Evaluation of Common Genetic Variants in 82 Candidate Genes As
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Identification of Transcriptomic Differences Between Lower
International Journal of Molecular Sciences Article Identification of Transcriptomic Differences between Lower Extremities Arterial Disease, Abdominal Aortic Aneurysm and Chronic Venous Disease in Peripheral Blood Mononuclear Cells Specimens Daniel P. Zalewski 1,*,† , Karol P. Ruszel 2,†, Andrzej St˛epniewski 3, Dariusz Gałkowski 4, Jacek Bogucki 5 , Przemysław Kołodziej 6 , Jolanta Szyma ´nska 7 , Bartosz J. Płachno 8 , Tomasz Zubilewicz 9 , Marcin Feldo 9,‡ , Janusz Kocki 2,‡ and Anna Bogucka-Kocka 1,‡ 1 Chair and Department of Biology and Genetics, Medical University of Lublin, 4a Chod´zkiSt., 20-093 Lublin, Poland; [email protected] 2 Chair of Medical Genetics, Department of Clinical Genetics, Medical University of Lublin, 11 Radziwiłłowska St., 20-080 Lublin, Poland; [email protected] (K.P.R.); [email protected] (J.K.) 3 Ecotech Complex Analytical and Programme Centre for Advanced Environmentally Friendly Technologies, University of Marie Curie-Skłodowska, 39 Gł˛ebokaSt., 20-612 Lublin, Poland; [email protected] 4 Department of Pathology and Laboratory Medicine, Rutgers-Robert Wood Johnson Medical School, One Robert Wood Johnson Place, New Brunswick, NJ 08903-0019, USA; [email protected] 5 Chair and Department of Organic Chemistry, Medical University of Lublin, 4a Chod´zkiSt., Citation: Zalewski, D.P.; Ruszel, K.P.; 20-093 Lublin, Poland; [email protected] St˛epniewski,A.; Gałkowski, D.; 6 Laboratory of Diagnostic Parasitology, Chair and Department of Biology and Genetics, Medical University of Bogucki, J.; Kołodziej, P.; Szyma´nska, Lublin, 4a Chod´zkiSt., 20-093 Lublin, Poland; [email protected] J.; Płachno, B.J.; Zubilewicz, T.; Feldo, 7 Department of Integrated Paediatric Dentistry, Chair of Integrated Dentistry, Medical University of Lublin, M.; et al. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Neuronal Network Dysfunction in a Human Model for Kleefstra Syndrome Mediated by Enhanced NMDAR Signaling
bioRxiv preprint doi: https://doi.org/10.1101/585596; this version posted March 21, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Neuronal network dysfunction in a human model for Kleefstra syndrome mediated by enhanced NMDAR signaling Monica Frega1,2†, Katrin Linda1†, Jason M. Keller1, Güvem Gümüş-Akay1, Britt Mossink1, Jon- Ruben van Rhijn3, Moritz Negwer1, Teun Klein Gunnewiek4, Katharina Foreman3, Nine Kompier3, Chantal Schoenmaker1, Willem van den Akker1, Astrid Oudakker1, Huiqing Zhou1,5, Tjitske Kleefstra1, Dirk Schubert3, Hans van Bokhoven1,3, Nael Nadif Kasri1,3* 1Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behaviour, 6500 HB Nijmegen, the Netherlands 2Department of Clinical neurophysiology, University of Twente, 7522 NB Enschede, the Netherlands 3Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB Nijmegen, the Netherlands 4Department of Anatomy, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB Nijmegen, the Netherlands 5Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, the Netherlands †These authors contributed equally to the work *Corresponding Author dr. Nael Nadif Kasri Email: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/585596; this version posted March 21, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Epigenetic regulation of gene transcription plays a critical role in neural network development and in the etiology of Intellectual Disability (ID) and Autism Spectrum Disorder (ASD). -
Supp Table 6.Pdf
