rna polymerase and associated factors, part a

Preface One cannot fully understand the biology of a cell without understanding the central role that gene expression and its regulation play. RNA polymer- ase was discovered in eukaryotes in 1959 and in prokaryotes in 1960, and the subject of transcription regulation was reported in the early 1960s. Although many breakthrough experiments were performed in the 1970s, there has been, unquestionably, an explosion in our knowledge in the field since the 1980s thanks to the rapid development and use of powerful genetic, biochemical, and physical techniques. As a result, many plausible, some- times unexpected, ideas have been generated. More encouragingly, some of the ideas have been accepted. Volumes 273 and 274 of Methods in Enzymology cover, for the first time, methods and other analytical approaches for the study of transcription and its regulation in prokaryotes and eukaryotes. The chapters in these two volumes describe steps of transcription; component machinery and their specificity; purification, assays, and properties of RNA polymerases and their intrinsic and extrinsic (including regulatory) factors that guide transcription initiation, elongation, and termination; and the assembly of RNA polymerase holoenzymes and many regulatory protein-protein and nucleoprotein complexes, including chromatins. A few chapters dealing with specialized techniques analyzing transcriptional regulation are also in- cluded. These volumes will help further exploration of how transcription con- trois cellular adaptation, development, and differentiation. We underscore the importance of DNA-protein interactions in studying transcription and its regulation, a subject covered in Volume 208 of this series. SANKAR ADHYA xiii Contributors to Volume 273 Article numbers are in parentheses following the names of contributors. Affiliations listed are current. GORY ABATE-SHEN (6), Center for Advanced Biotechnology and Medicine and Depart- ment of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854 CHANG BA1 (27), Verna and Marrs McLean Department of Biochemistry, Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030 STEVAN BJORKLUND (15), Stanford University School of Medicine, Stanford, California 94305 RICHARD R. BURGESS (12), McArdle Labora- tory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin 53706 DAVID M. CHAO (16), Whitehead Institute for Biomedical Research, Cambridge, Massa- chusetts 02142; and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 JIN-LONG CHEN (19), Department of Biology, Tularik Incorporated, South San Francisco, California 94080 JOAN WELIKY CONAWAY (18), Program in Molecular and Cell Biology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104 RONALD G. GONAWAY (18), Program in Mo- lecular and Cell Biology, Oklahoma Medi- cal Research Foundation, Oklahoma City, Oklahoma 73104 CHRISTINE CONESA (22), Service de Biochimie et de G~n~tique Mol~culaire, Commissariat d l'Energie Atomique, Saclay, F91191 Gif sur Yvette Cedex, France MICHAEL E. DAHMUS (17), Section of Molecu- lar and Cellular Biology, Division of Bio- logical Sciences, University of California, Davis, Davis, California 95616 BENOIT de CROMBRUGGHE (20), Department of Molecular Genetics, M.D. Anderson Cancer Center, University of Texas, Hous- ton, Texas 77030 GIORGIO DIECI (22), Service de Biochimie et de Gdn~tique Moldculaire, Commissariat d l'Energie Atomique, Saclay, F91191 Gif sur Yvette Cedex, France ALICIA J. DOMBROSKI (11), Department of Microbiology and Molecular Genetics, Uni- versity of Texas Medical School, Houston, Texas 77030 RICHARD H. EBRIGHT (10), Department of Chemistry and