1993: DNA & Chromosomes, Vol. LVIII
Organizer: Bruce Stillman, Bruce Alberts
Symposium Participants v Foreword xix Gene Expression Chromatin Structure of Transcriptionally Active Genes D. Clark, M. Reitman, V. Studitsky, J. Chung, H. Westphal, E. Lee, and G. Felsenfeld 1 Regulation of Human Globin Gene Switching F. Grosveld, M. Antoniou, M. Berry, E. de Boer, N. Dillon, J. Ellis, P. Fraser, J. Hurst, A. Imam, D. Meijer, S. Philipsen, S. Pruzina, J. Strouboulis, and D. Whyatt 7 Chromatin Structure of the b-Globin Chromosomal Domain in Adult Chicken Erythrocytes A. Verreault and J.O. Thomas 15 Structural-Functional Organization of Chromosomal DNA Domains S.V. Razin, R. Hancock, O. Iarovaia, O. Westergaard, I. Gromova, and G.P. Georgiev 25 Chromatin Domains Constitute Regulatory Units for the Control of Eukaryotic Genes A.E. Sippel, G. Schäfer, N. Faust, H. Saueressig, A. Hecht, and C. Bonifer 37 Genetic and Molecular Analysis of Chromatin Domains J. Vazquez, G. Farkas, M. Gaszner, A. Udvardy, M. Muller, K. Hagstrom, H. Gyurkovics, L. Sipos, J. Gausz, M. Galloni, I. Hogga, F. Karch, and P. Schedl 45 Generation of Transgenic Mice with Yeast Artificial Chromosomes L. Montoliu, A. Schedl, G. Kelsey, P. Lichter, Z. Larin, H. Lehrach, and G. Schütz 55 Influence of Chromatin Structure on the Binding of Transcription Factors to DNA G.L. Hager, T.K. Archer, G. Fragoso, E.H. Bresnick, Y. Tsukagoshi, S. John, and C.L. Smith 63 The High Mobility Group Protein HMG I(Y) Is an Essential Structural Component of a Virus-inducible Enhancer Complex D. Thanos, W. Du, and T. Maniatis 73 Role of Chromatin Structure in Regulating Gene Expression: The hsp26 Gene of Drosophila melanogaster S.C.R. Elgin, H. Granok, Q. Lu, and L.L. Wallrath 83 Role of Enhancer Sequences in Regulating Accessibility of DNA in Nuclear Chromatin T. Jenuwein, W.- Forrester, and R. Grosschedl 97 Control of Antigenic Variation in African Trypanosomes P. Borst, J.H. Gommers- Ampt, M.J.L. Ligtenberg, G. Rudenko, R. Kieft, M.C. Taylor, P.A. Blundell, and F. van Leeuwen 105 Transcription of DNA and Chromatin DNA Bending in Transcription Initiation J.D. Kahn and D.M. Crothers 115 X-ray Crystallographic Studies of Eukaryotic Transcription Factors S.K. Burley, K.L. Clark, A. Ferré-D'Amaré, J.L. Kim, and D.B. Nikolov 123 Stereochemistry of Specific Steroid Receptor-DNA Interactions W Xu, I. Alroy, L.F. Freedman, and P.B. Sigler 133 The Cocrystal Structures of Two Zinc-stabilized DNA-binding Domains Illustrate Different Ways of Achieving Sequence-specific DNA Recognition J.W.R. Schwabe, L. Fairall, L. Chapman, J.T. Finch, R.N. Dutnall, and D. Rhodes 141 Hydration of Biological Macromolecules in Solution: Surface Structure and Molecular Recognition K. Wuthrich 149 Structure and DNA Binding of the Yeast MATa2 Homeodomain C. Wolberger 159 Combinatorial Control of Transcription: The Herpes Simplex Virus VP16-induced Complex A.C. Wilson, M.A. Cleary, J.