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The Symposia, 1933 — 2003

1998:   Mechanisms of Transcription, Vol. LXIII

Organizer: Bruce Stillman


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Symposium Participants    v
Foreword    xix Dedication    xxv Promoter Recognition and Initiation Transcription Regulation by Repressosome and by RNA Polymerase Contact S. Adhya, M. Geanacopoulos, D.E.A. Lewis, S. Roy, and T. Aki    1 RNA Polymerase-DNA Interaction: Structures of Intermediate, Open, and Elongation Complexes R.H. Ebright    11 The Initiator Element: A Paradigm for Core Promoter Heterogeneity within Metazoan Protein-coding Genes S.T. Smale, A. Jain, J. Kaufmann, K.H. Emami, K. Lo, and I.P. Garraway     21 X-ray Crystallographic Studies of Eukaryotic Transcription Factors S.K. Burley    33 Transcription in Archaea S.D. Bell and S.P. Jackson    41 Polarity of Transcription on Pol II and Archaeal Promoters: Where Is the "One-way Sign" and How Is It Read? F.T.F. Tsai, O. Littlefield, P.F. Kosa, J.M. Cox, A. Schepartz, and P.B. Sigler    53 Transcriptional Regulation by DNA Structural Transitions and Single-stranded DNA-binding Proteins L.B. Rothman-Denes, X. Dai, E. Davydova, R. Carter, and K. Kazmierczak    63 The DPE, a Conserved Downstream Core Promoter Element That Is Functionally Analogous to the TATA Box T.W. Burke, P.J. Willy, A.K. Kutach, J.E.F. Butler, and J.T. Kadonaga     75 The RNA Polymerase II General Transcription Factors: Past, Present, and Future D. Reinberg,G. Orphanides, R. Ebright, S. Akoulitchev, J. Carcamo, H. Cho, P. Cortes, R. Drapkin, O. Flores, I. Ha, J.A. Inostroza, S. Kim, T.-K. Kim, P. Kumar, T. Lagrange, G. LeRoy, H. Lu, D.-M. Ma, E. Maldonado, A. Merino, F. Mermelstein, I. Olave, M. Sheldon, R. Shiekhattar, N. Stone, X. Sun, L. Weis, K. Yeung, and L. Zawel     83 Ten Years of TFIIH F. Coin and J.-M. Egly    105 Crossing the Line between RNA Polymerases: Transcription of Human snRNA Genes by RNA Polymerases II and III R.W. Henry, E. Ford, R. Mital, V. Mittal, and N. Hernandez    111 Transcription Factor IIIB: The Architecture of Its DNA Complex, and Its Roles in Initiation of Transcription by RNA Polymerase III A. Kumar, A. Grove, G.A. Kassavetis, and E.P. Geiduschek    121 Strength and Regulation without Transcription Factors: Lessons from Bacterial rRNA Promoters R.L. Gourse, T. Gaal, S.E. Aiyar, M.M. Barker, S.T. Estrem, C.A. Hirvonen, and W. Ross    131 Activation The Functional and Regulatory Roles of Sigma Factors in Transcription C.A. Gross, C. Chan, A. Dombroski, T. Gruber, M. Sharp, J. Tupy, and B. Young    141 The Bacterial Enhancer-binding Protein NtrC as a Molecular Machine I. Rombel, A. North, I. Hwang, C. Wyman, and S. Kustu    157 Gene Transcription by Recruitment Z. Zaman, A.Z. Ansari, L. Gaudreau, J. Nevado, and M. Ptashne    167 Use of Artificial Activators to Define a Role for Protein-Protein and Protein-DNA Contacts in Transcriptional Activation S.L. Dove and A. Hochschild    173 Activation and the Role of Reinitiation in the Control of Transcription by RNA Polymerase II S. Hahn    181 Cofactor Requirements for Transcriptional Activation by Sp1 A.M. När, S. Ryu, and R. Tjian    189Role of General and Gene-specific Cofactors in the Regulation of Eukaryotic Transcription R.G. Roeder    201 Functional Analysis of TFIID Components W.-C. Shen, L.M. Apone, C.-M.A. Virbasius, X.-Y. Li, M. Monsalve, and M.R. Green    219 Mechanism and Regulation of Yeast RNA Polymerase II Transcription R.D. Kornberg    229 Functional and Structural Analysis of the Subunits of Human Transcription Factor TFIID I. Davidson, C. Romier, A.-C. Lavigne, C. Birck, G. Mengus, O. Poch, and D. Moras    233 Mechanisms of Viral Activators A.J. Berk, T.G. Boyer, A.N. Kapanidis, R.H. Ebright N.N. Kobayashi, P.J. Horn, S.M. Sullivan, R. Koop, M.A. Surby, and S.J. Triezenberg    243 Cooperative Assembly of RNA Polymerase II Transcription Complexes K. Ellwood, T. Chi, W. Huang, K. Mitsouras, and M. Carey     253 RNA Polymerase

