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The Symposia, 1933 — 2003

2000:   Biological Responses to DNA Damage, Vol. LXV

Organizer: Bruce Stillman


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Symposium Participants    v
Foreword    xxiMutation Response and Error BypassUnderstanding the Complexity of an Organism's Responses to DNA Damage G.C. Walker    1DNA Repair Systems and Bacterial Evolution M. Radman, F. Taddei, and I. Matic    11Adaptive Mutation in Escherichia coli P.L. Foster    21The Biochemical Basis and In Vivo Regulation of SOS-induced Mutagenesis Promoted byEscherichia coli DNA Polymerase V (UmuD´2C) M.F. Goodman and R. Woodgate    31Human DNA Polymerase k: A Novel DNA Polymerase of Unknown Biological FunctionEncoded by the DINB1 Gene V.L. Gerlach, W.J. Feaver, P.L. Fischhaber, J.A. Richardson, L. Aravind, E.V. Koonin, K. Bebenek, T.A. Kunkel, and E.C. Friedber    41Role of Yeast and Human DNA Polymerase h in Error-free Replication of Damaged DNAS. Prakash, R.E. Johnson, M.T. Washington, L. Haracska, C.M. Kondratick, and L. Prakash    51Roles of DNA Polymerase z and Rev1 Protein in Eukaryotic Mutagenesis and Translesion Replication C.W. Lawrence, P.E.M. Gibbs, R.S. Murante, X.-D. Wang, Z. Li, T.P. McManus, W.G. McGregor, J.R. Nelson, D.C. Hinkle, and V.M. Maher    61Xeroderma Pigmentosum Variant: From a Human Genetic Disorder to a Novel DNA PolymeraseC. Masutani, R. Kusumoto, A. Yamada, M. Yuasa, M. Araki, T. Nogimori, M. Yokoi, T. Eki, S. Iwai, and F. Hanaoka    71Streisinger Revisited: DNA Synthesis Errors Mediated by Substrate Misalignments K. Bebenek and T.A. Kunkel    81Base Recognition and Excision RepairRoles of Watson-Crick and Minor Groove Hydrogen Bonds in DNA Replication E.T. Kool    93Structural and Mechanistic Studies on Repair of 8-Oxoguanine in Mammalian Cells S.D. Bruner, D.P.G. Norman, J.C. Fromme, and G.L. Verdine    103Envisioning the Fourth Dimension of the Genetic Code: The Structural Biology of Macromolecular Recognition and Conformational Switching in DNA Repair K.-P. Hopfner, S.S. Parikh, and J.A. Tainer    113Repair of Endogenous DNA Damage T. Lindahl and D.E. Barnes    127Base Removers and Strand Scissors: Different Strategies Employed in Base Excision and Strand Incision at Modified Base Residues in DNA E. Seeberg, L. Luna, I. Morland, L. Eide, B. Johnsen, E. Larsen, I. Alseth, F. Dantzer, K. Baynton, R. Aamodt, K.I. Kristiansen, T. Rognes, A. Klungland, and M. Bjørås    135DNA Polymerase b and Mammalian Base Excision Repair S.H. Wilson, R.W. Sobol, W.A. Beard, J.K. Horton, R. Prasad, and B.J. Vande Berg    143Photolyase/Cryptochrome Family Blue-light Photoreceptors Use Light Energy to Repair DNA or Set the Circadian Clock A. Sancar, C. Thompson, R.J. Thresher, F. Araujo, J. Mo, S. Ozgur, E. Vagas, L. Dawut, and C.P. Selby    157Nucleotide Excision RepairDNA Damage Recognition and Nucleotide Excision Repair in Mammalian Cells R.D. Wood, S.J. Araújo, R.R. Ariza, D.P. Batty, M. Biggerstaff, E. Evans, P.-H. Gaillard, D. Gunz, B. Köberle, I. Kuraoka, J.G. Moggs, J.K. Sandall, and M.K.K. Shivji    173Regulation of Nucleotide Excision Repair in Bacteria and Mammalian Cells P.C. Hanawalt, D.J. Crowley, J.M. Ford, A.K. Ganesan, D.R. Lloyd, T. Nouspikel, C.A. Smith, G. Spivak, and S. Tornaletti    183Three-dimensional Structure and Function of Replication Protein A G. Mer, A. Bochkarev, W.J. Chazin, and A.M. Edwards    193Transcription-coupled Repair of Oxidative DNA Damage in Human Cells: Mechanisms and Consequences S. Tsutakawa and P.K. Cooper    201Mismatch RepairSignaling Mismatch Repair: The Mechanics of an Adenosine-Nucleotide Molecular Switch R. Fishel, S. Acharya, M. Berardini, T. Bocker, N. Charbonneau, A. Cranston, S. Gradia, S. Guerrette, C.D. Heinen, A. Mazurek, T. Snowden, C. Schmutte, K.-S. Shim, G. Tombline, and T. Wilson    217DNA Mismatch Repair: From Structure to Mechanism W. Yang, M.S. Junop, C. Ban, G. Obmolova, and P. Hsieh    225New Recognition Mode for a TG Mismatch: The Atomic Structure of a Very Short Patch Repair Endonuclease-DNA Complex S.E. Tsutakawa and K. Morikawa    233Temporary and Permanent Mutators Lacking the Mismatch Repair System: The Enhancement of Mutators in Cell Populations J.H. Miller, A. Yeung, P. Funchain, E. Mao, J. Stewart, W.M. Clendenin, and M.M. Slupska    241Telomeres and the Stability of DNA EndsMolecular Manifestations and Molecular Determinants of Telomere Capping E.H. Blackburn, S. Chan, J. Chang, T.B. Fulton, A. Krauskopf, M. McEachern, J. Prescott, J. Roy, C. Smith, and H. Wang    253A New Connection at Human Telomeres: Association of the Mre11 Complex with TRF2 T. de Lange and J.H.J. Petrini    265Telomere Length, Telomere-binding Proteins, and DNA Damage Signaling M.T. Hemann, J. Hackett, A. IJpma, and C.W. Greider    275All Things Must End: Telomere Dynamics in Yeast M.L. DuBois, S.J. Diede, A.E. Stellwagen, and D.E. Gottschling    281Sir2: An NAD-dependent Histone Deacetylase That Connects Chromatin Silencing, Metabolism, and Aging S. Imai, F.B. Johnson, R.A. Marciniak, M. McVey, P.U. Park, and L. Guarente    297Arrest, Adaptation, and Recovery following a Chromosome Double-strand Break in Saccharomyces cerevisiae S.E. Lee, A. Pellicioli, J. Demeter, M.P. Vaze, A.P. Gasch, A. Malkova, P.O. Brown, D. Botstein, T. Stearns, M. Foiani, and J.E. Haber    303Double-strand Break Repair in Human Cells S.C. West, C. Chappell, L.A. Hanakahi, J.-Y. Masson, M.J. McIlwraith, and E. Van Dyck    315Damage Control during Replication and MitosisControlling S-phase Onset in Fission Yeast Z. Lygerou and P. Nurs    323

