging. age where chronic diseases become prevalent [1, 2]. With an ex- that appear to regulate the aging process [4,5]. These include the ponential increase in health care costs, it follows that the chronic insulin and IGF-1 signaling cascades [4], protein synthesis and diseases that accumulate in an aging population poses a serious quality control [6], regulation of cell proliferation through factors socioeconomic problem. Finding treatments to age related dis- such as mTOR [7], stem cell maintenance 8 as well as mitochon- eases, therefore becomes increasingly more pertinent as the pop- drial preservation [9]. Most of these pathways are conserved ulation ages. Even more so since there appears to be a continu- through evolution and appear to regulate aging in many lower or- ous increase in the prevalence of chronic diseases in the aging ganisms. -
Patient Mutations Alter ATRX Targeting to PML Nuclear Bodies
European Journal of Human Genetics (2008) 16, 192–201 & 2008 Nature Publishing Group All rights reserved 1018-4813/08 $30.00 www.nature.com/ejhg ARTICLE Patient mutations alter ATRX targeting to PML nuclear bodies Nathalie G Be´rube´1,3,4, Jasmine Healy1,4, Chantal F Medina1, Shaobo Wu1, Todd Hodgson1, Magdalena Jagla1 and David J Picketts*,2 1Molecular Medicine Program, Ottawa Health Research Institute, Ottawa, Ontario, Canada; 2Departments of Medicine and Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada ATRX is a SWI/SNF-like chromatin remodeling protein mutated in several X-linked mental retardation syndromes. Gene inactivation studies in mice demonstrate that ATRX is an essential protein and suggest that patient mutations likely retain partial activity. ATRX associates with the nuclear matrix, pericentromeric heterochromatin, and promyelocytic leukemia nuclear bodies (PML-NBs) in a speckled nuclear staining pattern. Here, we used GFP–ATRX fusion proteins to identify the specific domains of ATRX necessary for subnuclear targeting and the effect of patient mutations on this localization. We identified two functional nuclear localization signals (NLSs) and two domains that target ATRX to nuclear speckles. One of the latter domains is responsible for targeting ATRX to PML-NBs. Surprisingly, this domain encompassed motifs IV–VI of the SNF2 domain suggesting that in addition to chromatin remodeling, it may also have a role in subnuclear targeting. More importantly, four different patient mutations within this domain resulted in an B80% reduction in the number of transfected cells with ATRX nuclear speckles and PML colocalization. These results demonstrate that patient mutations have a dramatic effect on subnuclear targeting to PML-NBs. -
X-Linked Diseases: Susceptible Females
REVIEW ARTICLE X-linked diseases: susceptible females Barbara R. Migeon, MD 1 The role of X-inactivation is often ignored as a prime cause of sex data include reasons why women are often protected from the differences in disease. Yet, the way males and females express their deleterious variants carried on their X chromosome, and the factors X-linked genes has a major role in the dissimilar phenotypes that that render women susceptible in some instances. underlie many rare and common disorders, such as intellectual deficiency, epilepsy, congenital abnormalities, and diseases of the Genetics in Medicine (2020) 22:1156–1174; https://doi.org/10.1038/s41436- heart, blood, skin, muscle, and bones. Summarized here are many 020-0779-4 examples of the different presentations in males and females. Other INTRODUCTION SEX DIFFERENCES ARE DUE TO X-INACTIVATION Sex differences in human disease are usually attributed to The sex differences in the effect of X-linked pathologic variants sex specific life experiences, and sex hormones that is due to our method of X chromosome dosage compensation, influence the function of susceptible genes throughout the called X-inactivation;9 humans and most placental mammals – genome.1 5 Such factors do account for some dissimilarities. compensate for the sex difference in number of X chromosomes However, a major cause of sex-determined expression of (that is, XX females versus XY males) by transcribing only one disease has to do with differences in how males and females of the two female X chromosomes. X-inactivation silences all X transcribe their gene-rich human X chromosomes, which is chromosomes but one; therefore, both males and females have a often underappreciated as a cause of sex differences in single active X.10,11 disease.6 Males are the usual ones affected by X-linked For 46 XY males, that X is the only one they have; it always pathogenic variants.6 Females are biologically superior; a comes from their mother, as fathers contribute their Y female usually has no disease, or much less severe disease chromosome. -
Structure of the SWI2/SNF2 Chromatin-Remodeling Domain of Eukaryotic Rad54