Waksman Institute, Rutgers University, New Brunswick, New Jersey O8855 STEPHEN J. ELLEDGE (27), Verna and Marrs McLean Department of Biochemistry, Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030 HAo FAN (23), Center for Gene Research, Na- goya University, Nagoya 464-01, Japan JAN S. FASSLER (1), Department of Biological Sciences, University of Iowa, Iowa City, Iowa 52242 NOBUYUKI FUJITA (9), Department of Molec- ular Genetics, National lnstitute of Genetics, Mishima, Shizuoka 411, Japan KARLA PFEIL GARRETT (18), Program in Mo- lecular and Cell Biology, Oklahoma Medi- cal Research Foundation, Oklahoma City, Oklahoma 73104 ALEX GOLDFARB (10), Public Health Re- search Institute, New York, New York 10016 JAY D. GRALLA (7), Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095 MICHAEL R. GREEN (8), Program in Molecu- lar Medicine, Howard Hughes Medical In- stitute Research Laboratories, University of Massachusetts Medical Center, Worcester, Massachusetts 01605 ix X CONTRIBUTORS TO VOLUME 273 INGRID GRUMMT (21), Division of Molecular Biology of the Cell 11/0120, German Cancer Research Center, D-69120 Heidelberg, Germany GARY N. GUSSIN (1, 3), Department of Biolog- ical Sciences, University of lowa, Iowa City, lowa 52242 REGINE HAKENBECK (24), Max-Planck Insti- tut far Molekulare Genetik, D-14195 Ber- lin, Germany LUCIE S. HEATH (5), Department of Biological Sciences, University of Alabama, Tusca- loosa, Alabama 35487 GERALD Z. HERTZ (2), Department of Molec- ular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colo- rado 80309 LILIAN M. HSU (4), Program in Biochemistry, Mount Holyoke College, South Hadley, Massachusetts 01075 JANINE HUET (22), Service de Biochimie et de Gdn~tique Mol~culaire, Commissariat d l'Energie Atomique, Saclay, F91191 Gif sur Yvette Cedex, France NANCY ILER (6), Center for Advanced BiD- technology and Medicine and Graduate Program in Microbiology and Molecular Genetics, Rutgers University, Piscataway, New Jersey 08854 AKIRA ISHIHAMA (9), Department of Molecu- lar Genetics, National Institute of Genetics, Mishima, Shizuoka 411, Japan VINAY K. JAIN (26), Baylor University Medi- cal Center, Dallas, Texas 75246 DING JUN JIN (25), Developmental Genetics Section, Laboratory of Molecular Biology, Division of Basic Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892 YOUNG-JooN KIM (15), Stanford University School of Medicine, Stanford, California 94305 YOUNGGYU KIM (10), Department of Chemis- try and Waksman Institute, Rutgers Univer- sity, New Brunswick, New Jersey 08855 ANTHONY J. KOLESKE (16), Department of Bi- ology, Massachusetts Institute of Technol- ogy, Cambridge, Massachusetts 02139 RO6ER D. KORNBERG (15), Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305 OLIVIER LEFEBVRE (22), Service de Biochimie et de G~n~tique Moldculaire, Commissariat d l'Energie Atomique, Saclay, F91191 Gif sur Yvette Cedex, France YANG LI (15), Department of Structural Biol- ogy, Stanford University School of Medi- cine, Stanford, California 94305 CHONGGUANG LIU (5), Department of Cell Bi- ology and Physiology, University of Pitts- burgh, Pittsburgh, Pennsylvania 15260 SANKAR N. MAITY (20), Department of Mo- lecular Genetics, M.D. Anderson Cancer Center, University of Texas, Houston, Texas 77030 NATHALIE MANAUD (22), Service de Biochi- mie et de G~ndtique Mol~culaire, Commis- sariat d l'Energie Atomique, Saclay, F91191 Gif sur Yvette Cedex, France CHARLES P. MORAN, JR. (13), Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322 Gl;RALD PEYROCHE (22), Service de Bioehi- mie et de G~ndtique Moldculaire, Commis- sariat gt l'Energie Atomique, Saclay, F91191 Gif sur Yvette Cedex, France WADE