Zooming in on Transcription Preinitiation
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A Versatile Group of Transcriptional Regulators in Archaea
Extremophiles (2014) 18:925–936 DOI 10.1007/s00792-014-0677-2 SPECIAL ISSUE: REVIEW 10th International Congress on Extremophiles The TrmB family: a versatile group of transcriptional regulators in Archaea Antonia Gindner • Winfried Hausner • Michael Thomm Received: 14 March 2014 / Accepted: 10 July 2014 / Published online: 13 August 2014 Ó The Author(s) 2014. This article is published with open access at Springerlink.com Abstract Microbes are organisms which are well adapted and Wheelis in 1990 (Woese et al. 1990). This was con- to their habitat. Their survival depends on the regulation of firmed later by studies of the Archaeal biochemistry and gene expression levels in response to environmental signals. molecular biology. What distinguishes Archaea from the The most important step in regulation of gene expression other two domains is the fact that they possess both bacterial takes place at the transcriptional level. This regulation is and eukaryal properties. On the one hand, they have tran- intriguing in Archaea because the eu-karyotic-like tran- scription, translation and DNA replication machineries scription apparatus is modulated by bacterial-like tran- which are similar to those of eukaryotic organisms (Keeling scription regulators. The transcriptional regulator of mal and Doolittle 1995; Langer et al. 1995; Dennis 1997; Gra- operon (TrmB) family is well known as a very large group of bowski and Kelman 2003). On the other hand, many genes regulators in Archaea with more than 250 members to date. involved in metabolic processes are more similar to those One special feature of these regulators is that some of them encoded in bacterial genomes (Koonin et al. -
Evolution of Two Modes of Intrinsic RNA Polymerase Transcript Cleavage
Dissertation zur Erlangung des Doktorgrades der Fakultät für Chemie und Pharmazie der Ludwig-Maximilians-Universität München Evolution of two modes of intrinsic RNA polymerase transcript cleavage Wenjie Ruan aus Anhui, P.R.China 2011 Dissertation zur Erlangung des Doktorgrades der Fakultät für Chemie und Pharmazie der Ludwig-Maximilians-Universität München Evolution of two modes of intrinsic RNA polymerase transcript cleavage Wenjie Ruan aus Anhui, P.R.China 2011 Erklärung II Erklärung Diese Dissertation wurde im Sinne von §13 Abs. 3 der Promotionsordnung vom 29. Januar 1998 (in der Fassung der vierten Änderungssatzung vom 26. November 2004) von Herrn Prof. Dr. Patrick Cramer betreut. Ehrenwörtliche Versicherung Diese Dissertation wurde selbständig und ohne unerlaubte Hilfe erarbeitet. München, den 06. April 2011 ______________________________ Wenjie Ruan Dissertation eingereicht am 07. April 2011 1. Gutachter: Prof. Dr. Patrick Cramer 2. Gutachter: Prof. Dr. Dietmar Martin Mündliche Prüfung am 11.Mai 2011 Acknowledgements III Acknowledgements Five years ago, on the beautiful fall of 2006, when I first set foot on this land, colorful leaves, blue sky, smiling and courteous people, were the first impressions Deutschland gave me. This was my first time coming abroad, touching a completely different world and culture. During the last years, I harvested a lot, both on academic life, and on mentality, grown up to be a strong person. The long journey would not have been possible without the help of many people. I wish to give them my sincere thanks here. Prof. Patrick Cramer, you are the first and most important person I want to thank. As a foreign student, huge differences on culture and language once gave me a lot of pressure. -
Characterization of Regulatory Sequences in Alternative Promoters of Hypermethylated Genes Associated with Tumor Resistance to Cisplatin
408 MOLECULAR AND CLINICAL ONCOLOGY 3: 408-414, 2015 Characterization of regulatory sequences in alternative promoters of hypermethylated genes associated with tumor resistance to cisplatin MOHAMMED A. IBRAHIM-ALOBAIDE1, ABDELSALAM G. ABDELSALAM2,3, HYTHAM ALOBYDI4, KAKIL IBRAHIM RASUL5, RUIWEN ZHANG6 and KALKUNTE S. SRIVENUGOPAL1 1Department of Biomedical Sciences and Cancer Biology Research Center, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX 79106, USA; 2Department of Mathematics, Statistics and Physics, College of Arts and Sciences, Qatar University, Doha, Qatar; 3Department of Statistics, Faculty of Economics and Political Sciences, Cairo University, Giza 12613, Egypt; 4Biomedica, LLC, Sterling Heights, MI 48310, USA; 5Weill Cornell Medical College and Hamad Medical Corporation, Doha, Qatar; 6Department of Pharmaceutical Sciences and Cancer Biology Research Center, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX 79106, USA Received October 7, 2014; Accepted October 23, 2014 DOI: 10.3892/mco.2014.468 Abstract. The development of cisplatin resistance in human TATA-8 and were found in all the promoters. B recognition cancers is controlled by multiple genes and leads to therapeutic element (BRE) sequences were present only in alternative failure. Hypermethylation of specific gene promoters is a key promoters harboring CGIs, but CCAAT and TAACC were event in clinical resistance to cisplatin. Although the usage of found in both types of alternative promoters, whereas down- multiple promoters is frequent in the transcription of human stream promoter element sequences were significantly less genes, the role of alternative promoters and their regulatory frequent. Therefore, it was hypothesized that BRE and CGI sequences have not yet been investigated in cisplatin resistance sequences co-localized in alternative promoters of cisplatin genes. -
