J E Haber

..In addition, MAT switching provides a remarkable example of a small locus control region--the Recombination Enhancer--that controls recombination along an entire chromosome arm...

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..Donor preference is regulated by a 250 bp recombination enhancer, that controls recombination of the entire left arm of chromosome III. Recent studies have shown how this locus-control region is turned on and off...

..Recent studies with the yeast Saccharomyces cerevisiae have identified some of the key players that link homologous recombination to synaptonemal complex formation...

..We suggest that Tid1p participates in monitoring the extent of single-stranded DNA produced by resection of DNA ends in a fashion that is distinct from its role in recombination...

..The similar genetic requirements for BIR and telomere maintenance in the absence of telomerase also suggest that these two processes proceed by similar mechanisms...

..This review encompasses these different aspects of DSB-induced recombination in Saccharomyces and attempts to relate genetic, molecular biological, and biochemical studies of the processes of DNA repair and recombination...

..We interpret these results in terms of the formation and resolution of alternative intermediates of a synthesis-dependent strand annealing mechanism...

..3' tails shorter than 30 nt are removed by another mechanism that depends at least in part on the 3'-to-5' proofreading activity of DNA polymerase delta...

..Thus, the end of a linearized DNA fragment can initiate new DNA synthesis by BIR in which the newly synthesized DNA is displaced and subsequently forms circles by NHEJ...

..cerevisiae. The S. servazzii region contains a sequence that supports autonomous DNA replication in S. cerevisiae and may represent a homologue of ARS304. The S. servazziii sequence has Genbank Accession No. BankIt359091 AF307954...

..The XRS2 gene encodes an 854-amino-acid protein with no obvious similarity to the Rad50 protein or to any other protein in the database. Overexpression of RAD50 does not complement the defects in xrs2 or vice versa...

..Nej1 regulates the subcellular distribution of Lif1. A green fluorescent protein (GFP)-Lif1 fusion protein accumulates in the nucleus in cells expressing NEJ1 but is largely cytoplasmic when NEJ1 is repressed...

..We conclude that the presence of nonhomologous ends alters the mechanism of DSB repair, likely through early recruitment of repair proteins including Msh2p and Rad1p, resulting in more frequent contractions of repeated sequences...

..Mating-type regulation of genes specific to haploid or diploid cells plays a key role in determining which pathways are used to repair DSBs...

..We conclude that the ability of a recombination-induced replication fork to copy > 130 kb to the end of the chromosome depends on a special site that enhances assembly of a processive repair replication fork...

..Mus81 proteins in yeasts and humans appear to have many, but not all, of the expected properties of eukaryotic Holliday junction resolvases, with intriguing connections to DNA replication checkpoints...

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..Mismatch repair proteins Msh6, Pms1, and Mlh1 are not required. We suggest Msh2 and Msh3 recognize not only heteroduplex loops and mismatched bp, but also branched DNA structures with a free 3' tail...

..A msh3 rad59 double mutant was more severely defective in SSA than either single mutant...

..Many of these pathways compete actively for the repair of a double-strand break. Which of these repair pathways is used appears to be regulated developmentally, genetically and during the cell cycle...

..We suggest that escape from the DNA damage-induced G2/M checkpoint depends on the extent of ssDNA created at broken chromosome ends. RPA appears to play a key intermediate step in this adaptation...

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..Our results provide a molecular basis for understanding the role of yeast nucleotide excision repair gene and their human homologs in DSB-induced recombination and repair...

..These data suggest RAD1 is required to remove nonhomologous DNA from the 3' ends of recombining DNA, a process analogous to the excision of photodimers during repair of ultraviolet-damaged DNA...

..Replication is terminated by capture of the second end of the DSB...

..We conclude that MOP2 (SLA2) encodes a plasma membrane-associated protein that is required for the accumulation and/or maintenance of plasma membrane H(+)-ATPase on the cell surface...

..Thus, Mcm1 is critically responsible for the activation as well as the Matalpha2-Mcm1-mediated repression of RE activity...

..Surprisingly, the TSM1 open reading frame of 1,410 amino acids extends into the MAT locus, such that the 3'-end of the MAT alpha 1 transcript ends 15 bp from the 3'-end of the TSM1 open reading frame...

..We also describe two new methods for the enrichment of auxotrophic mutations from a wild-type yeast strain...

..Following DNA repair, the checkpoint pathway is inactivated in a process termed recovery. A related but genetically distinct process, adaptation, controls cell cycle re-entry in the face of unrepairable damage...

..These rearrangements can occur from ectopic gene conversions accompanied by crossing-over, break-induced replication, single-strand annealing or non-homologous end-joining...

..In addition, the putative helicase Chl1, previously involved in donor preference, functions in the SBF pathway...

..Recent studies in budding yeast, including in this issue of Cell, have provided new insights into the role of palindromic sequences in gene amplification...

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..All three recombination-defective mutations are made more sensitive by deletions of Rad6 and of the histone deacetylases Rpd3 and Ume6, although these mutations are not themselves CPT or phleomycin sensitive...

..Additional BIR events can then copy the elongated sequence to all other telomeres...

..We propose that RE's targets are anchor sites that tether chromosome III-L in MATalpha cells thus reducing its mobility in the nucleus...