POWELL (18), Department of Biochem- istry, Emory University School of Medicine, Atlanta, Georgia 30322 FENGXIA QI (5), Department of Oral Biology, University of Alabama at Birmingham, Bir- mingham, Alabama 35294 DANIEL REINES (18), Department of Bio- chemistry, Emory University School of Medicine, Atlanta, Georgia 30322 MICHEL RIVA (22), Service de Biochimie et de Gdndtique Moldculaire, Commissariat ?t l'Energie Atomique, Saclay, F91191 Gif sur Yvette Cedex, France STEFAN G, E. ROBERTS (8), Wellcome Sci- ences Institute, Department of Biochemis- try, University of Dundee, Dundee DD1 4HN, United Kingdom CONTRIBUTORS TO VOLUME 273 xi ROBERT G. ROEDER (14), Laboratory of Bio- chemistry and Molecular Biology, The Rockefeller University, New York, New York 10021 ANNY RUET (22), Service de Biochimie et de Gdndtique Mol~culaire, Commissariat l'Energie Atomique, Saclay, F91191 Gif sur Yvette Cedex, France ANDREAS SCHNAPP (21), Division of Molecu- lar Biology of the Cell 11/0120, German Cancer Research Center, D-69120 Heidel- berg, Germany ANDRI~ SENTENAC (22), Service de Biochimie et de Gdndtique Moldculaire, Commissariat h l'Energie Atomique, Saclay, F91191 Gif sur Yvette Cedex, France KONSTANTINE SEVERINOV (10), The Rockefel- ler University, New York, New York 10021 JEEFRY B. STOCK (24), Department of Mo- lecular Biology, Princeton University, Princeton, New Jersey 08544 GARY D. STORMO (2), Department of Molecu- lar, Cellular, and Developmental Biology, University of Colorado, Boulder, Colo- rado 80309 MASAHIRO SUGIURA (23), Center for Gene Research, Nagoya University, Nagoya 464- 01, Japan HONG TANG (10), Department of Chemistry and Waksman Institute, Rutgers University, New Brunswick, New Jersey 08855 KATHLEEN M. TATTI (13), Department of Mi- crobiology and Immunology, Emory Uni- versity School of Medicine, Atlanta, Geor- gia 30322 ROBERT TJIAN (19), Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California 94720 CHARLES L. TURNBOUGH, JR. (5), Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294 RICHARD A. YOUNG (16), Whitehead Institute for Biomedical Research, Cambridge, Mas- sachusetts 02142; and Department of Biol- ogy, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 HAILAN ZHANG (6), CenterforAdvanced Bio- technology and Medicine and Graduate Program in Molecular Genetics and Micro- biology, Robert Wood Johnson Medical School, University of Medicine and Den- tistry of New Jersey, Piscataway, New Jer- sey 08854 YAN NING ZHOU (25), Developmental Genet- ics Section, Laboratory of Molecular Biol- ogy, Division of Basic Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892 METHODS IN ENZYMOLOGY VOLUME I. Preparation and Assay of Enzymes Edited by SIDNEY P. COLOWICK AND NATHAN O. KAPLAN VOLUME II. Preparation and Assay of Enzymes Edited by SIDNEY P. COLOWICK AND NATHAN O. KAPLAN VOLUME III. Preparation and Assay of Substrates Edited by SIDNEY P. COLOWICK AND NATHAN O. KAPLAN VOLUME IV. 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VOLUME 273 RNA Polymerase and Associated Factors (Part A) Edited by SANKARADHYA VOLUME 274 RNA Polymerase and Associated Factors (Part B) Edited by SANKARADHYA VOLUME 275 Viral Polymerases and Related Proteins (in preparation) Edited by LAWRENCEC Kuo, DAVID B OLSEN, AND STEVENS CARROLL VOLUME 276 Macromolecular Crystallography, Part A (in preparation) Edited by CHARLESW CARTER, JR., AND ROBERT M SWEET... Choy, S.