Characterization of Labelled Regulatory Elements in Embryonic Stem Cells and Macrophages Using Quantitative and Qualitative Methods
THESIS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY (PHD) Characterization of labelled regulatory elements in embryonic stem cells and macrophages using quantitative and qualitative methods by Attila Horváth UNIVERSITY OF DEBRECEN DOCTORAL SCHOOL OF MOLECULAR CELL AND IMMUNE BIOLOGY DEBRECEN, 2019 THESIS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY (PHD) Characterization of labelled regulatory elements in embryonic stem cells and macrophages using quantitative and qualitative methods by Attila Horváth Supervisor: Prof. Dr. László Nagy Co-Supervisor: Dr. Benedek Nagy UNIVERSITY OF DEBRECEN DOCTORAL SCHOOL OF MOLECULAR CELL AND IMMUNE BIOLOGY DEBRECEN, 2019 2 TABLE OF CONTENT 1. ABBREVIATIONS ..................................................................................................................................... 6 2. INTRODUCTION .................................................................................................................................... 10 Transcription regulation in Eukaryotes ......................................................................................................... 10 The concept of enhancer ............................................................................................................................. 12 Identification of enhancer regions................................................................................................................ 13 Histone modifications ................................................................................................................................. -
Repression of RNA Polymerase by the Archaeo-Viral Regulator
Edinburgh Research Explorer Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP Citation for published version: Sheppard, C, Blombach, F, Belsom, A, Schulz, S, Daviter, T, Smollett, K, Mahieu, E, Erdmann, S, Tinnefeld, P, Garrett, R, Grohmann, D, Rappsilber, J & Werner, F 2016, 'Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP', Nature Communications, vol. 7, 13595. https://doi.org/10.1038/ncomms13595 Digital Object Identifier (DOI): 10.1038/ncomms13595 Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: Nature Communications General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 06. Oct. 2021 ARTICLE Received 4 May 2016 | Accepted 18 Oct 2016 | Published 24 Nov 2016 DOI: 10.1038/ncomms13595 OPEN Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP Carol Sheppard1, Fabian Blombach1, Adam Belsom2, Sarah Schulz3, Tina Daviter1, Katherine Smollett1, Emilie Mahieu1, Susanne Erdmann4, Philip Tinnefeld3, Roger Garrett4, Dina Grohmann3,w, Juri Rappsilber2,5 & Finn Werner1 Little is known about how archaeal viruses perturb the transcription machinery of their hosts. -
The General Transcription Factors of RNA Polymerase II
Downloaded from genesdev.cshlp.org on October 7, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW The general transcription factors of RNA polymerase II George Orphanides, Thierry Lagrange, and Danny Reinberg 1 Howard Hughes Medical Institute, Department of Biochemistry, Division of Nucleic Acid Enzymology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854-5635 USA Messenger RNA (mRNA) synthesis occurs in distinct unique functions and the observation that they can as- mechanistic phases, beginning with the binding of a semble at a promoter in a specific order in vitro sug- DNA-dependent RNA polymerase to the promoter re- gested that a preinitiation complex must be built in a gion of a gene and culminating in the formation of an stepwise fashion, with the binding of each factor promot- RNA transcript. The initiation of mRNA transcription is ing association of the next. The concept of ordered as- a key stage in the regulation of gene expression. In eu- sembly recently has been challenged, however, with the karyotes, genes encoding mRNAs and certain small nu- discovery that a subset of the GTFs exists in a large com- clear RNAs are transcribed by RNA polymerase II (pol II). plex with pol II and other novel transcription factors. However, early attempts to reproduce mRNA transcrip- The existence of this pol II holoenzyme suggests an al- tion in vitro established that purified pol II alone was not ternative to the paradigm of sequential GTF assembly capable of specific initiation (Roeder 1976; Weil et al. (for review, see Koleske and Young 1995). -
Regulation of Gene Expression