Coping with and Recovering from Hydroxyurea-induced Replication Fork Arrest in Budding Yeast J.F.X. Diffley, K. Bousset, K. Labib, E.A. Noton, C. Santocanale, and J.A. Tercero    333

Damage Response and dNTP Regulation: The Interaction between Ribonucleotide Reductase and Its Inhibitor, Sml1 B. Georgieva, X. Zhao, and R. Rothstein    343

Is Rad9p Upstream or Downstream from Mec1p? E.J. Foss    347

DNA Damage Checkpoint Control of Mitosis in Fission Yeast N. Rhind, B.A. Baber-Furnari, A. Lopez-Girona, M.N. Boddy, J.-M. Brondello, B. Moser, P. Shanahan, A. Blasina, C. McGowan, and P. Russell    353

Mitotic Checkpoints, Genetic Instability, and Cancer M. Dobles and P.K. Sorger    361

Microscopy-induced Radiation Damage, Microtubules, and Progression through the Terminal Stage of G2 (Prophase) in Vertebrate Somatic Cells C.L. Rieder and R. Cole    369

Genome Stability and Checkpoint Control

Complexity of Damage Produced by Ionizing Radiation J.F. Ward    377

Complex Transcriptional Responses to Macromolecular Damaging Agents: Regulatory Responses Specific for SN2 Alkylation and the MAG1 Gene T.J. Begley, S.A. Jelinsky, and L.D. Samson    383

