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Transcription Regulation in Eukaryotes HFSP Workshop Reports Transcription Regulation in Eukaryotes HFSP Workshop Reports Senior editor: Jennifer Altman Assistant editor: Chris Coath I. Coincidence Detection in the Nervous System, eds A. Konnerth, R. Y. Tsien, K. Mikoshiba and J. Altman (1996) II. Vision and Movement Mechanisms in the Cerebral Cortex, eds R. Caminiti, K.-P. Hoffmann, F. Laquaniti and J. Altman (1996) III. Genetic Control of Heart Development, eds R. P. Harvey, E. N. Olson, R. A. Schulz and J. S. Altman (1997) IV. Central Synapses: Quantal Mechanisms and Plasticity, eds D. S. Faber, H. Korn, S. J. Redman, S. M. Thompson and J. S. Altman (1998) V. Brain and Mind: Evolutionary Perspectives, eds M. S. Gazzaniga and J. S. Altman (1998) VI. Cell Surface Proteoglycans in Signalling and Development, eds A. Lander, H. Nakato, S. B. Selleck, J. E. Turnbull and C. Coath (1999) VII. Transcription Regulation in Eukaryotes, eds P. Chambon, T. Fukasawa, R. Kornberg and C. Coath (1999) Forthcoming VIII. Replicon Theory and Cell Division, eds M. Kohiyama, W. Fangman, T. Kishimoto and C. Coath IX. The Regulation of Sleep, eds A. A. Borbély, O. Hayaishi, T. Sejnowski and J. S. Altman X. Axis Formation in the Vertebrate Embryo, eds S. Ang, R. Behringer, H. Sasaki, J. S. Altman and C. Coath XI. Neuroenergetics: Relevance for Functional Brain Imaging, eds P. J. Magistretti, R. G. Shulman, R. S. J. Frackowiak and J. S. Altman WORKSHOP VII Transcription Regulation in Eukaryotes Copyright © 1999 by the Human Frontier Science Program Please use the following format for citations: “Transcription Regulation in Eukaryotes” Eds P. Chambon, T. Fukasawa, R. D. Kornberg and C. Coath. HFSP, Strasbourg, 1999 HFSP WORKSHOPS The HFSP workshops were initiated by Michel Cuénod (Secretary-General, HFSPO) with the support of the Board of Trustees and the Council of Scientists. The workshops, held in English, are organized at the HFSPO office in Strasbourg on specific scientific topics of particular timeliness in the two fields of research covered by HFSP: brain functions and biological functions at the molecular level. The guiding principles are general significance and novelty of the topic, treatment by leading experts, emphasis on discussion, and broad international, inter- continental and interdisciplinary representation. There is no general audience but the reports, edited by the organizers, present the issues discussed in a format attractive to specialists, post-doctoral trainees and students. The present report is based on a meeting held in Strasbourg from December 3–5, 1998. Acknowledgements The proposal for the workshop came from Pierre Chambon (Strasbourg), Toshio Fukasawa (Tokyo) and Roger Kornberg (Stanford) and the meeting was organized by them with the help of the HFSP staff. Our thanks go to the five rapporteurs who wrote the initial reports of the talks given at the meeting: Geneviève Almouzni (Paris): Kingston, Hörz, Struhl, Egly Stefan Björklund (Umeå): Kornberg, Sakurai, Green, Svejstrup Irwin Davidson (Strasbourg): Roeder, Meisterernst, Tora, Sentenac Karl Nightingale (Cambridge): Workman, Wu, Becker, Tjian Kerstin Weiss (Zürich): Richmond, Travers, Allis, Cairns These reports were edited and the book produced by Chris Coath (Norwich) and Jennifer Altman (London). We thank Valérie Dupé (London) and Olivia Wendling (Strasbourg) for technical support at the meeting, Stuart Molloy (Resolution Design Ltd, London) for the artwork, Alissa Surges (Ann Arbor) for compiling the bibliography and Solange Metzger (HFSPO, Strasbourg) for her unfailing support in administration and production. We acknowledge the following publishers for their permission to reproduce copy- righted figures: Academic Press (Fig. 9 from The Journal of Molecular Biology); The American Society for Microbiology (Fig. 62 from Molecular and Cellular Biology); Cell Press (Figs 18, 19, 20, 58 and Table 7 from Cell; Figs 21, 36, 37, 38, 41, 42, 60, 68, 69, 70 from Molecular Cell); Cold Spring Harbor Laboratory Press (figure in Box 1 from Cold Spring Harbor Symposium on Quantitative Biology; Fig. 61 from Genes and Development); The National Academy of Sciences USA (Figs 43, 44 from The Proceedings of the National Academy of Sciences USA). HFSP secretariat Secretary-General: Michel Cuénod Deputy Secretary-General: Yoshiki Kurihara Directors for Research Grants: Martin Reddington, Takashi Shimizu Director for Fellowships and Workshops: Danuta Krotoski Director for Administration and Finance: Olivier Laustriat Administrative Officer: Takuya Okamoto Secretarial staff: Pascale Beudin, Laurence Lapp, Solange Metzger, Sarah Naett, Marie-Claude Perdiguès, Carine Schmitt, Dominique Tanguy 2 HFSP WORKSHOP 7 CONTENTS Participants . 3 Glossary and Abbreviations . 7 INTRODUCTION (Roger D. Kornberg) . 