Regulation of Gene Expression Gene Expression Can be Regulated at Many of the Steps in the Pathway from DNA to RNA to Protein : (1) controlling when and how often a given gene is transcribed (2) controlling how an RNA transcript is spliced or otherwise processed (3) selecting which mRNAs are exported from the nucleus to the cytosol (4) selectively degrading certain mRNA molecules (5) selecting which mRNAs are translated by ribosomes (6) selectively activating or inactivating proteins after they have been made * most genes the main site of control is step 1: transcription of a DNA sequence into RNA. * Chromatin remodeling * controlling when and how often a given gene is transcribed ! DNA regulation ! Chromatin ! double helix accessibility ! gene and its surroundings ! Promoter/Operator (Bacteria) ! Promoter + enhancing region (Eukaryote ) ! Overview of Eukaryotic gene regulation Mechanisms similar to those found in bacteria-most genes controlled at the transcriptional level ! Gene regulation in eukaryotes is more complex than it is in prokaryotes because of: ! The larger amount of DNA ! Larger number of chromosomes ! Spatial separation of transcription and translation ! mRNA processing ! RNA stability ! Cellular differentiation in eukaryotes Transcription is the Most Regulated Step ! Transcription; from DNA to RNA, is catalyzed by the enzyme RNA polymerase. ! Initiation of transcription requires the formation of a complex between the promoter on the DNA and RNA polymerase. ! Initiation rate is largely controlled by the rate of formation of the complex DNA (promoter) - RNA polymerase. Rate = number of events per unit time. Transcriptional Control The Latin prefix cis translates to “on this side” “next to” ! cis-acting “next to” elements (cis-Regulatory Elements) (CREs) are regions of non-coding DNA which regulate the transcription of nearby genes ! trans-acting “across from” elements usually considered to be proteins, that bind to the cis-acting sequences to control gene expression. -
Reconstitution of a Polii-Like RNA Polymerase and Contribution of Subunit E’ and Structural Elements in the Active Center to RNA Polymerase Functions
Reconstitution of a PolII-like RNA Polymerase and Contribution of Subunit E’ and Structural Elements in the Active Center to RNA Polymerase Functions Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften (Dr. rer. nat.) der Naturwissenschaftlichen Fakultät III – Biologie und Vorklinische Medizin der Universität Regensburg vorgelegt von Souad Naji aus Rabat, Marokko Regensburg, im August 2006 Promotionsgesuch eingereicht am: 18.07.2006 Die Arbeit wurde angeleitet von: Prof. Dr. M. Thomm Pruefungsausschuss: Vorsitzender: Prof. Dr. R. Wirth 1. Gutachter und Pruefer: Prof. Dr. M. Thomm 2. Gutachter und Pruefer: Prof. Dr. H. Tschochner 3. Pruefer Prof. Dr. R. Sterner Table of contents 1 Table of contents Table of contents .........................................................1 I Introduction .................................................................5 1. The transcription cycle......................................................................................... 5 2. DNA-dependent RNA polymerase....................................................................... 6 2.1 Bacterial RNAP ...................................................................................................... 7 2.2 Eukaryotic RNAPs.................................................................................................. 7 2.3 Archaeal RNAP .................................................................................................... 10 3. General RNAP architecture.............................................................................. -
Regulation of RNA Polymerase II Transcription
Regulation of RNA polymerase II transcription Ronny Drapkin, Alejandro Merino and Danny Reinberg Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, USA Transcription initiation plays a central role in the regulation of gene expression. Exciting developments in the last year have furthered our understanding of the interactions between general transcription factors and how these factors respond to modulators of transcription. Current Opinion in Cell Biology 1993, 5:469-476 Introduction TFIIJ. Formation of the DAB--polFEHJ complex, in the presence of each of four ribonucleoside triphosphates, Cellular growth and differentiation employ precise mech- enables RNAPII to clear the promoter region and initiate anisms to regulate the expression of various genes. One RNA synthesis from a specific start site [ 51. of the most rudimentary mechanisms for a cell to control The past year has seen intense activity aimed at elucidat- the functional levels of a protein is to modulate the lev- ing the molecular mechanisms underlying transcription els of mRNA encoding that polypeptide. It is therefore not initiation. In particular, the interactions that GTFs can surprising that most of the genetic programs that main- mediate, the GTF requirements for initiation, the role tain the cell in a constant state of flux mediate their effects of RNAPII phosphorylation, and the phenomenon of by impinging on mechanisms that control transcription antirepression in the process of activation have been initiation. the subject of many studies. These most recent develop- In contrast to prokaryotic RNA polymerase, eukaryotic ments are the focus of this review. enzymes require multiple accessory proteins to acquire promoter specificity. -
Expression of Mhc Ii Genes