Supplementary Table 6. Processes associated to the 2037 SCL candidate target genes ID Symbol Entrez Gene Name Process NM_178114 AMIGO2 adhesion molecule with Ig-like domain 2 adhesion NM_033474 ARVCF armadillo repeat gene deletes in velocardiofacial syndrome adhesion NM_027060 BTBD9 BTB (POZ) domain containing 9 adhesion NM_001039149 CD226 CD226 molecule adhesion NM_010581 CD47 CD47 molecule adhesion NM_023370 CDH23 cadherin-like 23 adhesion NM_207298 CERCAM cerebral endothelial cell adhesion molecule adhesion NM_021719 CLDN15 claudin 15 adhesion NM_009902 CLDN3 claudin 3 adhesion NM_008779 CNTN3 contactin 3 (plasmacytoma associated) adhesion NM_015734 COL5A1 collagen, type V, alpha 1 adhesion NM_007803 CTTN cortactin adhesion NM_009142 CX3CL1 chemokine (C-X3-C motif) ligand 1 adhesion NM_031174 DSCAM Down syndrome cell adhesion molecule adhesion NM_145158 EMILIN2 elastin microfibril interfacer 2 adhesion NM_001081286 FAT1 FAT tumor suppressor homolog 1 (Drosophila) adhesion NM_001080814 FAT3 FAT tumor suppressor homolog 3 (Drosophila) adhesion NM_153795 FERMT3 fermitin family homolog 3 (Drosophila) adhesion NM_010494 ICAM2 intercellular adhesion molecule 2 adhesion NM_023892 ICAM4 (includes EG:3386) intercellular adhesion molecule 4 (Landsteiner-Wiener blood group)adhesion NM_001001979 MEGF10 multiple EGF-like-domains 10 adhesion NM_172522 MEGF11 multiple EGF-like-domains 11 adhesion NM_010739 MUC13 mucin 13, cell surface associated adhesion NM_013610 NINJ1 ninjurin 1 adhesion NM_016718 NINJ2 ninjurin 2 adhesion NM_172932 NLGN3 neuroligin -
Methylated Spirits: Epigenetic Hypotheses of Psychiatric Disorders
Trends in Psychopharmacology Methylated Spirits: Epigenetic Hypotheses of Psychiatric Disorders Stephen M. Stahl, MD, PhD NEW TREND IN various brain circuits and creating risk for develop- PSYCHOPHARMACOLOGY ing a symptom of a mental illness. Now comes the Our spirits may be regulated by the methylation role of epigenetic actions in mental illnesses. If nor- of our genes. Methylation, acetylation, and other mal genes make normal gene products but at the biochemical processes are the molecular switches wrong time, either being epigenetically expressed for turning genes on and off. There is evidence in neurons when they should be silenced or epi- now that certain behaviors, feelings, and psychiat- genetically silenced in neurons when they should ric symptoms may be modified by turning various be expressed, particularly under the influence of genes on or off. If classical genetics is the sequence environmental factors and stress, this, too, can of DNA that is inherited, then epigenetics is a par- contribute to inefficient information processing in allel process determining whether a given gene brain circuits, increasing the chance of develop- (ie, a sequence of DNA coding for transcription) is ing symptoms of a psychiatric disorder. Here we expressed into its RNA or is silenced. Epigenetics describe the role of epigenetics and methylomics is now entering psychiatry with the hypothesis (methylating or demethylating upstream genes that normal genes as well as risk genes can both and downstream molecules) in various psychiatric contribute to a mental disorder. That is, it has long disorders, emphasizing schizophrenia, and demon- been hypothesized that when “abnormal” genes strate whether your spirits can be truly methylated. -
Histone Lysine Methyltransferases As Anti-Cancer Targets for Drug Discovery
Acta Pharmacologica Sinica (2016) 37: 1273–1280 © 2016 CPS and SIMM All rights reserved 1671-4083/16 www.nature.com/aps Review Histone lysine methyltransferases as anti-cancer targets for drug discovery Qing LIU1, 2, 3, Ming-wei WANG1, 2, 3, * 1The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; 2The National Center for Drug Screening, Shanghai 201203, China; 3School of Pharmacy, Fudan University, Shanghai 201203, China Post-translational epigenetic modification of histones is controlled by a number of histone-modifying enzymes. Such modification regulates the accessibility of DNA and the subsequent expression or silencing of a gene. Human histone methyltransferases (HMTs) constitute a large family that includes histone lysine methyltransferases (HKMTs) and histone/protein arginine methyltransferases (PRMTs). There is increasing evidence showing a correlation between HKMTs and cancer pathogenesis. Here, we present an