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The Symposia, 1933 — 2003

1993:   DNA & Chromosomes, Vol. LVIII

Organizer: Bruce Stillman, Bruce Alberts


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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

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-García    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