The Activation of TC10, a Rho Small Gtpase, Contributes to V-Rel-Mediated Transformation
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The Nurd Complex Cooperates with Dnmts to Maintain Silencing of Key Colorectal Tumor Suppressor Genes
Oncogene (2014) 33, 2157–2168 & 2014 Macmillan Publishers Limited All rights reserved 0950-9232/14 www.nature.com/onc ORIGINAL ARTICLE The NuRD complex cooperates with DNMTs to maintain silencing of key colorectal tumor suppressor genes Y Cai1,6, E-J Geutjes2,6, K de Lint2, P Roepman3, L Bruurs2, L-R Yu4, W Wang1, J van Blijswijk2, H Mohammad1, I de Rink5, R Bernards2 and SB Baylin1 Many tumor suppressor genes (TSGs) are silenced through synergistic layers of epigenetic regulation including abnormal DNA hypermethylation of promoter CpG islands, repressive chromatin modifications and enhanced nucleosome deposition over transcription start sites. The protein complexes responsible for silencing of many of such TSGs remain to be identified. Our previous work demonstrated that multiple silenced TSGs in colorectal cancer cells can be partially reactivated by DNA demethylation in cells disrupted for the DNA methyltransferases 1 and 3B (DNMT1 and 3B) or by DNMT inhibitors (DNMTi). Herein, we used proteomic and functional genetic approaches to identify additional proteins that cooperate with DNMTs in silencing these key silenced TSGs in colon cancer cells. We discovered that DNMTs and the core components of the NuRD (Mi-2/nucleosome remodeling and deacetylase) nucleosome remodeling complex, chromo domain helicase DNA-binding protein 4 (CHD4) and histone deacetylase 1 (HDAC1) occupy the promoters of several of these hypermethylated TSGs and physically and functionally interact to maintain their silencing. Consistent with this, we find an inverse relationship between expression of HDAC1 and 2 and these TSGs in a large panel of primary colorectal tumors. We demonstrate that DNMTs and NuRD cooperate to maintain the silencing of several negative regulators of the WNT and other signaling pathways. -
Human Prion-Like Proteins and Their Relevance in Disease
ADVERTIMENT. Lʼaccés als continguts dʼaquesta tesi queda condicionat a lʼacceptació de les condicions dʼús establertes per la següent llicència Creative Commons: http://cat.creativecommons.org/?page_id=184 ADVERTENCIA. El acceso a los contenidos de esta tesis queda condicionado a la aceptación de las condiciones de uso establecidas por la siguiente licencia Creative Commons: http://es.creativecommons.org/blog/licencias/ WARNING. The access to the contents of this doctoral thesis it is limited to the acceptance of the use conditions set by the following Creative Commons license: https://creativecommons.org/licenses/?lang=en Universitat Autònoma de Barcelona Departament de Bioquímica i Biologia Molecular Institut de Biotecnologia i Biomedicina HUMAN PRION-LIKE PROTEINS AND THEIR RELEVANCE IN DISEASE Doctoral thesis presented by Cristina Batlle Carreras for the degree of PhD in Biochemistry, Molecular Biology and Biomedicine from the Universitat Autònoma de Barcelona. The work described herein has been performed in the Department of Biochemistry and Molecular Biology and in the Institute of Biotechnology and Biomedicine, supervised by Prof. Salvador Ventura i Zamora. Cristina Batlle Carreras Prof. Salvador Ventura i Zamora Bellaterra, 2020 Protein Folding and Conformational Diseases Lab. This work was financed with the fellowship “Formación de Profesorado Universitario” by “Ministerio de Ciencia, Innovación y Universidades”. This work is licensed under a Creative Commons Attributions-NonCommercial-ShareAlike 4.0 (CC BY-NC- SA 4.0) International License. The extent of this license does not apply to the copyrighted publications and images reproduced with permission. (CC BY-NC-SA 4.0) Batlle, Cristina: Human prion-like proteins and their relevance in disease. Doctoral Thesis, Universitat Autònoma de Barcelona (2020) English summary ENGLISH SUMMARY Prion-like proteins have attracted significant attention in the last years. -
Termin Translat Trna Utr Mutat Protein Signal
