(NAS Colloquium) Links Between Recombination and Replication : Vital Roles of Recombination.

Colloquium on Links Between Recombination and Replication: Vital Roles of Recombination -- PNAS -- Contents -- Introduction Links between recombination and replication: Vital roles of recombination -- Colloquium Historical overview: Searching for replication help in all of the rec places -- THREAD 1: THE DISCOVERY OF RECOMBINATION GENES IN BACTERIA -- THREAD 2: IN VIVO CHARACTERIZATION OF BACTERIAL RECOMBINATION FUNCTIONS -- THREAD 3: EARLY LINKS BETWEEN REPLICATION FORKS AND RECOMBINATIONAL DNA REPAIR -- THREAD 4: Studies of the Bacterial SOS System -- THREAD 5: WORK ON BACTERIOPHAGE T4 DNA METABOLISM -- THREAD 6: ORIGIN-INDEPENDENT AND RDR RESTART DURING THE SOS RESPONSE -- THREAD 7: ISOLATION AND CHARACTERIZATION OF RECA PROTEIN AND PROKARYOTIC RECOMBINATION PROTEINS -- THREAD 8: RECOMBINATION MODEL DEVELOPMENT -- THREAD 9: EUKARYOTIC RECOMBINATION PROTEINS -- THREAD 10: THE RESTART (X174-TYPE) PRIMOSOME -- THREAD 11: TYING THE THREADS TOGETHER, GENETICALLY AND BIOCHEMICALLY -- THREAD 12: XERCD AND FREQUENCY ESTIMATES -- THE END MARKS A BEGINNING -- Colloquium Rescue of arrested replication forks by homologous recombination -- DNA SEQUENCES, OR MUTATIONS THAT CAUSE REPLICATION ARREST, INDUCE DNA REARRANGEMENTS -- THE REPLICATION FORK REVERSAL REACTION -- Colloquium Circles: The replication-recombination-chromosome segregation connection -- Colloquium Participation of recombination proteins in rescue of arrested replication forks in UV-irradiated Escherichia… -- A COMMON PATHWAY INVOLVING BOTH NUCLEOTIDE EXCISION REPAIR AND REC GENES -- Colloquium Effects of mutations involving cell division, recombination, and chromosome dimer resolution on a priA2::kan… -- MATERIALS AND METHODS -- RESULTS -- DISCUSSION -- Colloquium RecA protein promotes the regression of stalled replication forks in vitro -- MATERIALS AND METHODS -- RESULTS -- DISCUSSION.

Colloquium Topological challenges to DNA replication: Conformations at the fork -- CONFORMATIONS OF NONREPLICATING DNA -- CONFORMATIONS OF REPLICATING DNA -- DOMAINS -- Colloquium Rescue of stalled replication forks by RecG: Simultaneous translocation on the leading and lagging strand… -- MATERIALS AND METHODS -- RESULTS -- DISCUSSION -- Colloquium Formation of Holliday junctions by regression of nascent DNA in intermediates containing stalled replication… -- MATERIALS AND METHODS -- RESULTS -- DISCUSSION -- Colloquium Single-strand interruptions in replicating chromosomes cause double-strand breaks -- MATERIALS AND METHODS -- RESULTS -- DISCUSSION -- Colloquium Handoff from recombinase to replisome: Insights from transposition -- Colloquium Break-induced replication: A review and an example in budding yeast -- POSSIBLE MECHANISMS OF BIR -- BIR IN SACCHAROMYCES CEREVISIAE -- TWO (OR MORE) PATHWAYS OF BREAK-INDUCED REPLICATION IN S. CEREVISIAE -- YEAST TELOMERE MAINTENANCE IN THE ABSENCE OF TELOMERASE APPEARS TO EMPLOY BIR -- MAMMALIAN TELOMERE MAINTENANCE IN THE ABSENCE OF TELOMERASE: THE ALTERNATIVE LENGTHENING OF TELOMERES (ALT) PATHWAY -- BIR AND ITS RELATIONSHIP TO OTHER HOMOLOGOUS RECOMBINATION EVENTS -- GENE TARGETING MAY ALSO INVOLVE BIR-LIKE EVENTS -- BIR EVENTS COUPLED TO NONHOMOLOGOUS RECOMBINATION IN HIGHER EUKARYOTIC CELLS -- BIR EVENTS DURING TRANSFORMATION IN BUDDING YEAST -- MATERIALS AND METHODS -- RESULTS -- DISCUSSION -- Colloquium Links between replication and recombination in Saccharomyces cerevisiae: A hypersensitive requirement for… -- MATERIALS AND METHODS -- RESULTS AND DISCUSSION -- CONCLUDING REMARKS -- Colloquium Evidence that replication fork components catalyze establishment of cohesion between sister chromatids -- HISTORICAL OBSERVATIONS -- GENES REQUIRED TO MAINTAIN SISTER CHROMATID COHESION.

