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Regulation and Role of RNA Pol II CTD Phosphoryla-Tion in The MASTERARBEIT Regulation and role of RNA Pol II CTD phosphoryla- tion in the transcription cycle of the Nos2 gene Bernadette Stych, BSc angestrebter akademischer Grad Master of Science (MSc) Wien, 2014 Studienkennzahl lt. Studienblatt: A 066 830 Studienrichtung lt. Studienblatt: Molekulare Mikrobiologie, Mikrobielle Ökologie und Immunbiologie Betreuer: Univ.-Prof.Dr. Thomas Decker 111 CCCONTENT 1 Content .................................................................................................................................. 2 2 Zusammenfassung ................................................................................................................. 4 3 Abstract ................................................................................................................................. 6 4 Introduction .......................................................................................................................... 7 4.1 Listeria Monocytogenes and the innate immune system ............................................. 7 Listeria monocytogenes ........................................................................................ 7 Adherence, invasion and cell spreading ................................................................ 8 Innate immune response to L. monocytogenes - a small overview ....................... 8 Important inflammatory cytokines in L. monocytogenes infection ...................... 8 Response of phagocytes ........................................................................................ 9 Clearance of L. monocytogenes from infected mice ............................................. 9 Toll- like receptor signalling and activation of NFκB pathway ............................ 10 Induction of type I interferon .............................................................................. 11 Activation of the JAK/STAT pathway by type I IFN .............................................. 12 Genes expressed in macrophages after L. monocytogenes infection ................. 14 4.2 iNOS and the Nos2 gene ............................................................................................. 15 4.3 Serine phosphorylation at the CTD of RNA Polymerase II .......................................... 16 RNA Pol II and its carboxy-terminal domain ....................................................... 16 Modification of the CTD of RNA Pol II ................................................................. 16 Serine phosphorylation: Role in transcription and controversy in literature ..... 18 5 Aim of the project ............................................................................................................... 22 6 Results ................................................................................................................................. 23 6.1 induction of Gene expression by the type I IFN and NFκB pathways ......................... 23 6.2 phosphorylation of the RNA polymerase ctd at the Nos2 gene ................................. 24 Normalization and analysis of the ChIP data ...................................................... 25 RNA Pol II distribution at the Nos2 gene ............................................................. 26 Serine 2P of the Pol II CTD at different Nos2 exons ............................................ 27 Serine 5P of the Pol II CTD at different Nos2 exons ............................................ 28 Serine 7P of the Pol II CTD at different Nos2 exons ............................................ 29 6.3 iNOS expression in the Raw 264.7 macrophage cell line ............................................ 29 6.4 Cloning strategy for a NFκB p50 and Cdk7 or Cdk9 fusion gene ................................. 30 Cloning strategies ................................................................................................ 30 Optimization of the PCR protocol ....................................................................... 33 Sequencing data .................................................................................................. 34 Optimization of digestion and ligation step ........................................................ 34 Insertion of the p50 gene into a mammalian expression vector ........................ 35 7 Conclusion & Outlook.......................................................................................................... 36 7.1 Phosphorylation at Serine 2, 5 and 7 residues at the Nos2 gene ............................... 36 8 Materials & Methods .......................................................................................................... 39 8.1 Material ....................................................................................................................... 39 Mice and cell lines ............................................................................................... 39 Media .................................................................................................................. 39 Bacteria ............................................................................................................... 39 Interferon β ......................................................................................................... 39 Antibodies against ............................................................................................... 40 Primers ................................................................................................................ 40 Cloning system .................................................................................................... 42 2 Restriction enzymes ............................................................................................ 42 Enzymes and materials used for PCR, ChIP and cloning ..................................... 43 Kits ....................................................................................................................... 43 8.2 Methods ...................................................................................................................... 44 Cell culture .......................................................................................................... 44 Heat killed L. monocytogenes .............................................................................. 45 mRNA extraction and cDNA preparation ............................................................ 45 Chromatin Immunoprecipitation ........................................................................ 45 Competent cells ................................................................................................... 50 Digestion and ligation .......................................................................................... 51 Transformation of competent E. coli TOP10 ....................................................... 51 MiniPrep .............................................................................................................. 51 Gel- electrophoresis ............................................................................................ 51 9 References ........................................................................................................................... 52 10 Acknowlegment............................................................................................................... 57 3 222 ZZZUSAMMENFASSUNG Listeria monocytogenes ist eines der am besten charakterisierten und am meisten untersuchten intrazellulären Pathogene. Dieses Gram positive Bakterium wird oft verwendet, um das angebo- rene Immunsystem und die Abwehr gegen intrazelluläre Mikroben zu untersuchen. Es verur- sacht schwere Infektionen bei immunsupprimierten Individuen. Intravenös injizierte Bakterien in einem Mausmodell finden sich unverzüglich in der Milz und in der Leber wieder, und auf der zellulären Ebene gehören Makrophagen zu den ersten infizierten Zellen. L. monocytogenes ist in der Lage, aus dem Phagosom des infizierten Makrophagen zu entkommen, sich im Cytosol zu vermehren und auf benachbarte Zellen auszubreiten. Unser Labor untersucht, die Reaktion des angeborenen Immunsystems auf Listerien-Infektio- nen, und wie die Effektoren der Immunabwehr reguliert werden. Viele antimikrobielle Gene in infizierten Zellen werden von NFκB und dem Typ-I-interferon/ISGF3-Weg reguliert. Zu dieser Gruppe der koregulierten Gene gehört auch Nos2, das die induzierbare Stickstoffmonoxid-Syn- thase (iNOS) kodiert. Mein Projekt konzentrierte sich auf Phosphorylierungsereignisse an der carboxyterminalen Do- mäne (CTD) der RNA-Polymerase II (RNA Pol II) während des Transkriptionszykluses des Nos2 Gens. Die CTD ist aus einer sich oftmals wiederholenden siebenstelligen Aminosäuresequenz aufgebaut. Modifikationen, im Speziellen Phosphorylierungen dieser Domäne sind unerlässlich für RNA-Pol II Prozessivität sowie die Assemblierung von Proteinen, die an der pre-mRNA-Pro- zessierung beteiligt sind. Die beiden Cyclin-abhängigen Kinasen Cdk7 und Cdk9 phosphorylieren die CTD bei jeweils Serin 2 und Serin 5 während der Transkriptionsinitiation. Allerdings gibt es wenige Informationen über Veränderungen und Funktion dieser Modifikationen während der Elongation. Darüber hinaus ist bekannt, dass auch Serin 7 von Cdk7 und -9 phosphoryliert wird. Es ist aber unklar, ob dies bei der Initiation, Elongation oder Termination der Transkription eine Rolle spielt. Meine Studie zeigt, dass die Phosphorylierung von Serin 2 in BMDMs, stimuliert mit Listeria- abgeleiteten Signalen Richtung
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