Drugs & Chemicals 1: Tumor Suppressor Protein p53 2: Heterogeneous-Nuclear Ribonucleo- (1029) proteins (14) activ apoptosi arf cell express function inactiv induc altern assai associ bind mdm2 mutat p53 p73 pathwai protein regul complex detect exon famili genom respons suppress suppressor tumor wild-typ interact intron isoform nuclear protein sensit site specif splice suggest variant 3: RNA, Transfer (110) 4: DNA Primers (1987) codon contain differ eukaryot gene initi amplifi analysi chain clone detect dna express mrna protein region ribosom rna fragment gene genotyp mutat pcr sequenc site speci suggest synthesi polymorph popul primer reaction region restrict sequenc speci termin translat trna utr 5: Saccharomyces cerevisiae Proteins 6: Apoptosis Regulatory Proteins (291) (733) activ apoptosi apoptosis-induc albican bud candida cerevisia complex encod apoptot bcl-2 caspas caspase-8 cell eukaryot fission function growth interact involv death fasl induc induct ligand methyl necrosi pathwai program sensit surviv trail mutant pomb protein requir saccharomyc strain suggest yeast 7: Plant Proteins (414) 8: Membrane Proteins (1608) access arabidopsi cultivar flower hybrid leaf leav apoptosi cell conserv domain express function gene human identifi inhibitor line maiz plant pollen rice root seed mammalian membran mice mous mutant seedl speci thaliana tomato transgen wheat mutat protein signal suggest transport 1 9: Tumor Suppressor Proteins (815) 10: 1-Phosphatidylinositol 3-Kinase activ arrest cell cycl cyclin damag delet dna (441) 3-kinas activ -
Bicyclomycin Sensitivity and Resistance Affect Rho Factor-Mediated Transcription Termination in the Tna Operon of Escherichia Coli
JOURNAL OF BACTERIOLOGY, Aug. 1995, p. 4451–4456 Vol. 177, No. 15 0021-9193/95/$04.0010 Copyright 1995, American Society for Microbiology Bicyclomycin Sensitivity and Resistance Affect Rho Factor-Mediated Transcription Termination in the tna Operon of Escherichia coli CHARLES YANOFSKY* AND VIRGINIA HORN Department of Biological Sciences, Stanford University, Stanford, California 94305-5020 Received 13 March 1995/Accepted 27 May 1995 The growth-inhibiting drug bicyclomycin, known to be an inhibitor of Rho factor activity in Escherichia coli, was shown to increase basal level expression of the tryptophanase (tna) operon and to allow growth of a tryptophan auxotroph on indole. The drug also relieved polarity in the trp operon and permitted growth of a trp double nonsense mutant on indole. Nine bicyclomycin-resistant mutants were isolated and partially characterized. Recombination data and genetic and biochemical complementation analyses suggest that five have mutations that affect rho, three have mutations that affect rpoB, and one has a mutation that affects a third locus, near rpoB. Individual mutants showed decreased, normal, or increased basal-level expression of the tna operon. All but one of the resistant mutants displayed greatly increased tna operon expression when grown in the presence of bicyclomycin. The tna operon of the wild-type drug-sensitive parent was also shown to be highly expressed during growth with noninhibitory concentrations of bicyclomycin. These findings demonstrate that resistance to this drug may be acquired by mutations at any one of three loci, two of which appear to be rho and rpoB. Zwiefka et al. (24) found that the antibiotic bicyclomycin segment and interacts with the transcribing RNA polymerase (bicozamycin), an inhibitor of the growth of several gram- molecule, causing it to terminate transcription (7, 9). -
Downregulation of the Let‑7 Family of Micrornas May Promote Insulin Receptor/Insulin‑Like Growth Factor Signalling Pathways in Pancreatic Ductal Adenocarcinoma
ONCOLOGY LETTERS 20: 2613-2620, 2020 Downregulation of the let‑7 family of microRNAs may promote insulin receptor/insulin‑like growth factor signalling pathways in pancreatic ductal adenocarcinoma EKENE EMMANUEL NWEKE1 and MARTIN BRAND2,3 1Department of Surgery, 2School of Physiology, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193; 3Department of Surgery, Steve Biko Academic Hospital and The University of Pretoria, Pretoria 0002, South Africa Received October 18, 2019; Accepted May 27, 2020 DOI: 10.3892/ol.2020.11854 Abstract. Pancreatic ductal adenocarcinoma (PDAC) is may thus be an effective target for the development of INSR/ an aggressive cancer type characterized by