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. Special Techniques for the Enzymologist Edited by SIDNEY P. COLOWICK AND NATHAN O. KAPLAN VOLUME V. Preparation and Assay of Enzymes Edited by SIDNEY P. COLOWICK AND NATHAN O. KAPLAN VOLUME VI. Preparation and Assay of Enzymes (Continued) Preparation and Assay of Substrates Special Techniques Edited by SIDNEY P. COLOWICK AND NATHAN O. KAPLAN VOLUME VII. Cumulative Subject Index Edited by SIDNEY P. COLOWICK AND NATHAN O. KAPLAN VOLUME VIII. Complex Carbohydrates Edited by ELIZABETH F. NEUFELD AND VICTOR GINSBURG VOLUME IX. Carbohydrate Metabolism Edited by WILLIS A. WOOD VOLUME X. Oxidation and Phosphorylation Edited by RONALD W. ESTABROOK AND MAYNARD E. PULLMAN VOLUME XI. Enzyme Structure Edited by C. H. W. HIRS VOLUME XII. Nucleic Acids (Parts A and B) Edited by LAWRENCE GROSSMAN AND KIVIE MOLDAVE VOLUME XIII. Citric Acid Cycle Edited by J. M. LOWENSTEIN VOLUME XIV. Lipids Edited by J. M. LOWENSTEIN VOLUME XV. Steroids and Terpenoids Edited by RAYMOND B. CLAYTON XV xvi METHODS IN ENZYMOLOGY VOLUME XVI. Fast Reactions Edited by KENNETH KUSTIN VOLUME XVII. Metabolism of Amino Acids and Amines (Parts A and B) Edited by HERBERT TABOR AND CELIA WHITE TABOR VOLUME XVIII. Vitamins and Coenzymes (Parts A, B, and C) Edited by DONALD B. McCoRMICK AND LEMUEL D. WRIGHT VOLUME XIX. Proteolytic Enzymes Edited by GERTRUDE E. PERLMANN AND LASZLO LORAND VOLUME XX. Nucleic Acids and Protein Synthesis (Part C) Edited by KIVIE MOLDAVE AND LAWRENCE GROSSMAN VOLUME XXI. Nucleic Acids (Part D) Edited by LAWRENCE GROSSMAN AND KIVIE MOLDAVE VOLUME XXII. Enzyme Purification and Related Techniques Edited by WILLIAM B. JAKOBY VOLUME XXIII. Photosynthesis (Part A) Edited by ANTHONY SAN PIETRO VOLUME XXIV. Photosynthesis and Nitrogen Fixation (Part B) Edited by ANTHONY SAN PIETRO VOLUME XXV. Enzyme Structure (Part B) Edited by C. H. W. HIRS AND SERGE N. TIMASHEFF VOLUME XXVI. Enzyme Structure (Part C) Edited by C. H. W. HIRS AND SERGE N. TIMASHEFF VOLUME XXVII. Enzyme Structure (Part D) Edited by C. H. W. HIRS AND SERGE N. TIMASHEFF VOLUME XXVIII. Complex Carbohydrates (Part B) Edited by VICTOR GINSBURG VOLUME XXIX. Nucleic Acids and Protein Synthesis (Part E) Edited by LAWRENCE GROSSMAN AND KIVIE MOLDAVE VOLUME XXX. Nucleic Acids and Protein Synthesis (Part F) Edited by KIVtE MOLDAVE AND LAWRENCE GROSSMAN VOLUME XXXI. Biomembranes (Part A) Edited by SIDNEY FLEISCHER AND LESTER PACKER VOLUME XXXII. Biomembranes (Part B) Edited by SIDNEY FLEISCHER AND LESTER PACKER VOLUME XXXIII. Cumulative Subject Index Volumes I-XXX Edited by MARTHA G. DENNIS AND EDWARD A. DENNIS VOLUME XXXIV. Affinity Techniques (Enzyme Purification: Part B) Edited by WILLIAM B. JAKOBY AND ME1R WILCHEK METHODS IN ENZYMOLOGY xvii VOLUME XXXV. Lipids (Part B) Edited by JOHN M. LOWENSTEIN VOLUME XXXVI. Hormone Action (Part A: Steroid Hormones) Edited by BERT W. O'MALLEY AND JOEL G. HARDMAN VOLUME XXXVII. Hormone Action (Part B: Peptide Hormones) Edited by BERT W. O'MALLEY AND JOEL G. HARDMAN VOLUME XXXVIII. Hormone Action (Part C: Cyclic Nucleotides) Edited by JOEL G. HARDMAN AND BERT W. O'MALLEY VOLUME XXXIX. Hormone Action (Part D: Isolated Cells, Tissues, and Organ Systems) Edited by JOEL G. HARDMAN AND BERT W. O'MALLEY VOLUME XL. Hormone Action (Part E: Nuclear Structure and Function) Edited by BERT