-S. Lai, K. LaMarco, M.G. Peterson, and W. Herr 167 Coactivators and TAFs: A New Class of Eukaryotic Transcription Factors That Connect Activators to the Basal Machinery N. Tanese and R. Tjian 179 The Cycling of RNA Polymerase II during Transcription L. Zawel, H. Lu, L.J. Cisek, J.L. Corden, and D. Reinberg 187 How Eukaryotic Transcription Activators Increase Assembly of Preinitiation Complexes B. Choy, S.G.E. Roberts, L.A. Griffin, and M.R. Green 199 Biochemical Analysis of the Role of Chromatin Structure in the Regulation of Transcription by RNA Polymerase II R. T. Kamakaka and J. T. Kadonaga 205 Nucleosome Cores and Histone H1 in the Binding of GAL4 Derivatives and the Reactivation of Transcription from Nucleosome Templates In Vitro L.-J. Juan, P.P. Walter, I.C.A. Taylor, R.E. Kingston, and J.L. Workman 213 Transcription Factor Access to DNA in the Nucleosome A.P. Wolffe, G. Almuzni, K. Ura, D. Pruss, and J.J. Hayes 225 Nucleosome Positioning and Transcription R.T. Simpson, S.Y. Roth, R.H. Morse, H.-G. Patterton, J.P. Cooper, M. Murphy, M.P. Kladde, and M. Shimizu 237 Histones and the Regulation of Heterochromatin in Yeast J.S. Thompson, A. Hecht, and M. Grunstein 247 Role of Yeast SNF and SWI Proteins in Transcriptional Activation B.C. Laurent, I. Treich, and M. Carlson 257 Genome Structure Studies of Nucleosome Structure T.J. Richmond, T. Rechsteiner, and K. Luger 265 Structure of the Histone Octamer Core of the Nucleosome and Its Potential Interactions with DNA E.N. Moudrianakis and G. Arents 273 Functions for DNA Methylation in Vertebrates A.P. Bird l81 Parental Imprinting of the H19 and Igf2 Genes in the Mouse S.M. Tilghman, M.S. Bartolomei, A.L. Webber, M.E. Brunkow, J. Saam, P.A. Leighton, K. Pfeifer, and S. Zemel 287 DNA Methylation, Genomic Imprinting, and Mammalian Development E. Li, C. Beard, A.C. Forster, T.H. Bestor, and R. Jaenisch 297 Allele-specific Structures in the Mouse Igf2-H19 Domain M. Ariel, S. Selig, M. Brandeis, D. Kitsberg, T. Kafri, A. Weiss, I. Keshet, A. Razin, and H. Cedar 307 Epigenetic and Chromosomal Control of Gene Expression: Molecular and Genetic Analysis of X Chromosome Inactivation H.F. Willard, C.J. Brown, L. Carrel, B. Hendrich, and A.P. Miller 315 Dissection of the Signal for DNA Methylation in the z-h Region of Neurospora E.U. Selker, G.A. Richardson, P.W. Garrett-Engele, M.J. Singer, and V. Miao 323 Crystal Structure of the HhaI DNA Methyltransferase X. Cheng, S. Kumar, S. Klimasauskas, and R.J. Roberts 331 Human and Mouse T-Cell-receptor Loci: The Importance of Comparative Large-scale DNA Sequence Analyses L. Hood, B.F. Koop, L. Rowen, and K. Wang 339 Criterion for the Completeness of Large-scale Physical Maps of DNA M.V. Olson and P. Green 349 Mapping and Sequencing the Nuclear Genome of the Yeast Saccharomyces cerevisiae: Strategies and Results of the European Enterprise B. Dujon 357 The Genome of the Nematode Caenorhabditis elegans R. Waterston, R. Ainscough, K. Anderson, M. Berks, D. Blair, M. Connell, J. Cooper, A. Coulson, M. Craxton, S. Dear, Z. Du, R. Durbin, A. Favello, L. Fulton, P. Green, N. Halloran, T. Hawkins, L. Hillier, C. Huynh, L. Johnston, J. Kershaw, J. Kirsten, Y. Kozono, N. Laister, P. Latreille, B. Mortimore, D. Panussis, C. Percy, L. Rifkin, A. Roopra, R. Shownkeen, N. Smaldon, A. Smith, M. Smith, R. Staden, J. Sulston, J. Thierry-Mieg, M. Vaudin, K. Vaughan, L. Weinstock, R. Wilson, and P. Wohldmann 367 Integrated Mapping across the Whole Human Genome I. Chumakov, C. Bellanne- Chantelot, I. LeGall, and