Mechanisms of Transcription

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    189 Role 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 Polymerase G.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 Protein J. 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. Mizzen, M.-H. Kuo, E. Smith, J. Brownell, J. Zhou, R. Ohba, Y. Wei, L. Monaco, P. Sassone-Corsi, and C.D. Allis    469 Regulation of Transcription by Multisubunit Complexes That Alter Nucleosome Structure D.J. Steger, R.T. Utley, P.A. Grant, S. John, A. Eberharter, J. Côté, T. Owen-Hughes, K. Ikeda, and J.L. Workman    483 TBP-associated Factors in the PCAF Histone Acetylase Complex T. Kotani, X. Zhang, R.L. Schiltz, V.V. Ogryzko, T. Howard, M.J. Swanson, A. Vassilev, H. Zhang, J. Yamauchi, B.H. Howard, J. Qin, and Y. Nakatani    493 Structure of the Yeast Histone Acetyltransferase Hat1: Insights into Substrate Specificity and Implications for the Gcn5-related N-acetyltransferase Superfamily R.N. Dutnall, S.T. Tafrov, R. Sternglanz, and V. Ramakrishnan    501 The Establishment of Active Chromatin Domains A. Bell, J. Boyes, J. Chung, M. Pikaart, M.-N. Prioleau, F. Recillas, N. Saitoh, and G. Felsenfeld    509 Nuclear Matrix Attachment Regions Confer Long-range Function upon the Immunoglobulin m Enhancer L.A. Fernández, M. Winkler, W. Forrester, T. Jenuwein, and R. Grosschedl    515

Remodeling Chromatin

ATP-dependent Remodeling of Chromatin C. Wu, T. Tsukiyama, D. Gdula, P. Georgel, M. Martínez-Balbás, G. Mizuguchi, V. Ossipow, R. Sandaltzopoulos, and H.-M. Wang    525 A Model for Chromatin Remodeling by the SWI/SNF Family G.R. Schnitzler, S. Sif, and R.E. Kingston    535 SWI/SNF Complex: Dissection of a Chromatin Remodeling Cycle C.L. Peterson    545 The SAGA of Spt Proteins and Transcriptional Analysis in Yeast: Past, Present, and Future F. Winston and P. Sudarsanam    553 Specificity of ATP-dependent Chromatin Remodeling at the Yeast PHO5 Promoter E.S. Haswell and E.K. O'Shea    563 Role of Chromatin Structure and Distal Enhancers in Tissue-specific Transcriptional Regulation In Vitro R. Bagga, J.A. Armstrong, and B.M. Emerson    569

Regulatory Complexes and Pathways

The Transcriptional Basis of Steroid Physiology R.J. Lin, H.-Y. Kao, P. Ordentlich, and R.M. Evans    577 Building Transcriptional Regulatory Complexes: Signals and Surfaces K.R. Yamamoto, B.D. Darimont, R.L. Wagner, and J.A. Iñiguez-Lluhí    587 The Herpes Simplex Virus VP16-induced Complex: Mechanisms of Combinatorial Regulation W. Herr    599 Structure and Function of the Interferon-b Enhanceosome T. Maniatis, J.V. Falvo, T.H. Kim, T.K. Kim, C.H. Lin, B.S. Parekh, and M.G. Wathelet    609 Autoinhibition as a Transcriptional Regulatory Mechanism B.J. Graves, D.O. Cowley, T.L. Goetz, J.M. Petersen, M.D. Jonsen, and M.E. Gillespie    621 Mechanisms of Activation by CREB and CREM: Phosphorylation, CBP, and a Novel Coactivator, ACT G.M. Fimia, D. De Cesare, and P. Sassone-Corsi    631 Regulation of SRF Activity by Rho Family GTPases R. Treisman, A.S. Alberts, and E. Sahai    643 Summary: Three Decades after Sigma R. Losick    653