THE SMC1 SMC3 "COHESIN" COMPLEX -- SITES OF COHESION -- BUILDING CHROMATID BRIDGES OCCURS DURING S-PHASE -- TRF4P/DNA POLYMERASE Σ LINKS REPLICATION AND COHESION -- A POLYMERASE SWITCH MODEL FOR COHESION ESTABLISHMENT -- COHESION AND CANCER -- SOME UNANSWERED QUESTIONS -- Colloquium Rad52 forms DNA repair and recombination centers during S phase -- MATERIALS AND METHODS -- RESULTS -- DISCUSSION -- Colloquium A yeast gene, MGS1, encoding a DNA-dependent AAA+ ATPase is required to maintain genome stability -- MATERIALS AND METHODS -- RESULTS -- DISCUSSION -- Colloquium The tight linkage between DNA replication and double-strand break repair in bacteriophage T4 -- T4 RECOMBINATION-DEPENDENT REPLICATION -- RELATIONSHIP OF T4 RDR TO DSB REPAIR -- THREE MODELS OF DSB REPAIR -- A TWO-PLASMID SYSTEM FOR RDR AND DSB REPAIR -- REQUIREMENT FOR RECOMBINATION AND REPLICATION GENE PRODUCTS -- DO ANY OF THE DSB REPAIR MODELS EXPLAIN THE DSB REPAIR PRODUCTS? -- RECOMBINATION EVENTS STIMULATED BY REPLICATION FORKS BLOCKED AT TOPOISOMERASE CLEAVAGE COMPLEXES -- INTERPLASMID RECOMBINATION EVENTS SIMULATED BY A T4 ORIGIN OF REPLICATION ON ONE OF THE PLASMIDS -- THE TIGHT CONNECTIONS OF T4 REPLICATION, RECOMBINATION, AND DSB REPAIR -- Colloquium Mediator proteins orchestrate enzyme-ssDNA assembly during T4 recombination-dependent DNA replication and repair -- T4 RDR IN VITRO: MECHANISMS AND QUESTIONS -- ROLE OF UVSY PROTEIN IN ASSEMBLY OF THE T4 PRESYNAPTIC FILAMENT -- IS PRESYNAPSIS COUPLED TO THE NUCLEOLYTIC RESECTION OF DSDNA ENDS? -- MECHANISM OF DNA HELICASE LOADING BY GP59 -- SUPPRESSION OF GP59-DEPENDENT PRIMOSOME ASSEMBLY BY UVSX/UVSY -- ENZYME PARTITIONING IS ORCHESTRATED BY RMPS -- BUBBLE MIGRATION: A MECHANISM FOR LESION BYPASS? -- Colloquium Two recombination-dependent DNA replication pathways of bacteriophage T4, and their roles in mutagenesis and….