..The dephosphorylation of gammaH2AX by the HTP-C is necessary for efficient recovery from the DNA damage checkpoint...

..We further report that this Mec1-independent pathway converges with the Rad53/Dun1-regulated checkpoint kinase cascade and leads to the degradation of the ribonucleotide reductase inhibitor Sml1...

..In addition, we showed an absolute requirement for the MRX complex in signal joining, suggesting that the Mre11-Rad50-Nbs1 complex may be required for signal joint formation in mammalian cells as well...

..Our findings show that the Smc5-Smc6 complex is essential for genome stability as it promotes repair of DSBs by error-free sister-chromatid recombination (SCR), thereby suppressing inappropriate non-sister recombination events...

..However, this interpretation only considered half of the possible outcomes. The conjecture fails when all possible outcomes are examined...

..These results suggest that MRN-dependent generation of ssDNA oligos, which constitute a unique signal of ongoing DSB repair not encountered in normal DNA metabolism, stimulates ATM activity...

..Thus, there are at least two Rad52-independent recombination pathways in budding yeast...

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..We show that Sae2 oligomerizes independently of DNA damage and that oligomerization is required for its regulatory influence on the Mre11 nuclease and checkpoint functions...

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..We also note that Pol32 homologues have been identified both in fission yeast and in metazoans where telomerase-independent survivors with alternative telomere maintenance have also been identified...

..These results indicate that Slx4 has multiple functions in responding to DNA damage and that a subset of these are regulated by Mec1/Tel1-dependent phosphorylation...

..In yeast, we see a high level of constitutive gamma-H2AX in telomere regions in the absence of any exogenous DNA damage, suggesting that yeast chromosome ends are transiently detected as DSBs...

..We suggest that Mec1-dependent checkpoint signaling through Rad53 and Chk1 includes the repression of nuclear movements that are normally associated with the execution of anaphase...

..We propose that the completion of replication is not under the surveillance of known checkpoints...

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..Our findings might contribute to explaining some of the recombination defects of BLM cells...

..Once repair is initiated, the rate of repair replication during BIR is comparable to that of normal DNA replication, as copying of >100 kb is completed less than 30 min after repair DNA synthesis is detected close to the DSB...

..In addition, the interstrand cross-link repair gene PSO2 plays a role in end joining hairpin ends that is not seen in repair of linearized plasmids and may be involved in positioning transposase cleavage at the transposon ends...

..Srs2 promotes the noncrossover synthesis-dependent strand-annealing (SDSA) pathway, apparently by regulating Rad51 binding during strand exchange...

..We suggest that monitoring of the extent of DNA damage depends on independent binding of RPA and Rad52p to ssDNA, with Rad52p's activity modulated by Rad51p whereas RPA's action depends on Tid1p...

..The increased gamma ray sensitivity of rad1Delta rad52Delta yku70Delta strains compared to rad52Delta yku70Delta strains suggests that MMEJ also contributes to the repair of DSBs induced by ionizing radiation...

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..Cleaved signal ends are also transposed into new sites in DNA, allowing RAG-induced transposition to be studied in vivo...

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..In vivo and in vitro evidence suggests that phosphorylated forms of Ptc2 and Ptc3 specifically bind to the Rad53 FHA1 domain and inactivate Rad53-dependent pathways during adaptation and recovery by dephosphorylating Rad53...

..We propose that at least two separate activities associated with the N-terminus of Mre11p are required for its mitotic function...

..The differences between the RAD51- and RAD50/RAD59-dependent pathways account for the distinct ways that two different recombination processes maintain yeast telomeres in the absence of telomerase...

..Permanent preanaphase arrest of srs2Delta cells is reversed by the addition of caffeine after cells have arrested. Thus, in addition to its roles in recombination, Srs2p appears to be needed to turn off the DNA damage checkpoint...

..Deletion of FKH1 significantly reduces MATa's use of HML, as does mutation of the Fkh1/Fkh2-binding sites in a multimer of region A. We conclude that Fkh1p regulates MATa donor preference through direct interaction with RE...

..Thus, RPA appears to play a role in strand invasion as well as in facilitating Rad51 binding to ssDNA, possibly by stabilizing the displaced ssDNA...

..These data suggest there is constitutive tethering of HML, which is relieved in MATa cells through the action of RE...

..We also provide evidence that the DSB-induced cohesin domain functions in postreplicative repair...

..Our findings reveal a new role of ATP-dependent chromatin remodeling in nuclear processes and suggest that an ATP-dependent chromatin remodeling complex can read a DNA repair histone code...

..Here, we have examined the machinery that holds broken chromosome ends together, and we have explored the behavior of broken chromosomes as they pass through mitosis...

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..CDK1 is also important for a later step in homologous recombination, after strand invasion and before the initiation of new DNA synthesis...

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..We conclude that DNA synthesis during gene conversion is different from S-phase replication, involving only leading-strand polymerization...

..This conclusion is supported by the finding that deleting the SGS1 helicase also suppressed heteroduplex rejection...

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..Additional biochemical studies suggest the presence of an ssDNA complex containing both Rad51 and Rad52...

..A deeper knowledge of the role of SMC proteins in DSB repair should contribute to a better understanding of chromosome dynamics and stability...