The Interplay between Nonhomologous End-joining and Cell Cycle Checkpoint Factors in Development, Genomic Stability, and Tumorigenesis D.O. Ferguson, J.M. Sekiguchi, K.M. Frank, Y. Gao, N.E. Sharpless, Y. Gu, J. Manis, R.A. DePinho, and F.W. Al    395

S-phase Functions of the Mre11 Complex J.H.J. Petrini    405

The FHA Domain, a Phosphoamino Acid Binding Domain Involved in the DNA Damage Response Pathway M. Huang and S.J. Elledge    413

The FHA Domain in DNA Repair and Checkpoint Signaling D. Durocher, S.J. Smerdon, M.B. Yaffe, and S.P. Jackson    423

Details and Concerns Regarding the G2/M DNA Damage Checkpoint in Budding Yeast T. Weinert, E. Little, L. Shanks, A. Admire, R. Gardner, C. Putnam, R. Michelson, K. Nyberg, and P. Sundareshan    433

Establishment of and Recovery from Damage Checkpoint Requires Sequential Interactions of Crb2 with Protein Kinases Rad3, Chk1, and Cdc2 F. Esashi, S. Mochida, T. Matsusaka, T. Obara, A. Ogawa, K. Tamai, and M. Yanagida    443

Analysis of the Fission Yeast Checkpoint Rad Proteins T. Caspari, C. Davies, and A.M. Carr    451

A Conserved Role for the Hus1 Checkpoint Protein in Eukaryotic Genome Maintenance R.S. Weiss, P. Leder, and T. Enoch    457

DNA-damage-induced Checkpoint Pathways in the Nematode Caenorhabditis elegans E.R. Hofmann, S. Milstein, and M.O. Hengartner    467

53 and the DNA Damage Response

The Transcriptional Program following p53 Activation R. Zhao, K. Gish, M. Murphy, Y. Yin, D. Notterman, W.H. Hoffman, E. Tom, D.H. Mack, and A.J. Levine    475

Regulation of p53 after Different Forms of Stress and at Different Cell Cycle Stages V. Gottifredi, S.Y. Shieh, and C. Prives    483

The DNA Damage Checkpoint and Human Cancer L.B. Schultz, N.H. Chehab, A. Malikzay, R.A. DiTullio, Jr., E.S. Stavridi, and T.D. Halazonetis    489

DNA Damage Responses and Chemosensitivity in the Em-myc Mouse Lymphoma Model C.A. Schmitt, R.R. Wallace-Brodeur, C.T. Rosenthal, M.E. McCurrach, and S.W. Lowe    499

Genetic Instability, Oncogenes, and the p53 Pathway G. Wahl and O. Vafa    511

DNA Damage and Cancer Progression

Multiple Signaling Pathways Involving ATM M.B. Kastan, D.-S. Lim, S.-T. Kim, B. Xu, and C. Canman    521

ATM: Sounding the Double-strand Break Alarm Y. Shiloh    527

Interactions of the Nijmegen Breakage Syndrome Protein with ATM and BRCA1 X. Wu, G. Rathbun, W.S. Lane, D.T. Weaver, and D.M. Livingston    535

The Function of BRCA1 in DNA Damage Response J.-S. Lee, K. Collins, A. Brown, C.-H. Lee, and J.H. Chung    547

Recombination between Two Chromosomes: Implications for Genomic Integrity in Mammalian Cells C. Richardson and M. Jasin    553

Transcription-coupled Repair: A Multifunctional Signaling Pathway S.A. Leadon    561

Chromosomal Instability and Cancer Predisposition: Insights from Studies on the Breast Cancer Susceptibility Gene, BRCA2 A.R. Venkitaraman    567

Roles of RecQ Family Helicases in the Maintenance of Genome Stability L. Wu, S.L. Davies, and I.D. Hickson    573

Role of DNA Break-sensing Molecule Poly(ADP-ribose) Polymerase (PARP) in Cellular Function and Radiation Toxicity W.-M. Tong, D. Galendo, and Z.-Q. Wang    583

Summary: Biological Responses to DNA Damage: A Perspective in the New Millennium E.C. Friedberg    593