ARTICLES Structure of the SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54 Nicolas H Thomä1, Bryan K Czyzewski1,2, Andrei A Alexeev3, Alexander V Mazin4, Stephen C Kowalczykowski3 & Nikola P Pavletich1,2 SWI2/SNF2 chromatin-remodeling proteins mediate the mobilization of nucleosomes and other DNA-associated proteins. SWI2/SNF2 proteins contain sequence motifs characteristic of SF2 helicases but do not have helicase activity. Instead, they couple ATP hydrolysis with the generation of superhelical torsion in DNA. The structure of the nucleosome-remodeling domain of zebrafish Rad54, a protein http://www.nature.com/nsmb involved in Rad51-mediated homologous recombination, reveals that the core of the SWI2/SNF2 enzymes consist of two ␣/-lobes similar to SF2 helicases. The Rad54 helicase lobes contain insertions that form two helical domains, one within each lobe. These insertions contain SWI2/SNF2-specific sequence motifs likely to be central to SWI2/SNF2 function. A broad cleft formed by the two lobes and flanked by the helical insertions contains residues conserved in SWI2/SNF2 proteins and motifs implicated in DNA-binding by SF2 helicases. The Rad54 structure suggests that SWI2/SNF2 proteins use a mechanism analogous to helicases to translocate on dsDNA. Cellular processes such as transcription, replication, DNA repair and breaks by Rad51-mediated homologous recombination15–20. Like other recombination require direct access to DNA. This process is facilitated SWI2/SNF2 remodeling enzymes, Rad54 can translocate on DNA, gen- by the SWI2/SNF2 family of ATPases, which detach DNA from histones erate superhelical torsion and enhance the accessibility to nucleosomal and other bound proteins1,2. The SWI2/SNF2 chromatin remodeling DNA18,19,21. -
ATRX-Mutant Cancers to WEE1 Inhibition Junbo Liang1, Hong Zhao2,3, Bill H
Published OnlineFirst September 24, 2019; DOI: 10.1158/0008-5472.CAN-18-3374 CANCER RESEARCH | TRANSLATIONAL SCIENCE Genome-Wide CRISPR-Cas9 Screen Reveals Selective Vulnerability of ATRX-Mutant Cancers to WEE1 Inhibition Junbo Liang1, Hong Zhao2,3, Bill H. Diplas4, Song Liu5, Jianmei Liu2,3, Dingding Wang1, Yan Lu1, Qing Zhu6, Jiayu Wu1, Wenjia Wang1, Hai Yan4, Yi-Xin Zeng6, Xiaoyue Wang1, and Yuchen Jiao2,7 ABSTRACT ◥ The tumor suppressor gene ATRX is frequently mutated in a induced apoptosis. AZD1775 also selectively inhibited the prolif- variety of tumors including gliomas and liver cancers, which are eration of patient-derived primary cell lines from gliomas with highly unresponsive to current therapies. Here, we performed a naturally occurring ATRX mutations, indicating that the synthetic genome-wide synthetic lethal screen, using CRISPR-Cas9 genome lethal relationship between WEE1 and ATRX could be exploited in a editing, to identify potential therapeutic targets specific for ATRX- broader spectrum of human tumors. As WEE1 inhibitors have been mutated cancers. In isogenic hepatocellular carcinoma (HCC) cell investigated in several phase II clinical trials, our discovery provides lines engineered for ATRX loss, we identified 58 genes, including the the basis for an easily clinically testable therapeutic strategy specific checkpoint kinase WEE1, uniquely required for the cell growth of for cancers deficient in ATRX. ATRX null cells. Treatment with the WEE1 inhibitor AZD1775 robustly inhibited the growth of several ATRX-deficient HCC cell Significance: ATRX-mutant cancer cells depend on WEE1, lines in vitro, as well as xenografts in vivo. The increased sensitivity which provides a basis for therapeutically targeting WEE1 in to the WEE1 inhibitor was caused by accumulated DNA damage– ATRX-deficient cancers. -
ATRX and RECQ5 Define Distinct Homologous Recombination Subpathways
ATRX and RECQ5 define distinct homologous recombination subpathways Amira Elbakrya, Szilvia Juhásza,1, Ki Choi Chana, and Markus Löbricha,2 aRadiation Biology and DNA Repair, Technical University of Darmstadt, 64287 Darmstadt, Germany Edited by Stephen C. West, The Francis Crick Institute, London, United Kingdom, and approved December 10, 2020 (received for review May 25, 2020) Homologous recombination (HR) is an important DNA double- or by the resolvase GEN1 which induce asymmetrical or sym- strand break (DSB) repair pathway that copies sequence informa- metrical incisions in the two strands at each HJ, giving rise to tion lost at the break site from an undamaged homologous tem- both crossover (CO) and non-CO products (6–8). Additionally, plate. This involves the formation of a recombination structure dHJs can be dissolved by the BLM/TOPOIIIα/RMI1/2 (BTR) that is processed to restore the original sequence but also harbors complex, where the two HJs migrate toward each other and the potential for crossover (CO) formation between the participat- merge to form a hemicatenane that is then decatenated by top- ing molecules. Synthesis-dependent strand annealing (SDSA) is an oisomerases, thus separating the two molecules without ex- HR subpathway that prevents CO formation and is thought to change of genetic material (9–11). Under specific circumstances, predominate in mammalian cells. The chromatin remodeler ATRX a third subpathway termed break-induced replication (BIR) can promotes an alternative HR subpathway that has the potential to mediate conservative DNA synthesis initiated by the D-loop to form COs. Here, we show that ATRX-dependent HR outcompetes copy the entire chromosome arm (12, 13). -