EXPRESSION OF MHC II GENES 1 1 2,* GORAZD DROZINA , JIRI KOHOUTEK , NABILA JABRAN-FERRAT AND B. MATIJA 1,* PETERLIN 1Departments of Medicine, Microbiology and Immunology Rosalind Russell Medical Research Center University of California, San Francisco San Francisco, CA 94143 2Structural Immuno-Pharmacology Institute of Pharmacology and Structural Biology CNRS VMR 5089 31400 Toulouse France *Correspondence: [email protected] [email protected] 1 ABSTRACT Innate and adaptive immunity are connected via antigen processing and presentation (APP), which results in the presentation of antigenic peptides to T cells in the complex with the major histocompatibility (MHC) determinants. MHC class II (MHC II) determinants present antigens to CD 4+ T cells, which are the main regulators of the immune response. Their genes are transcribed from compact promoters that form first the MHC II enhanceosome, which contains DNA-bound activators and then the MHC II transcriptosome with the addition of the class II transactivator (CIITA). CIITA is the master regulator of MHC II transcription. It is expressed constitutively in dendritic cells (DC) and mature B cells and is inducible in most other cell types. Three isoforms of CIITA exist, depending on cell type and inducing signals. CIITA is regulated at the levels of transcription and post-translational modifications, which are still not very clear. Inappropriate immune responses are found in several diseases, which include cancer and autoimmunity. Since CIITA regulates the expression of MHC II genes, it is involved directly in the regulation of the immune response. The knowledge of CIITA will facilitate the manipulation of the immune response and might contribute to the treatment of these diseases. -
A Genetic Investigation of Archaeal Information-Processing Systems
A genetic investigation of archaeal information-processing systems. Thesis Presented in partial fulfillment of the requirements for the degree master of science in the Graduate School of The Ohio State University Travis H. Hileman B.S. Graduate Program in Microbiology The Ohio State University 2013 Thesis Committee: Dr. Thomas Santangelo, Advisor Dr. Irina Artsimovitch Dr. Tina Henkin Dr. Michael Ibba Copyright by Travis H. Hileman 2013 Abstract Studies of Archaea and their biology have been hindered by the lack of defined genetic systems. Thermococcus kodakarensis has emerged as a model organism with a near complete suite of genetic tools that can be used to investigate basic biological mechanisms in Archaea. This thesis is centered on two aspects of archaeal information processing systems, namely transcription and DNA replication. Properly regulated gene expression is necessary for cellular homeostasis and response to external signals. Much regulation occurs at the level of transcription initiation, but post-initiation events can also dramatically alter gene expression. Transcription termination represents a regulatory event; however, the mechanisms employed to direct transcription termination in Archaea remain undefined. Intrinsic transcription termination occurs within poly-T tracts encoded on the non-template strand of DNA, but the mechanism by which termination occurs is unknown. Utilizing the genetic system unique to T. kodakarensis, two selective schemes were constructed, and continued efforts should permit isolation of RNA polymerase variants that have aberrant termination phenotypes. DNA replication is similarly subject to many regulatory inputs, and these inputs are received by different components of the replication apparatus. The protein encoded by TK0808, a protein of previously unknown function, was shown to stably interact with replisome components in vivo. -
Transcription Syndromes and the Role of RNA Polymerase II General Transcription Factors in Human Disease
Transcription syndromes and the role of RNA polymerase II general transcription factors in human disease. T Aso, … , J W Conaway, R C Conaway J Clin Invest. 1996;97(7):1561-1569. https://doi.org/10.1172/JCI118580. Perspective Find the latest version: https://jci.me/118580/pdf Perspectives Transcription Syndromes and the Role of RNA Polymerase II General Transcription Factors in Human Disease Teijiro Aso, Ali Shilatifard, Joan Weliky Conaway, and Ronald C. Conaway Program in Molecular and Cell Biology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104 Messenger RNA synthesis is a major site for the regulation of ing essential communication between DNA binding transacti- gene expression. Eukaryotic messenger RNA synthesis is cata- vators and RNA polymerase II, were discovered. Finally, in no lyzed by multisubunit RNA polymerase II (1–3) and proceeds area of research on the mechanism of eukaryotic messenger via multiple stages, which are designated preinitiation, initia- RNA synthesis has the pace of progress been more striking tion, elongation, and termination and which have come to be than in investigations of the “general” transcription factors, referred to collectively as the transcription cycle (Fig. 1). The which have been shown to play fundamental roles in all stages past decade was a watershed for biochemical studies of eu- of transcription by RNA polymerase II (32–34). As a conse- karyotic messenger RNA synthesis. A diverse collection of quence of an intense biochemical campaign, a large number of transcription factors and other nuclear proteins that govern general factors has been identified, purified to homogeneity, the activity of RNA polymerase II during messenger RNA their genes cloned, and working models for their roles in initia- synthesis was identified and characterized, and unprecedented tion and elongation established.