overview of representative HKMTs, including their biological and biochemical properties as well as the profiles of small molecule inhibitors for a comprehensive understanding of HKMTs in drug discovery. Keywords: histone methyltransferases; adenosylmethionine; small molecule inhibitors; anti-cancer drugs; epigenetic modification; drug discovery Acta Pharmacologica Sinica (2016) 37: 1273–1280; doi: 10.1038/aps.2016.64; published online 11 Jul 2016 Introduction vivo, suggesting the possibility of using HKMTs as targets for Post-translational epigenetic modifications of histones are cancer therapy. Here, we discuss individual histone lysine controlled by histone-modifying enzymes, including histone methylation with the currently available small molecule inhib- methyltransferases (HMTs), histone demethylases, histone itors and their applications in cancer treatment. acetyltransferases, histone deacetylases (HDACs), ubiquitin ligases, and other specific kinases phosphorylating serine HKMTs-catalyzed methylation residues on histones. -
EHMT2 Directs DNA Methylation for Efficient Gene Silencing in Mouse Embryos
Downloaded from genome.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press Research EHMT2 directs DNA methylation for efficient gene silencing in mouse embryos Ghislain Auclair,1 Julie Borgel,2,3,4 Lionel A. Sanz,2,3,5 Judith Vallet,1 Sylvain Guibert,1 Michael Dumas,1 Patricia Cavelier,2 Michael Girardot,2 Thierry Forné,2 Robert Feil,2 and Michael Weber1 1CNRS, University of Strasbourg, UMR7242 Biotechnology and Cell Signaling, 67412 Illkirch, France; 2Institute of Molecular Genetics, CNRS UMR5535, University of Montpellier, 34293 Montpellier, France The extent to which histone modifying enzymes contribute to DNA methylation in mammals remains unclear. Previous studies suggested a link between the lysine methyltransferase EHMT2 (also known as G9A and KMT1C) and DNA methyl- ation in the mouse. Here, we used a model of knockout mice to explore the role of EHMT2 in DNA methylation during mouse embryogenesis. The Ehmt2 gene is expressed in epiblast cells but is dispensable for global DNA methylation in embryogenesis. In contrast, EHMT2 regulates DNA methylation at specific sequences that include CpG-rich promoters of germline-specific genes. These loci are bound by EHMT2 in embryonic cells, are marked by H3K9 dimethylation, and have strongly reduced DNA methylation in Ehmt2−/− embryos. EHMT2 also plays a role in the maintenance of germ- line-derived DNA methylation at one imprinted locus, the Slc38a4 gene. Finally, we show that DNA methylation is instru- mental for EHMT2-mediated gene silencing in embryogenesis. Our findings identify EHMT2 as a critical factor that facilitates repressive DNA methylation at specific genomic loci during mammalian development. -
Catalytic Inhibition of H3k9me2 Writers Disturbs Epigenetic Marks
www.nature.com/scientificreports OPEN Catalytic inhibition of H3K9me2 writers disturbs epigenetic marks during bovine nuclear reprogramming Rafael Vilar Sampaio 1,3,4*, Juliano Rodrigues Sangalli1,4, Tiago Henrique Camara De Bem 1, Dewison Ricardo Ambrizi1, Maite del Collado 1, Alessandra Bridi 1, Ana Clara Faquineli Cavalcante Mendes de Ávila1, Carolina Habermann Macabelli 2, Lilian de Jesus Oliveira1, Juliano Coelho da Silveira 1, Marcos Roberto Chiaratti 2, Felipe Perecin 1, Fabiana Fernandes Bressan1, Lawrence Charles Smith3, Pablo J Ross 4 & Flávio Vieira Meirelles1* Orchestrated events, including extensive changes in epigenetic marks, allow a somatic nucleus to become totipotent after transfer into an oocyte, a process termed nuclear reprogramming. Recently, several strategies have been applied in order to improve reprogramming efciency, mainly focused on removing repressive epigenetic marks such as histone methylation from the somatic nucleus. Herein we used the specifc and non-toxic chemical probe UNC0638 to inhibit the catalytic activity of the histone methyltransferases EHMT1 and EHMT2. Either the donor