dysregulated IGF pathway‑specific treatment strategies. cell signalling pathways and resistance to treatment. The insulin-like growth factor (IGF) signalling pathway has Introduction been identified to have a role in tumour progression and therapy resistance. However, its regulatory roles in PDAC According to 2018 GLOBOCAN statistics, pancreatic cancer have remained to be fully elucidated. In the present study, had 458,918 new cases and 432,242 mortalities, which dysregulated microRNAs (miRNAs) in PDAC were explored accounted for 4.5% of cancer-associated deaths world- with a focus on those that may be involved in regulating the wide (1,2). Pancreatic ductal adenocarcinoma (PDAC), the insulin/IGF signalling pathway. A total of 208 patients were most common type of pancreatic cancer, has a poor prog- recruited, comprising 112 patients with PDAC, 50 patients nosis with a five‑year overall survival rate of 5%, which has with chronic pancreatitis (CP) and 46 subjects as a control not significantly improved over the last two decades despite group (CG). -
Structure of the Rho Transcription Terminator: Mechanism of Mrna Recognition and Helicase Loading
Cell, Vol. 114, 135–146, July 11, 2003, Copyright 2003 by Cell Press Structure of the Rho Transcription Terminator: Mechanism of mRNA Recognition and Helicase Loading Emmanuel Skordalakes and James M. Berger* this process by a number of factors, such as NusG, Department of Molecular and Cell Biology which serve as antiterminators to ameliorate the termi- University of California, Berkeley nation properties of the enzyme (Sullivan and Gottes- 239 Hildebrand Hall, #3206 man, 1992). Berkeley, California 94720 Tethering of Rho to a rut site is independent of ATP binding and/or hydrolysis (Galluppi and Richardson, 1980; McSwiggen et al., 1988) and is mediated by an Summary N-terminal domain in each protomer of the Rho hexamer (Martinez et al., 1996a, 1996b; Allison et al., 1998; Bri- In bacteria, one of the major transcriptional termina- ercheck et al., 1998). Previous high-resolution NMR and tion mechanisms requires a RNA/DNA helicase known X-ray crystal structures of the N-terminal mRNA binding as the Rho factor. We have determined two structures domain of Rho have provided a structural view of this of Rho complexed with nucleic acid recognition site fold and its interactions with target substrates (Allison mimics in both free and nucleotide bound states to et al., 1998; Briercheck et al., 1998; Bogden et al., 1999). 3.0 A˚ resolution. Both structures show that Rho forms The domain consists of a three-helix bundle that rests a hexameric ring in which two RNA binding sites—a on top of a five-stranded  barrel. The barrel belongs primary one responsible for target mRNA recognition to the oligonucleotide/oligossacharide binding (OB) pro- and a secondary one required for mRNA translocation tein superfamily and is primarily responsible for Rho’s and unwinding—point toward the center of the ring. -
Identification of Transcriptional Mechanisms Downstream of Nf1 Gene Defeciency in Malignant Peripheral Nerve Sheath Tumors Daochun Sun Wayne State University
Wayne State University DigitalCommons@WayneState Wayne State University Dissertations 1-1-2012 Identification of transcriptional mechanisms downstream of nf1 gene defeciency in malignant peripheral nerve sheath tumors Daochun Sun Wayne State University, Follow this and additional works at: http://digitalcommons.wayne.edu/oa_dissertations Recommended Citation Sun, Daochun, "Identification of transcriptional mechanisms downstream of nf1 gene defeciency in malignant peripheral nerve sheath tumors" (2012). Wayne State University Dissertations. Paper 558. This Open Access Dissertation is brought to you for free and open access by DigitalCommons@WayneState. It has been accepted for inclusion in Wayne State University Dissertations by an authorized administrator of DigitalCommons@WayneState. IDENTIFICATION OF TRANSCRIPTIONAL MECHANISMS DOWNSTREAM OF NF1 GENE DEFECIENCY IN MALIGNANT PERIPHERAL NERVE SHEATH TUMORS by DAOCHUN SUN DISSERTATION Submitted to the Graduate School of Wayne State University, Detroit, Michigan in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY 2012 MAJOR: MOLECULAR BIOLOGY AND GENETICS