W. O'MALLEY AND JOEL G. HARDMAN VOLUME XLI. Carbohydrate Metabolism (Part B) Edited by W. A. WOOD VOLUME XLII. Carbohydrate Metabolism (Part C) Edited by W. A. WOOD VOLUME XLIII. Antibiotics Edited by JOHN H. HASH VOLUME XLIV. Immobilized Enzymes Edited by KLAUS MOSBACH VOLUME XLV. Proteolytic Enzymes (Part B) Edited by LASZLO LORAND VOLUME XLVI. Affinity Labeling Edited by WILLIAM B. JAKOBY AND MUIR WILCHEK VOLUME XLVII. Enzyme Structure (Part E) Edited by C. H. W. HIRS AND SERGE N. TIMASHEFF VOLUME XLVIII. Enzyme Structure (Part F) Edited by C. H. W. HIRS AND SERGE N. TIMASHEFF VOLUME XLIX. Enzyme Structure (Part G) Edited by C. H. W. HIRS AND SEROE N. TIMASHEFF VOLUME k. Complex Carbohydrates (Part C) Edited by VICTOR GINSBURG VOLUME LI. Purine and Pyrimidine Nucleotide Metabolism Edited by PATRICIA A. HOFFEE AND MARY ELLEN JONES VOLUME LIE Biomembranes (Part C: Biological Oxidations) Edited by SIDNEY FLEISCHER AND LUSTER PACKER VOLUME LIII. Biomembranes (Part D: Biological Oxidations) Edited by SIDNEY FLEISCHER AND LUSTER PACKER xviii METHODS IN ENZYMOLOGY VOLUME LIV. Biomembranes (Part E: Biological Oxidations) Edited by SIDNEY FLEISCHER AND LESTER PACKER VOLUME LV. Biomembranes (Part F: Bioenergetics) Edited by SIDNEY FLZISCHER AND LESTER PACKER VOLUME LVI. Biomembranes (Part G: Bioenergetics) Edited by SIDNEY FLEISCHER AND LESTER PACKER VOLUME LVII. Bioluminescence and Chemiluminescence Edited by MARLENE A. DELUCA VOLUME LVIII. Cell Culture Edited by WILLIAM B. JAKOBY AND IRA PASTAN VOLUME LIX. Nucleic Acids and Protein Synthesis (Part G) Edited by KIVlE MOLDAVE AND LAWRENCE GROSSMAN VOLUME LX. Nucleic Acids and Protein Synthesis (Part H) Edited by KIVIE MOLDAVE AND LAWRENCE GROSSMAN VOLUME 61. Enzyme Structure (Part H) Edited by C. H. W. HIRS AND SERGE N. TIMASHEFF VOLUME 62. Vitamins and Coenzymes (Part D) Edited by DONALD B. McCORMICK AND LEMUEL D. WRIGHT VOLUME 63. Enzyme Kinetics and Mechanism (Part A: Initial Rate and Inhibitor Methods) Edited by DANIEL L. PURICH VOLUME 64. Enzyme Kinetics and Mechanism (Part B: Isotopic Probes and Com- plex Enzyme Systems) Edited by DANIEL L, PURICH VOLUME 65. Nucleic Acids (Part I) Edited by LAWRENCE GROSSMAN AND KIVIE MOLDAVE VOLUME 66. Vitamins and Coenzymes (Part E) Edited by DONALD B. McCORMICK AND LEMUEL D. WRIGHT VOLUME 67. Vitamins and Coenzymes (Part F) Edited by DONALD B. McCoRMICK AND LEMUEL D. WRIGHT VOLUME 68. Recombinant DNA Edited by RAY Wu VOLUME 69. Photosynthesis and Nitrogen Fixation (Part C) Edited by ANTHONY SAN PIETRO VOLUME 70. Immunochemical Techniques (Part A) Edited by HELEN VAN VUNAKIS AND JOHN J. LANGONE VOLUME 71. Lipids (Part C) Edited by JOHN M. LOWENSTEIN METHODS IN ENZYMOLOGY xix VOLUME 72. Lipids (Part D) Edited by JOHN M. LOWENSTEIN VOLUME 73. Immunochemical Techniques (Part B) Edited by JOHN J. LANGONE AND HELEN VAN VUNAKIS VOLUME 74. Immunochemical Techniques (Part C) Edited by JOHN J. LANGONE AND HELEN VAN VUNAKIS VOLUME 75. Cumulative Subject Index Volumes XXXI, XXXII, XXXIV-LX Edited by EDWARD A. DENNIS AND MARTHA G. DENNIS VOLUME 76. Hemoglobins Edited by ERALDO ANTONINI, LUIGI ROSsI-BERNARDI, AND EMILIA CHIANCONE VOLUME 77. Detoxication and Drug Metabolism Edited by WILLIAM B. JAKOBY VOLUME 78. Interferons (Part A) Edited by SIDNEY PESTKA VOLUME 79. Interferons (Part B) Edited by SIDNEY PESTKA VOLUME 80. Proteolytic