cell (before reconstruction) or the early embryo was exposed to the probe to assess its efect on developmental rates and epigenetic marks. First, we showed that the treatment of bovine fbroblasts with UNC0638 did mitigate the levels of H3K9me2. Moreover, H3K9me2 levels were decreased in cloned embryos regardless of treating either donor cells or early embryos with UNC0638. Additional epigenetic marks such as H3K9me3, 5mC, and 5hmC were also afected by the UNC0638 treatment. Therefore, the use of UNC0638 did diminish the levels of H3K9me2 and H3K9me3 in SCNT-derived blastocysts, but this was unable to improve their preimplantation development. -
Methyltransferase (NSP16) from SARS-Cov-2 to Tackle the COVID-19 Disease
Supplementary Material Interfering with mRNA methylation by the 2'O- Methyltransferase (NSP16) from SARS-CoV-2 to tackle the COVID-19 disease Content Table S1. Protein Data Bank ID codes of human betacoronavirus NSP16/NSP10 complexes with ligands and/or RNA. Figure S1. Molecular docking of SFG to NSP16. Figure S2. Structure of the 44367977/NSP16 complex with SFG superimposed. Figure S3. Ligand interaction diagrams of NSP16 with SFG, 44367977, 25203154, 71008334 and 44601604. Table S2. PubChem indexed biological assays data of SFG and the newly identified molecules. Table S1. Protein Data Bank ID codes of human betacoronavirus NSP16/NSP10 complexes with ligands and/or RNA. Code mRNA binding Cofactor/Inhibitor Ions groove binding site SARS-CoV 2XYQ ---- SAH Cl/Mg/Na/Zn Nsp16/10 complex 2XYR ---- SFG Cl/Mg/Na/Zn 2XYV ---- SAH Cl/Mg/Na/Zn 3R24 ---- SAM Zn 5YN5 --- --- Zn 5YN6 ---- SAM Zn 5YN8 ---- SAH Zn 5YNB ---- SFG Zn 5YNF m7GpppA ---- Zn MERS-CoV 5YNI m7GpppG SAM Zn Nsp16/10 complex 5YNJ m7GpppG ---- Zn 5YNN m7GpppG SFG Zn 5YNO m7GpppA SAH Zn 5YNP m7GpppA SFG Zn 5YNQ m7GpppG SAH Zn 6W4H ---- SAM SO3, Zn 6W61 ---- SAM Cl/Zn 6W75 (dimer) ---- SAM Na/Zn 6WJT (dimer) ---- SAH Na/Zn SARS-CoV-2 6WKQ(dimer) ---- SFG Na/Zn Nsp16/10 complex 6WKS m7GpppA SAM Zn 6WQ3 m7GpppA SAH SO4/Zn 6WVN M7GpppA SAM Cl/SO4/Zn 6YZ1 ---- SFG Zn 7C2J ---- SAM Zn Figure S1. Molecular docking of SFG to NSP16. Yellow dashed lines represent hydrogen bonds, magenta dashed lines represent salt bridges and blue dashed lines show aromatic stacking; non- polar hydrogens are not shown for the sake of clarity. -
High-Affinity Alkynyl Bisubstrate Inhibitors of Nicotinamide N-Methyltransferase (NNMT) Rocco L
Subscriber access provided by JUBILANT ORGANOSYS LTD Article High-Affinity Alkynyl Bisubstrate Inhibitors of Nicotinamide N-Methyltransferase (NNMT) Rocco L. Policarpo, Ludovic Decultot, Elizabeth May, Petr Kuzmic, Samuel Carlson, Danny Huang, Vincent Chu, Brandon A. Wright, Saravanakumar Dhakshinamoorthy, Aimo Kannt, Shilpa Rani, Sreekanth Dittakavi, Joseph D. Panarese, Rachelle Gaudet, and Matthew D. Shair J. Med. Chem., Just Accepted Manuscript • DOI: 10.1021/acs.jmedchem.9b01238 • Publication Date (Web): 07 Oct 2019 Downloaded from pubs.acs.org on October 8, 2019 Just Accepted “Just Accepted” manuscripts have been peer-reviewed and accepted for publication. They are posted online prior to technical editing, formatting for publication and author proofing. The American Chemical Society provides “Just Accepted” as a service to the research community to expedite the dissemination of scientific material as soon as possible after acceptance. “Just Accepted” manuscripts appear in full in PDF format accompanied by an HTML abstract. “Just Accepted” manuscripts have been fully peer reviewed, but should not be considered the official version of record. They are citable by the Digital Object Identifier (DOI®). “Just Accepted” is an optional service offered to authors. Therefore, the “Just Accepted” Web site may not include all articles that will be published in the journal. After a manuscript is technically edited and formatted, it will be removed from the “Just Accepted” Web site and published as an ASAP article. Note that technical editing may introduce minor changes to the manuscript text and/or graphics which could affect content, and all legal disclaimers and ethical guidelines that apply to the journal pertain. ACS cannot be held responsible for errors or consequences arising from the use of information contained in these “Just Accepted” manuscripts. -