RESULTS AND DISCUSSION -- CONCLUSIONS -- Colloquium Bacteriophage T4 gene 41 helicase and gene 59 helicase-loading protein: A versatile couple with role in… -- T4 GENE 59 HELICASE-LOADING PROTEIN -- ROLE OF THE HELICASE AND HELICASE-LOADING PROTEIN DURING ORIGIN-DEPENDENT REPLICATION -- THE VERSATILITY OF T4 41 HELICASE AND 59 HELICASE-LOADING PROTEIN COUPLES REPLICATION AND RECOMBINATION -- COMPARISON WITH OTHER HELICASES AND LOADING PROTEINS -- Colloquium Instability of repetitive DNA sequences: The role of replication in multiple mechanisms -- MATERIALS AND METHODS -- RESULTS AND DISCUSSION -- Colloquium Repeat expansion by homologous recombination in the mouse germ line at palindromic sequences -- MATERIALS AND METHODS -- RESULTS -- DISCUSSION -- Colloquium Stationary-phase mutation in the bacterial chromosome: Recombination protein and DNA polymerase IV dependence -- MATERIALS AND METHODS -- RESULTS -- DISCUSSION -- FURTHER DISCUSSION -- Colloquium Managing DNA polymerases: Coordinating DNA replication, DNA repair, and DNA recombination -- Colloquium Roles of DNA polymerases V and II in SOS-induced error-prone and error-free repair in Escherichia coli -- COPING WITH DNA DAMAGE IN E. COLI -- FUTURE PERSPECTIVES -- Colloquium Accuracy of lesion bypass by yeast and human DNA polymerase -- THE RAD6-DEPENDENT PATHWAYS OF DAMAGE BYPASS -- ROLE OF DNA POLΗ IN THE ERROR-FREE BYPASS OF UV LESIONS -- FIDELITY AND PROCESSIVITY OF DNA POLΗ -- INEFFICIENT EXTENSION OF MISMATCHED BASE PAIRS BY DNA POLΗ -- MATERIALS AND METHODS -- RESULTS AND DISCUSSION -- Colloquium ATP bound to the origin recognition complex is important for preRC formation -- MATERIALS AND METHODS -- RESULTS -- DISCUSSION -- Colloquium Creating a dynamic picture of the sliding clamp during T4 DNA polymerase holoenzyme assembly by using… -- MATERIALS AND METHODS -- RESULTS -- DISCUSSION.

Colloquium Interaction of the β sliding clamp with MutS, ligase, and DNA polymerase I -- THE SLIDING CLAMP IN REPLICATION -- PCNA AND GP45 PARTICIPATE IN MANY DNA METABOLIC PROCESSES -- INTERACTION OF Β WITH POL III H.E., POL II, AND POL V -- INTERACTION OF Β WITH MUTS -- WHAT ROLE MAY THE Β-MUTS INTERACTION PLAY IN MISMATCH REPAIR? -- THE Β CLAMP INTERACTS WITH POL I AND LIGASE -- CONCLUSIONS -- Colloquium Defining the roles of individual residues in the single-stranded DNA binding site of PcrA helicase -- MATERIALS AND METHODS -- RESULTS -- DISCUSSION -- Colloquium Homologous DNA recombination in vertebrate cells -- CHICKEN DT40 CELLS AS AN EXPERIMENTAL SYSTEM TO ANALYZE HOMOLOGOUS RECOMBINATION (HR) -- HETEROALLELIC HR PLAYS AN IMPORTANT ROLE IN DNA DOUBLE-STRAND BREAK (DSB) REPAIR IN YEAST BUT NOT IN VERTEBRATE CELLS -- HOMOLOGOUS DNA RECOMBINATION IS ESSENTIAL FOR THE VIABILITY OF VERTEBRATE CELLS -- THE DIFFERING ROLES OF RAD52 IN VERTEBRATE AND YEAST CELLS -- ACTIVITIES OF RAD51-LIKE MOLECULES IN YEAST AND VERTEBRATES -- DT40 CELLS DEFICIENT IN BOTH RAD52 AND XRCC3, A RAD51 PARALOG, ARE NOT VIABLE -- OTHER RAD51-INTERACTING PROTEINS -- CONCLUSIONS -- Colloquium Meiotic recombination and chromosome segregation in Schizosaccharomyces pombe -- GENETIC AND PHYSIOLOGIC CONTROL OF THE ENTRY INTO MEIOSIS -- CONTROL OF MEIOTIC REC GENE EXPRESSION -- REP1(REC16) LINKS MEIOTIC REPLICATION AND RECOMBINATION -- GENE PRODUCTS REQUIRED FOR MEIOTIC RECOMBINATION -- THE M26 MEIOTIC RECOMBINATION HOTSPOT -- DNA BREAKS ASSOCIATED WITH MEIOTIC RECOMBINATION -- NUCLEAR REORGANIZATION AND MOVEMENT -- LINEAR ELEMENTS NOT SYNAPTONEMAL COMPLEX -- SISTER CHROMATID COHESION (SCC), RECOMBINATION AND MEIOTIC SEGREGATION -- MEIOTIC SEGREGATION IN THE ABSENCE OF RECOMBINATION -- PERSPECTIVES -- Colloquium Manipulating the mammalian genome by homologous recombination.

TRANSIENT ALTERATION OF GENE EXPRESSION.

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