D. Cohen 377 Replication of the Genome The Replicon: Thirty Years Later F. Jacob 383 Transcription Stimulates the Establishment of Bidirectional l DNA Replication In Vitro B. Learn, A.W. Karzai, and R. McMacken 389 Site-specific DNA-binding Proteins Important for Replication and Transcription Have Multiple Activities R. Li, L. Yang, E. Fouts, and M.R. Botchan 403 Analysis of Replication Origin Function on Chromosome III of Saccharomyces cerevisiae C.S. Newlon, I. Collins, A. Dershowitz, A.M. Deshpande, S.A. Green-feder,L. Y. Ong, and J.F. Theis 415 The Topography of Chromosome Replication in Yeast B.J. Brewer, J.D. Diller, K.L. Friedman, K.M. Kolor, M.K. Raghuraman, and W.L. Fangman 425
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The Replicon Model and Eukaryotic Chromosomes S.P. Bell, Y. Marahrens, H. Rao, and B. Stillman 435 A Transcriptional Silencer as a Specialized Origin of Replication That Establishes Functional Domains of Chromatin C.A. Fox, S. Loo, D.H. Rivier, M.A. Foss,and J. Rine 443 The Mechanism of Fission Yeast Mating-type Interconversion: Evidence for Two Types of Epigenetically Inherited Chromosomal Imprinted Events A.J.S. Klar and M.J. Bonaduce 457 Initiation of Replication at a Mammalian Chromosomal Origin J.L. Hamlin, P.J. Mosca, P.A. Dijkwel, and H.-B. Lin 467 Site-specific Initiation of DNA Replication in Metazoan Chromosomes and the Role of Nuclear Organization D.M. Gilbert, H. Miyazawa, F.S. Nallaseth, J.M. Ortega, J.J. Blow, and M.L. DePamphilis 475 DNA Amplification in DNA Puff 1I/9A of Sciara coprophila S.A. Gerbi, C. Liang, N. Wu, S.M. DiBartolomeis, B. Bienz-Tadmor, H.S. Smith, and F.D. Urnov 487 Two DNA Polymerases: HIV Reverse Transcriptase and the Klenow Fragment of Escherichia coli DNA Polymerase I T.A. Steitz, S. Smerdon, J. Jäger, J. Wang, L.A. Kohlstaedt, J.M. Friedman, L.S. Beese, and P.A. Rice 495 Recombination, Repair, and Genome Stability Role of Gin and FIS in Site-specific Recombination P. Merker, G. Muskhelishvili, A. Deufel, K. Rusch, and R. Kahmann 505 Target Site Selection in Transposition of Phage Mu M. Mizuuchi and K. Mizuuchi 515 Late Steps in Genetic Recombination: Branch Migration and Holliday Junction Resolution by RuvA, RuvB, and RuvC Proteins S.C. West, I.R. Tsaneva, K. Hiom, and F.E. Benson 525 Retroviral Integration Machinery as a Probe for DNA Structure and Associated Proteins H.-P. Muller, P.M. Pryciak, and H.E. Varmus 533 Chiasma Interference and the Distribution of Exchanges in Drosophila melano- gaster R. Lande and F.W. Stahl 543 Potential Advantages of Unstable Interactions for Pairing of Chromosomes in Meiotic, Somatic, and Pre meiotic Cells N. Kleckner and B.M. Weiner 553 RecA-like Recombination Proteins in Eukaryotes: Functions and Structures of RAD51 Genes T. Ogawa, A. Shinohara, A. Nabetani, T. Ikeya, X. Yu, E.H. Egelman, and H. Ogawa 567 Characterization of Sequences Responsible for trans-Inactivation of the Drosophila brown Gene L.E. Martin-Morris, K. Loughney, E.O. Kershisnik, G. Poortinga, and S. Henikoff 577 Position Effect Variegation and Genomic Instability A. C. Spradling 585 Mismatch Repair and Genetic Stability in Human Cells W-H. Fang, G.