Approved by: _______________________________________ Advisor Date _______________________________________ _______________________________________ _______________________________________ © COPYRIGHT BY DAOCHUN SUN 2012 All Rights Reserved DEDICATION This work is dedicated to my parents and my wife Ze Zheng for their continuous support and understanding during the years of my education. I could not achieve my goal without them. ii ACKNOWLEDGMENTS I would like to express tremendous appreciation to my mentor, Dr. Michael Tainsky. His guidance and encouragement throughout this project made this dissertation come true. I would also like to thank my committee members, Dr. Raymond Mattingly and Dr. John Reiners Jr. for their sustained attention to this project during the monthly NF1 group meetings and committee meetings, Dr. -
For Personal Use. Only Reproduce with Permission from the Lancet
Correlation to non-HGNT Accesion group 2 Description AA897204 1.479917 ESTs T85111 1.286576 null T60168 | AI821353 1.274487 thyroid transcription factor 1 AA600173 1.183065 ubiquitin-conjugating enzyme E2A (RAD6 homolog) R55745 1.169339 ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D) AA400492 1.114935 ESTs AA864791 1.088826 hypothetical protein FLJ21313 N53758 1.070402 EST AI216628 1.067763 ESTs AI167637 1.058561 ESTs AA478265 1.056331 similar to transmembrane receptor Unc5H1 AA969924 1.039315 EST AI074650 1.039043 hypothetical protein FLJ13842 R20763 1.035807 ELAV (embryonic lethal, abnormal vision, Drosophila)-like 3 (Hu antigen C) AI347081 1.034518 Ca2+-dependent activator protein for secretion R44386 1.028005 ESTs AA976699 1.027227 chromogranin A (parathyroid secretory protein 1) AA634475 1.026766 KIAA1796 protein AA496809 1.02432 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 H16572 1.013059 null H29013 1.002117 seizure related 6 homolog (mouse)-like AI299731 1.001053 Homo sapiens nanos mRNA, partial cds AA400194 0.9950039 EST AI216537 | AI820870 0.9737153 Homo sapiens cDNA FLJ39674 fis, clone SMINT2009505 AA426408 0.9728649 type I transmembrane receptor (seizure-related protein) AA971742 | AI733380 0.9707561 achaete-scute complex-like 1 (Drosophila) R41450 0.9655133 ESTs AA487505 0.9636143 immunoglobulin superfamily, member 4 AA404337 0.957686 thymus high mobility group box protein TOX N68578 0.9552571 ESTs R45008 0.9422938 ELAV (embryonic lethal, abnormal -
Theoretical Principles of in Vitro Selection Using Combinatorial
Theoretical Principles of In Vitro Selection UNIT 9.1 Using Combinatorial Nucleic Acid Libraries Over the past decade, a new paradigm for binding proteins, peptides, and small organic drug discovery (Gold, 1995) and biological molecules (reviewed in Klug and Famulok, research (Gold et al., 1995) has been developed 1994; Gold, 1995; Gold et al., 1995). This unit from technologies that integrate combinatorial presents a theoretical overview of in vitro af- chemistry with rounds of selection and ampli- finity selection using SELEX technology. fication, a technique that is called in vitro se- A schematic representation of the SELEX lection. Systematic Evolution of Ligands by process is shown in Figure 9.1.1 and may be EXponential enrichment, or SELEX (Ellington used to describe SELEX performed with librar- and Szostak, 1990; Tuerk and Gold, 1990) is a ies of RNA, RNA derivatives, or DNA. For the flexible and extremely successful form of this purposes of developing a mathematical model, technology that uses combinatorial libraries of the SELEX process for affinity binding may be oligonucleotides containing regions of ran- summarized in four steps: (1) generation of a domized sequence as potential ligands. Oli- library of potential ligands, (2) binding of the gonucleotide libraries (containing randomized library to the target molecule, (3) partitioning regions) provide, after selection, compounds of the bound ligands from the unbound ligands, that bind tightly to the intended target. The and (4) amplification of the partitioned ligands process of in vitro selection was called SELEX to generate a new, enriched library, leading by Tuerk and Gold (1990), while the selected again to step 1. -
Abdullahi, Akilu Nuclear 80S Ribosomes Increase Upon Serum Starvation 51