Enzymes (Part C) Edited by LASZLO LORAND VOLUME 81. Biomembranes (Part H: Visual Pigments and Purple Mem- branes, I) Edited by LESTER PACKER VOLUME 82. Structural and Contractile Proteins (Part A" Extracellular Matrix) Edited by LEON W. CUNNINGHAM AND DIXIE W. FREDERIKSEN VOLUME 83. Complex Carbohydrates (Part D) Edited by VICTOR GINSBURG VOLUME 84. Immunochemical Techniques (Part D: Selected Immunoassays) Edited by JOHN J. LANGONE AND HELEN VAN VUNAKIS VOLUME 85. Structural and Contractile Proteins (Part B" The Contractile Appara- tus and the Cytoskeleton) Edited by DIXIE W. FREDERIKSEN AND LEON W. CUNNINGHAM VOLUME 86. Prostaglandins and Arachidonate Metabolites Edited by WILLIAM E. M. LANDS AND WILLIAM L. SMITH VOLUME 87. Enzyme Kinetics and Mechanism (Part C: Intermediates, Stereo- chemistry, and Rate Studies) Edited by DANIEL L. PURICH VOLUME 88. Biomembranes (Part I: Visual Pigments and Purple Mem- branes, II) Edited by LESTER PACKER VOLUME 89. Carbohydrate Metabolism (Part D) Edited by WILLIS A. WOOD XX METHODSIN ENZYMOLOGY VOLUME 90. Carbohydrate Metabolism (Part E) Edited by WILLIS A. WOOD VOLUME 91. Enzyme Structure (Part I) Edited by C. H. W. HIRS AND SERGE N. TIMASHEFF VOLUME 92. Immunochemical Techniques (Part E: Monoclonal Antibodies and General Immunoassay Methods) Edited by JOHN J. LANGONE AND HELEN VAN VUNAKIS VOLUME 93. Immunochemical Techniques (Part F: Conventional Antibodies, Fc Receptors, and Cytotoxicity) Edited by JOHN J. LANGONE AND HELEN VAN VUNAKIS VOLUME 94. Polyamines Edited by HERBERT TABOR AND CELIA WHITE TABOR VOLUME 95. Cumulative Subject Index Volumes 61-74, 76-80 Edited by EDWARD A. DENNIS AND MARTHA G. DENNIS VOLUME 96. Biomembranes [Part J: Membrane Biogenesis: Assembly and Tar- geting (General Methods; Eukaryotes)] Edited by SIDNEY FLEISCHER AND BECCA FLEISCHER VOLUME 97. Biomembranes [Part K: Membrane Biogenesis: Assembly and Tar- geting (Prokaryotes, Mitochondria, and Chloroplasts)] Edited by SIDNEY FLEISCHER AND BECCA FLEISCHER VOLUME 98. Biomembranes (Part L: Membrane Biogenesis: Processing and Re- cycling) Edited by SIDNEY FLEISCHER AND BECCA FLEISCHER VOLUME 99. Hormone Action (Part F: Protein Kinases) Edited by JACKIE D. CORB1N AND JOEL G. HARDMAN VOLUME 100. Recombinant DNA (Part B) Edited by RAY Wu, LAWRENCE GROSSMAN, AND KIVIE MOLDAVE VOLUME 101. Recombinant DNA (Part C) Edited by RAY Wu, LAWRENCE GROSSMAN, AND KIVIE MOLDAVE VOLUME 102. Hormone Action (Part G: Calmodulin and Calcium-Binding Pro- teins) Edited by ANTHONY R. MEANS AND BERT W. O'MALLEY VOLUME 103. Hormone Action (Part H: Neuroendocrine Peptides) Edited by P. MICHAEL CONN VOLUME 104. Enzyme Purification and Related Techniques (Part C) Edited by WILLIAM B. JAKOBY VOLUME 105. Oxygen Radicals in Biological Systems Edited by LESTER PACKER VOLUME 106. Posttranslational Modifications (Part A) Edited by FINN WOLD AND KIVIE MOLDAVE [...]... 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. Viral Polymerases and. Separation and Analysis of Biological Macromole- cules (Part A: Fundamentals) Edited by BARRY L. KARGER AND WILLIAM S. HANCOCK VOLUME 271. High Resolution Separation and Analysis of Biological. VOGT AND INDER M. VERMA VOLUME 255. Small GTPases and Their Regulators (Part A: Ras Family) Edited by W. E. BALCH, CHANNING J. DER, AND ALAN HALL VOLUME 256. Small GTPases and Their Regulators