Transcription Regulation, Initiation, and "DNA Scrunching" by T7 RNA PolymeraseG.M.T. Cheetham, D. Jeruzalmi, and T.A. Steitz    263

Structural Studies of Escherichia coli RNA Polymerase S.A. Darst, A. Polyakov, C. Richter, and G. Zhang    269

Interaction of Escherichia coli s70 with Core RNA Polymerase R.R. Burgess, T.M. Arthur, and B.C. Pietz    277

The Transition from Initiation to Elongation by RNA Polymerase II D.S. Luse and I. Samkurashvili    289

Role of RNA Polymerase II Carboxy-terminal Domain in Coordinating Transcription with RNA Processing S. McCracken, E. Rosonina, N. Fong, M. Sikes, A. Beyer, K. O'Hare, S. Shuman, and D. Bentley    301

Fractions to Functions: RNA Polymerase II Thirty Years Later N.A. Woychik    311

Elongation and Termination

Antitermination by Bacteriophage l Q Protein J.W. Roberts, W. Yarnell, E. Bartlett, J. Guo, M. Marr, D.C. Ko, H. Sun, and C.W. Roberts    319

Structure and Mechanism in Transcriptional Antitermination by the Bacteriophage l N ProteinJ. Greenblatt, T.-F. Mah, P. Legault, J. Mogridge, J. Li, and L.E. Kay    327

Mechanistic Model of the Elongation Complex of Escherichia coli RNA Polymerase N. Korzheva, A. Mustaev, E. Nudler, V. Nikiforov, and A. Goldfarb    337

Promoter-associated Pausing in Promoter Architecture and Postinitiation Transcriptional Regulation J. Lis    347

Mechanism of Promoter Escape by RNA Polymerase II J.W. Conaway, A. Dvir, R.J. Moreland, Q. Yan, B.J. Elmendorf, S. Tan, and R.C. Conaway    357

RNA Polymerase II Elongation Control J. Peng, M. Liu, J. Marion, Y. Zhu, and D.H. Price    365

HIV-1 Tat Interacts with Cyclin T1 to Direct the P-TEFb CTD Kinase Complex to TAR RNA M.E. Garber, P. Wei, and K.A. Jones    371

The Yeast RNA Polymerase III Transcription Machinery: A Paradigm for Eukaryotic Gene Activation S. Chédin, M.L. Ferri, G. Peyroche, J.C. Andrau, S. Jourdain, O. Lefebvre, M. Werner, C. Carles, and A. Sentenac    381

Repression Mechanisms

The Regulation of Gene Activity by Histones and the Histone Deacetylase RPD3 N. Suka, A.A. Carmen, S.E. Rundlett, and M. Grunstein    391

Targeting Sir Proteins to Sites of Action: A General Mechanism for Regulated Repression M. Cockell, M. Gotta, F. Palladino, S.G. Martin, and S.M. Gasser    401

Activation and Repression Mechanisms in Yeast K. Struhl, D. Kadosh, M. Keaveney, L. Kuras, and Z. Moqtaderi    413

The Mad Protein Family Links Transcriptional Repression to Cell Differentiation G.A. McArthur, C.D. Laherty, C. Quéva, P.J. Hurlin, L. Loo, L. James, C. Grandori P. Gallant, Y. Shiio, W.C. Hokanson, A.C. Bush, P.F. Cheng, Q.A. Lawrence, B. Pulverer, P.J. Koskinen, K.P. Foley, D.E. Ayer, and R.N. Eisenman    423

Histone Deacetylase Directs the Dominant Silencing of Transcription in Chromatin: Association with MeCP2 and the Mi-2 Chromodomain SWI/SNF ATPase P.A. Wade, P.L. Jones, D. Vermaak, G.J.C. Veenstra, A. Imhof, T. Sera, C. Tse, H. Ge, Y.-B. Shi, J.C. Hansen, and A.P. Wolffe    435

Gene Regulation by the Yeast Ssn6-Tup1 Corepressor M. Wahi, K. Komachi, and A.D. Johnson    447

In Vivo Functions of Histone Acetylation/Deacetylation in Tup1p Repression and Gcn5p Activation D.G. Edmondson, W. Zhang, A. Watson, W. Xu, J.R. Bone, Y. Yu, D. Stillman, and S.Y. Roth    459

Chromosome Structure and Transcription

Signaling to Chromatin through Histone Modifications: How Clear Is the Signal? C. Mi