17 PART I - CHROMATIN STRUCTURE IN GENE REGULATION Introduction (Karl Nightingale) . 23 The nucleosome core structure at 2.0 Å resolution (Timothy J. Richmond) . 28 Nucleosomal location of the linker histone and its role in transcriptional repression (Andrew A. Travers). 36 Linking histone modifications to gene activation (C. David Allis) . 42 Function and composition of transcription adaptor histone acetyltransferase complexes (Jerry L. Workman) . 50 ATP-dependent chromatin remodelling by NURF and transcriptional activation (Carl Wu) . 57 CHRAC, a chromatin remodelling complex driven by the ATPase ISWI (Peter B. Becker). 65 New components of the chromatin remodelling complexes RSC and SWI/SNF (Bradley R. Cairns) . 72 Regulation of human chromatin remodelling (Robert E. Kingston) . 80 Chromatin remodelling in vivo (Wolfram Hörz) . 88 PART II - FACTORS REQUIRED FOR ACTIVATED TRANSCRIPTION Introduction (Stefan Björklund) . 97 The Mediator complex and in vitro transcriptional activation in yeast (Roger D. Kornberg) . 100 Regulation of transcription through general and gene-specific coactivators (Robert G. Roeder) . 106 Transcriptional activation by Sp1: a biochemical journey (Robert Tjian). 122 TRANSCRIPTION REGULATION IN EUKARYOTES 3 Structure and function of proteins that modulate RNA polymerase II transcription (Michael Meisterernst). 130 Functional correlation between Gal11, TFIIE and TFIIH in S. cerevisiae (Hiroshi Sakurai) . 138 Functional analysis of the components of yeast TFIID in vivo (Michael R. Green) . 146 Mechanism for in vivo transcriptional activation and repression in yeast (Kevin Struhl). 155 The role of TAFII30-containing complexes in vertebrate gene regulation (Làszlò Tora) . 162 TFIIH and the transcription-repair syndromes (Jean-Marc Egly) . 171 Elongator, a component of the elongating RNA polymerase II holoenzyme (Jesper Q. Svejstrup) . 176 Molecular interactions leading to the recruitment of RNA polymerase III (André Sentenac). 183 CONCLUSION (Toshio Fukasawa) . 193 BIBLIOGRAPHY . 200 4 HFSP WORKSHOP 7 PARTICIPANTS* C. David ALLIS Irwin DAVIDSON Department of Biochemistry Institut de Génétique et de Biologie and Molecular Genetics Moléculaire et Cellulaire University of Virginia Université Louis Pasteur Charlottesville, USA Illkirch, FRANCE Geneviève ALMOUZNI Valérie DUPÉ UMR 144 CNRS Department of Developmental Institut Curie, Section Recherche Neurobiology Paris, FRANCE Guy’s and St Thomas Medical and Dental School Jennifer S. ALTMAN London, UK Senior Editor London, UK Jean-Marc EGLY Peter B. BECKER Institut de Génétique et de Biologie Adolf-Butenandt- Institut, Moléculaire et Cellulaire Molekularbiologie Université Louis Pasteur Ludwig-Maximilians-Universität Illkirch, FRANCE München, GERMANY Toshio FUKASAWA Stefan BJÖRKLUND Department of Microbiology Department of Medical Biochemistry Keio University School of Medicine and Biophysics Tokyo, JAPAN Umeå University Umeå, SWEDEN Michael R. GREEN Howard Hughes Medical Institute Bradley R. CAIRNS University of Massachusets Department of Oncological Sciences Medical School Huntsman Cancer Institute Worcester, USA University of Utah Salt Lake City, USA Wolfram HÖRZ Institut für Physiologische Chemie Pierre CHAMBON Ludwig-Maximilians-Universität Institut de Génétique et de Biologie München, GERMANY Moléculaire et Cellulaire Université Louis Pasteur Illkirch, FRANCE Robert E. KINGSTON Department of Molecular Biology Harvard University Chris COATH Editor Boston, USA Norwich, UK Roger D. KORNBERG Michel CUÉNOD Department of Structural Biology Secretary-General Stanford University School of Human Frontier Science Program Medicine Strasbourg, FRANCE Stanford, USA * Collaborators have the same affiliation as the participant presenting the paper unless shown in a footnote to the relevant article. TRANSCRIPTION REGULATION IN EUKARYOTES 5 Danuta KROTOSKI Jesper Q. SVEJSTRUP Director of Fellowships Mechanism of Gene Transcription and Workshops Laboratory Human Frontier Science Program Imperial Cancer Research Fund Strasbourg, FRANCE South Mimms, UK Michael MEISTERERNST Robert TJIAN Laboratory for Molecular Biology – Department of Molecular and Cell Genzentrum Biology Ludwig-Maximilians-Universität University of California/HHMI München, GERMANY Berkeley, USA Karl NIGHTINGALE Department of Biochemistry Làszlò TORA University of Cambridge Institut de Génétique et de Biologie Cambridge, UK Moléculaire et Cellulaire Université Louis Pasteur Martin REDDINGTON Illkirch, FRANCE Director of Research Grants Human Frontier Science Program Andrew A. TRAVERS Strasbourg, FRANCE Division of Cell Biology MRC Laboratory of Molecular Timothy J. RICHMOND Biology Institut für Molekularbiologie Cambridge, UK und Biophysik ETH Hönggerberg Kerstin WEISS Zürich, SWITZERLAND Institut für Molekularbiologie Robert
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