-W Park, T Aki, P Parrack, N Fujita, A Ishihama, and S Adhya, E M B O J., 14, 4523 (1995) 14 PROMOTER ELEMENTS AND R N A POLYMERASE COMPONENTS [1] Eukaryotic Promoters and RNA Polymerases Polymerase Core Enzymes Specialization of eukaryotic RNA polymerases (RNA polymerase I, II, and III or Pol I, II, and III) is one alternative to the use in eubacteria of different sigma factors to transcribe... activator and RNAP [An alternative method of achieving contact between a DNA-binding activator and RNAP bound at a (T4 late) promoter requires tracking of the activator along the intervening DNA; tracking can initiate at a site upstream or downstream from the promoter, and can span several hundreds base pairs] °] A long-standing question, which has not been conclusively answered, is whether any activator... PACKER VOLUME 270 High Resolution Separation and Analysis of Biological Macromolecules (Part A: Fundamentals) Edited by BARRY L KARGERAND WILLIAMS HANCOCK VOLUME 271 High Resolution Separation and Analysis of Biological Macromolecules (Part B: Applications) Edited by BARRY L KARGERAND WILLIAMS HANCOCK VOLUME 272 Cytochrome P450 (Part B) Edited by ERIC F JOHNSONAND MICHAELR WATERMAN VOLUME 273 RNA Polymerase. .. simultaneous binding 83 B Chen, B deCrombrugghe, W B Anderson, M E Gottesman, I Pastan, and R L Perlman, Nature N e w Biol 233, 67 (1971) ea j Majors, Proc Natl Acad Sci U.S .A 72, 4394 (1975) 85 A Schmitz and D J Galas, Nucleic Acids Res 6, 111 (1979) 86 S B Straney and D M Crothers, Cell 51, 699 (1987) s7 A Majumdar and S Adhya, unpublished data, cited by S Adhya and A Majumdar, in "RNA Polymerase and. .. Coagulation, Fibrinolysis, and Complement Activation (Part A: Mammalian Blood Coagulation Factors and Inhibitors) Edited by LASZLO LORAND AND KENNETH G MANN VOLUME223 Proteolytic Enzymes in Coagulation, Fibrinolysis, and Complement Activation (Part B: Complement Activation, Fibrinolysis, and Nonmammalian Blood Coagulation Factors) Edited by LASZLO LORAND AND KENNETH G MANN VOLUME224 Molecular Evolution: Producing... Santero, S Porter, and S Kustu, Cell 63, 11 (1990) 69 F Claverie-Martin and B Magasanik, Proc Natl Acad Sci U.S .A 88, 1631 (1988) 70 G M Sanders, G A Kassavetis, and E P Geiduschek, Proc Natl Acad Sci U.S .A 91, 7703 (1994) 71 L Bracco, D Kotlarz, A Kolb, S Diekman, and H Buc, E M B O J 8, 4289 (1989) 72 j Perez-Martin and M Espinosa, J MoL Biol 241, 7 (1994) 73 S Adhya, M Gottesman, S Garges, and A. .. GIUSEPPE M ATTARDI AND ANNE CHOMYN VOLUME261 Nuclear Magnetic Resonance and Nucleic Acids Edited by THOMAS L JAMES VOLUME262 DNA Replication Edited by JUD1TH L CAMPBELL XXX METHODSINENZYMOLOGY VOLUME263 Plasma Lipoproteins (Part C: Quantitation) Edited by WILLIAMA BRADLEY,SANDRAH GIANTURCO ,AND JERE P SEGREST VOLUME 264 Mitochondrial Biogenesis and Genetics (Part B) Edited by GIUSEPPEM ATTARDIAND ANNE CHOMYN... Phosphorylation (Part B: Analysis of Protein Phosphorylation, Protein Kinase Inhibitors, and Protein Phosphatases) Edited by TONY HUNTER AND BARTHOLOMEW M SEFTON VOLUME 202 Molecular Design and Modeling: Concepts and Applications (Part A: Proteins, Peptides, and Enzymes) Edited by JOHN J LANGONE VOLUME 203 Molecular Design and Modeling: Concepts and Applications (Part B: Antibodies and Antigens, Nucleic Acids,... at ara02 (at -276) and araI1 (at -64) interact through D N A looping to repress the araPBAo promoter in the absence of arabinose, while dimers bound at ara02 and ara01 interact to repress araPc.65"9°'91In neither case is there evidence for RNAP binding under repressing conditions In the absence of looping, GalR bound only to the external operator Oz can partially repress open complex formation at galP1 . 273. RNA Polymerase and Associated Factors (Part A) Edited by SANKAR ADHYA VOLUME 274. RNA Polymerase and Associated Factors (Part B) Edited by SANKAR ADHYA VOLUME 275. 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