Catalytic Inhibition of H3k9me2 Writers Disturbs Epigenetic Marks During Bovine Nuclear
bioRxiv preprint doi: https://doi.org/10.1101/847210; this version posted November 20, 2019. 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-NC-ND 4.0 International license. 1 1 Catalytic inhibition of H3K9me2 writers disturbs epigenetic marks during bovine nuclear 2 reprogramming. 3 1,3,4Sampaio RV*, 1,4Sangalli JR, 1De Bem THC, 1Ambrizi DR, 1 del Collado M, 1 Bridi A, 1 Ávila 4 ACFCM, 2Macabelli CH, 1Oliveira LJ, 1da Silveira JC, 2Chiaratti MR, 1Perecin F,1Bressan FF; 5 3Smith LC, 4Ross PJ, 1Meirelles FV. 6 1 Departament of Veterinary Medicine, Faculty of Animal Science and Food Engineering, 7 University of Sao Paulo, Pirassununga, SP, Brazil. 2Departament of Genetic and Evolution, 8 Federal University of São Carlos, São Carlos, SP, Brazil. 3 Université de Montréal, Faculté de 9 médecine vétérinaire, Centre de recherche en reproduction et fertilité, St. Hyacinthe, Québec, 10 postcode: H3T 1J4, Canada.4Department of Animal Science, University of California Davis, 11 USA. 12 *Correspondence 13 Rafael Vilar Sampaio, Department of Veterinary Medicine, Faculty of Food Engineering and 14 Animal Science, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil. Email: 15 [email protected] 16 Abstract 17 Orchestrated events, including extensive changes in epigenetic marks, allow a somatic nucleus to 18 become totipotent after transfer into an oocyte, a process termed nuclear reprogramming. 19 Recently, several strategies have been applied in order to improve reprogramming efficiency, 20 mainly focused on removing repressive epigenetic marks such as histone methylation from the 21 somatic nucleus. -
Protein Interactions Allow Functional Regulation of Homocysteine Metabolism
HIGHLIGHTS - Protein interactions allow functional regulation of homocysteine metabolism - Homocysteine metabolism establishes pathway interplays through protein interactions - Intermolecular interactions within homocysteine metabolism may support substrate channeling - Homocysteine metabolism interaction networks are altered in oncogenesis - Proteins of homocysteine metabolism interact with oncogenes for gene regulation PROTEIN-PROTEIN INTERACTIONS INVOLVING ENZYMES OF THE MAMMALIAN METHIONINE AND HOMOCYSTEINE METABOLISM Francisco Portillo1,2,3,4, Jesús Vázquez5,6, María A. Pajares2,7* 1Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Arturo Duperier 4, 28029 Madrid, Spain 2Instituto de Investigación Sanitaria La Paz (IdiPAZ), Paseo de la Castellana 261, 28046 Madrid, Spain 3Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid, Arzobispo Morcillo 4, 28029 Madrid, Spain 4Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain. 5Laboratory of Cardiovascular Proteomics, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández de Almagro 3, 28029 Madrid, Spain. 6CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain. 7Departamento de Biología Estructural y Química, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain. *Corresponding author: Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain. (Phone: 34-918373112; FAX: 34-915360432; email: [email protected]). ABBREVIATIONS: AdoMet, S-adenosylmethionine; AdoHcy, S- adenosylhomocysteine; AHCY, S-adenosylhomocysteine hydrolase; AP, affinity 1 purification; BHMT and BHMT2, betaine homocysteine S-methyltransferases 1 and 2; CBS, cystathionine b-synthase; CTH, cystathionine g-lyase; GSH and GSSG, glutathione reduced and oxidized forms; Hcy, homocysteine; MAT, methionine adenosyltransferase; MS, mass spectrometry; MTR, methionine synthase; NNMT, nicotinamide N- methyltransferase; PDRG1, p53 and DNA damage-regulated gene 1.