Posters A-Z Abdullahi, Akilu Nuclear 80S ribosomes increase upon serum starvation 51 Abernathy, Emma Virus-induced global cytoplasmic mRNA degradation impacts 52 transcription rates in mammalian cells Acosta-Alvear, Diego Blueprint of the mammalian IRE1 interactome revealed by unbiased 53 systems-level analyses Afroz, Tariq A fly-trap mechanism provides sequence-specific RNA recognition by 54 CPEB proteins Agarwala, Prachi 5' UTR localized G-quadruplexes synergistically modulate TGFß2 55 expression Ali Khan, Abrar Functional genetic variations in proximal promoter alter the expression 56 of 3-hydroxy-3-methyl glutaryl-coenzyme A reductase gene in spontaneously hypertensive rat ALqosaibi, Amany I. The role of some genes in Telomere Position Effect appears to involve 57 post-transcriptional regulation of a sub-telomeric reporter gene Alshiekh, Alak Targeting BRCA1 mRNA by tunable miR mimics 58 Alves, Lysangela The mRNAs associated to a zinc finger protein shift during stress 59 conditions: The zinc finger protein TcZC3H39 and the stress response in Trypanosoma cruzi Andries, Vanessa Role of NANOS3 in tumor progression 60 Antic, Sanja mRNA degradation on the ribosome in Drosophila cells 61 EMBO | EMBL Symposia: The Complex Life of mRNA Archambaud, Cristel The intestinal microbiota interferes with the microRNA response upon 62 oral Listeria infection Arnese, Renato Generation of a knock-in mouse model for the in vivo study of local 63 protein synthesis: a preliminary screening Babour, Anna Licensing mRNP for nuclear export: a role for chromatin -
Regulatory Interplay Between Small Rnas and Transcription Termination Factor Rho Lionello Bossi, Nara Figueroa-Bossi, Philippe Bouloc, Marc Boudvillain
Regulatory interplay between small RNAs and transcription termination factor Rho Lionello Bossi, Nara Figueroa-Bossi, Philippe Bouloc, Marc Boudvillain To cite this version: Lionello Bossi, Nara Figueroa-Bossi, Philippe Bouloc, Marc Boudvillain. Regulatory interplay be- tween small RNAs and transcription termination factor Rho. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms , Elsevier, 2020, pp.194546. 10.1016/j.bbagrm.2020.194546. hal-02533337 HAL Id: hal-02533337 https://hal.archives-ouvertes.fr/hal-02533337 Submitted on 6 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Regulatory interplay between small RNAs and transcription termination factor Rho Lionello Bossia*, Nara Figueroa-Bossia, Philippe Bouloca and Marc Boudvillainb a Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France b Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France * Corresponding author: [email protected] Highlights Repression -
Struktur-Funktionsbeziehungen Der Rho- Und Der Plexin-Proteinfamilien
Struktur-Funktionsbeziehungen der Rho- und der Plexin-Proteinfamilien Inauguraldissertation zur Erlangung des Doktorgrades der Fakultät für Chemie der Ruhr-Universität Bochum vorgelegt von Dennis Franz-Josef Fiegen aus Kleve April 2005 INHALTSVERZEICHNIS _______________________________________________________________________________________________________________________________________________________________________________________________________________ Inhaltsverzeichnis Inhaltsverzeichnis .................................................................................................................... III Abbildungsverzeichnis ............................................................................................................ IX Tabellenverzeichnis ................................................................................................................. XI Abkürzungsverzeichnis ..........................................................................................................XII 1. Einleitung ........................................................................................................................ 1 1.1 GTP-bindende Proteine als Elemente der Signaltransduktion ..................................... 2 1.2 Die Ras-Superfamilie ..................................................................................................... 3 1.3 Die GTPasen der Rho-Familie ....................................................................................... 7 1.4 Regulatoren und Effektoren der RhoGTPasen