The Chromatin Remodeller ATRX: a Repeat Offender in Human Disease
Review The chromatin remodeller ATRX: a repeat offender in human disease David Clynes, Douglas R. Higgs, and Richard J. Gibbons MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK The regulation of chromatin structure is of paramount collaboration with its interaction partner death-associated importance for a variety of fundamental nuclear process- protein 6 (DAXX), functions as a histone chaperone complex es, including gene expression, DNA repair, replication, for the deposition of the histone variant H3.3 into peri- and recombination. The ATP-dependent chromatin- centric, telomeric, and ribosomal repeat sequences [7–10]. remodelling factor ATRX (a thalassaemia/mental retar- ATR-X syndrome is characterised by a variety of clini- dation X-linked) has emerged as a key player in each of cal features that include mental retardation, facial, skel- these processes. Exciting recent developments suggest etal, and urogenital abnormalities, as well as mild a- that ATRX plays a variety of key roles at tandem repeat thalassaemia (a blood disorder characterised by an im- sequences within the genome, including the deposition balance of globin chain synthesis and anaemia) [11,12]. of a histone variant, prevention of replication fork stal- The latter is attributable to reduced expression of the a ling, and the suppression of a homologous recombina- globin genes located on chromosome 16. ATRX was hence tion-based pathway of telomere maintenance. Here, we considered to be an X-chromosome-encoded trans-acting provide a mechanistic overview of the role of ATRX in factor that facilitates the expression of a select repertoire each of these processes, and propose how they may be of disparate genes. -
Werner Syndrome Protein Participates in a Complex with RAD51, RAD54
Erratum Werner syndrome protein participates in a complex with RAD51, RAD54, RAD54B and ATR in response to ICL-induced replication arrest Marit Otterlei, Per Bruheim, Byungchan Ahn, Wendy Bussen, Parimal Karmakar, Kathy Baynton and Vilhelm A. Bohr Journal of Cell Science 119, 5215 (2006) doi:10.1242/jcs.03359 There was an error in the first e-press version of the article published in J. Cell Sci. 119, 5137-5146. The first e-press version of this article gave the page range as 5114-5123, whereas it should have been 5137-5146. We apologise for this mistake. Research Article 5137 Werner syndrome protein participates in a complex with RAD51, RAD54, RAD54B and ATR in response to ICL-induced replication arrest Marit Otterlei1,2,*, Per Bruheim1,3,§, Byungchan Ahn1,4,§, Wendy Bussen5, Parimal Karmakar1,6, Kathy Baynton7 and Vilhelm A. Bohr1 1Laboratory of Molecular Gerontology, National Institute on Aging, NIH, 5600 Nathan Shock Dr., Baltimore, MD 21224, USA 2Department of Cancer Research and Molecular Medicine, Laboratory Centre, Faculty of Medicine, Norwegian University of Science and Technology, Erling Skjalgsons gt. 1, N-7006 Trondheim, Norway 3Department of Biotechnology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway 4Department of Life Sciences, University of Ulsan, Ulsan 680-749, Korea 5Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar St, SHM-C130, New Haven, CT 06515, USA 6Department of Life Science and Biotechnology, Jadavpur University, Kolkata-700 032, WB, -
ATRX Promotes Heterochromatin Formation to Protect Cells from G-Quadruplex DNA-Mediated Stress
ARTICLE https://doi.org/10.1038/s41467-021-24206-5 OPEN ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress Yu-Ching Teng1, Aishwarya Sundaresan1, Ryan O’Hara1, Vincent U. Gant1, Minhua Li1, Sara Martire 1, ✉ Jane N. Warshaw1, Amrita Basu2 & Laura A. Banaszynski 1 1234567890():,; ATRX is a tumor suppressor that has been associated with protection from DNA replication stress, purportedly through resolution of difficult-to-replicate G-quadruplex (G4) DNA structures. While several studies demonstrate that loss of ATRX sensitizes cells to chemical stabilizers of G4 structures, the molecular function of ATRX at G4 regions during replication remains unknown. Here, we demonstrate that ATRX associates with a number of the MCM replication complex subunits and that loss of ATRX leads to G4 structure accumulation at newly synthesized DNA. We show that both the helicase domain of ATRX and its H3.3 chaperone function are required to protect cells from G4-induced replicative stress. Fur- thermore, these activities are upstream of heterochromatin formation mediated by the his- tone methyltransferase, ESET, which is the critical molecular event that protects cells from G4-mediated stress. In support, tumors carrying mutations in either ATRX or ESET show increased mutation burden at G4-enriched DNA sequences. Overall, our study provides new insights into mechanisms by which ATRX promotes genome stability with important impli- cations for understanding impacts of its loss on human disease. 1 Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children’s Medical Center Research Institute, Harold. C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical ✉ Center, Dallas, TX, USA.