-M. Li, M., Longley, J. Holmes, W. Thilly, and P. Modrich 597 Excision Repair in Man and the Molecular Basis of Xeroderma Pigmentosum Syndrome J. T. Reardon, L.H. Thompson, and A. Sancar 605 DNA Joining in Mammalian Cells T. Lindahl, C. Prigent, D.E. Barnes, A.R. Lehmann, M.S. Satoh, E. Roberts, R.A. Nash, P. Robins, and G. Daly 619 Nucleotide Excision Repair of DNA by Mammalian Cell Extracts and Purified Proteins R.D. Wood, A. Aboussekhra, M. Biggerstaff, C.J. Jones, A. O'Donovan, M.K.K. Shivji, and D.E. Szymkowski 625 Chromosomal Fragile Sites: Molecular Test of the Delayed-replication Model C.D. Laird, R.S. Hansen, T.K. Canfield, M.M. Lamb, and S.M. Gartler 633 Coupling DNA Replication to the Cell Cycle T.J. Kelly, P. Nurse, and S.L. Forsburg 637 Loss of Chromosomal Integrity in Neoplasia T.D. Tlsty, P. Jonczyk, A. White, M. Sage, I. Hall, D. Schaefer, A. Briot, E. Livanos, H. Roelofs, B. Poulose, and J. Sanchez 645 Cell Cycle Regulation of Gene Amplification A. Di Leonardo, S.P. Linke, Y. Yin, and G.M. Wahl 655 Centromeres and Telomeres Molecular Analysis of the Budding Yeast Centromere/Kinetochore W. Jiang and J. Carbon 669 Structure and Function of Chromosomes in Mitosis of Budding Yeast V. Guacci, A. Yamamoto, A. Strunnikov, J. Kingsbury, E. Hogan, P. Meluh, and D. Koshland 677 Structure and Function of Schizosaccharomyces pombe Centromeres L. Clarke, M. Baum, L.G. Marschall, V.K. Ngan, and N.C. Steiner 687 The INCENPs: Structural and Functional Analysis of a Family of Chromosome Passenger Proteins A.M. Mackay and W.C. Earnshaw 697 In Vivo and In Vitro Studies of Telomeres and Telomerase M.S. Lee, R.C. Gallagher, J. Bradley, and E.H. Blackburn 707 Telomerase and Telomere-length Regulation: Lessons from Small Eukaryotes to Mammals C.W. Greider 719 Structural and Temporal Analysis of Telomere Replication in Yeast R.J. Wellinger, A.J. Wolf, and V.A. Zakian 725 The Positioning of Yeast Telomeres Depends on SIR3, SIR4, and the Integrity of the Nuclear Membrane F. Palladino, T. Laroche, E. Gilson, L. Pillus, and S.M. Gasser 733 Nuclear Structure Snurposomes and Coiled Bodies Z. Wu, C. Murphy, C.-H.H. Wu, A. Tsvetkov, and J.G. Gall 747 From the Chromosomal Loops and the Scaffold to the Classic Bands of Metaphase Chromosomes Y. Saitoh and U.K. Laemmli 755 Studies of Metaphase and Interphase Chromosomes Using Fluorescence In Situ Hybridization B.J. Trask, S. Allen, H. Massa, A. Fertitta, R. Sachs, G. van den Engh, and M. Wu 767 Role of Chromosome Territories in the Functional Compartmentalization of the Cell Nucleus T. Cremer, A. Kurz, R. Zirbel, S. Dietzel, B. Rinke, E. Schröck, M.R. Speicher, U. Mathieu, A. Jauch, P. Emmerich, H. Scherthan, T. Ried, C. Cremer, and P. Lichter 777 Mechanisms of Intracellular Transcript Localization and Export in Early Drosophila Embryos I. Davis, H. Francis-Lang, and D. Ish-Horowicz 793 Dynamics of Transcription and Pre-mRNA Splicing within the Mammalian Cell Nucleus D.L. Spector, R.T. O'Keefe, and L.F. Jiménez-GarcÃÂa 799 Probing Functional Organization within the Nucleus: Is Genome Structure Integrated with RNA Metabolism? J.B. Lawrence, K.C. Carter, and X. Xing 807 Summary: Genetic Tinkering-Local Problems, Local Solutions H. Weintraub 819
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