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1.  Recombination-restarted replication makes inverted chromosome fusions at inverted repeats 
Nature  2012;493(7431):246-249.
Summary
Impediments to DNA replication are known to induce gross chromosomal rearrangements (GCR) and copy number variations (CNV). GCRs/CNVs underlie human genomic disorders1 and are a feature of cancer2. During cancer development environmental factors and oncogene-driven proliferation promote replication stress. Resulting GCRs/CNVs are proposed to contribute to cancer development and therapy resistance3. When stress arrests replication, the replisome remains associated with the fork DNA (stalled fork) and is protected by the inter-S phase checkpoint. Stalled forks efficiently resume when the stress is relieved. However, if the polymerases dissociate from the fork (fork collapse) or the fork structure breaks (broken fork), replication restart can proceed either by homologous recombination (HR) or microhomology-primed re-initiation (FoSTeS/MMBIR)4,5. Here we ascertain the consequences of replication with a fork restarted by HR. We identify a new mechanism of chromosomal rearrangement: recombination-restarted forks have an exceptionally high propensity to execute a U-turn at small inverted repeats (up to 1:40 replication events). We propose that the error-prone nature of restarted forks contributes to the generation of GCRs and gene amplification in cancer and to non-recurrent CNVs in genomic disorders.
doi:10.1038/nature11676
PMCID: PMC3605775  PMID: 23178809
2.  GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome 
Time-resolved ChIP-chip can be utilized to monitor the genome-wide dynamics of the GINS complex, yielding quantitative information on replication fork movement.Replication forks progress at remarkably uniform rates across the genome, regardless of location.GINS progression appears to be arrested, albeit with very low frequency, at sites of highly transcribed genes.Comparison of simulation with data leads to novel biological insights regarding the dynamics of replication fork progression
In mitotic division, cells duplicate their DNA in S phase to ensure that the proper genetic material is passed on to their progeny. This process of DNA replication is initiated from several hundred specific sites, termed origins of replication, spaced across the genome. It is essential for replication to begin only after G1 and finish before the initiation of anaphase (Blow and Dutta, 2005; Machida et al, 2005). To ensure proper timing, the beginning stages of DNA replication are tightly coupled to the cell cycle through the activity of cyclin-dependent kinases (Nguyen et al, 2001; Masumoto et al, 2002; Sclafani and Holzen, 2007), which promote the accumulation of the pre-RC at the origins and initiate replication. Replication fork movement occurs subsequent to the firing of origins on recruitment of the replicative helicase and the other fork-associated proteins as the cell enters S phase (Diffley, 2004). The replication machinery itself (polymerases, PCNA, etc.) trails behind the helicase, copying the newly unwound DNA in the wake of the replication fork.
One component of the pre-RC, the GINS complex, consists of a highly conserved set of paralogous proteins (Psf1, Psf2, Psf3 and Sld5 (Kanemaki et al, 2003; Kubota et al, 2003; Takayama et al, 2003)). Previous work suggests that the GINS complex is an integral component of the replication fork and that its interaction with the genome correlates directly to the movement of the fork (reviewed in Labib and Gambus, 2007). Here, we used the GINS complex as a surrogate to measure features of the dynamics of replication—that is, to determine which origins in the genome are active, the timing of their firing and the rates of replication fork progression.
The timing of origin firing and the rates of fork progression have also been investigated by monitoring nascent DNA synthesis (Raghuraman et al, 2001; Yabuki et al, 2002). Origin firing was observed to occur as early as 14 min into the cell cycle and as late as 44 min (Raghuraman et al, 2001). A wide range of nucleotide incorporation rates (0.5–11 kb/min) were observed, with a mean of 2.9 kb/min (Raghuraman et al, 2001), whereas a second study reported a comparable mean rate of DNA duplication of 2.8±1.0 kb/min (Yabuki et al, 2002). In addition to these observations, replication has been inferred to progress asymmetrically from certain origins (Raghuraman et al, 2001). These data have been interpreted to mean that the dynamics of replication fork progression are strongly affected by local chromatin structure or architecture, and perhaps by interaction with the machineries controlling transcription, repair and epigenetic maintenance (Deshpande and Newlon, 1996; Rothstein et al, 2000; Raghuraman et al, 2001; Ivessa et al, 2003). In this study, we adopted a complementary ChIP-chip approach for assaying replication dynamics, in which we followed GINS complexes as they traverse the genome during the cell cycle (Figure 1). These data reveal that GINS binds to active replication origins and spreads bi-directionally and symmetrically as S phase progresses (Figure 3). The majority of origins appear to fire in the first ∼15 min of S phase. A small fraction (∼10%) of the origins to which GINS binds show no evidence of spreading (category 3 origins), although it remains possible that these peaks represent passively fired origins (Shirahige et al, 1998). Once an active origin fires, the GINS complex moves at an almost constant rate of 1.6±0.3 kb/min. Its movement through the inter-origin regions is consistent with that of a protein complex associated with a smoothly moving replication fork. This progression rate is considerably lower and more tightly distributed than those inferred from previous genome-wide measurements assayed through nascent DNA production (Raghuraman et al, 2001; Yabuki et al, 2002). Our study leads us to a different view of replication fork dynamics wherein fork progression is highly uniform in rate and little affected by genomic location.
In this work, we also observe a large number of low-intensity persistent features at sites of high transcriptional activity (e.g. tRNA genes). We were able to accurately simulate these features by assuming they are the result of low probability arrest of replication forks at these sites, rather than fork pausing (Deshpande and Newlon, 1996). The extremely low frequency of these events in wild-type cells suggests they are due to low probability stochastic occurrences during the replication process. It is hoped that future studies will resolve whether these persistent features indeed represent rare instances of fork arrest, or are the result of some alternative process. These may include, for example, the deposition of GINS complexes (or perhaps more specifically Psf2) once a pause has been resolved.
In this work, we have made extensive use of modeling to test a number of different hypotheses and assumptions. In particular, iterative modeling allowed us to infer that GINS progression is uniform and smooth throughout the genome. We have also demonstrated the potential of simulations for estimating firing efficiencies. In the future, extending such firing efficiency simulations to the whole genome should allow us to make correlations with chromosomal features such as nucleosome occupancy. Such correlations may help in determining factors that govern the probability of replication initiation throughout the genome.
Previous studies have led to a picture wherein the replication of DNA progresses at variable rates over different parts of the budding yeast genome. These prior experiments, focused on production of nascent DNA, have been interpreted to imply that the dynamics of replication fork progression are strongly affected by local chromatin structure/architecture, and by interaction with machineries controlling transcription, repair and epigenetic maintenance. Here, we adopted a complementary approach for assaying replication dynamics using whole genome time-resolved chromatin immunoprecipitation combined with microarray analysis of the GINS complex, an integral member of the replication fork. Surprisingly, our data show that this complex progresses at highly uniform rates regardless of genomic location, revealing that replication fork dynamics in yeast is simpler and more uniform than previously envisaged. In addition, we show how the synergistic use of experiment and modeling leads to novel biological insights. In particular, a parsimonious model allowed us to accurately simulate fork movement throughout the genome and also revealed a subtle phenomenon, which we interpret as arising from low-frequency fork arrest.
doi:10.1038/msb.2010.8
PMCID: PMC2858444  PMID: 20212525
cell cycle; ChIP-chip; DNA replication; replication fork; simulation
3.  The Chromatin Assembly Factor 1 Promotes Rad51-Dependent Template Switches at Replication Forks by Counteracting D-Loop Disassembly by the RecQ-Type Helicase Rqh1 
PLoS Biology  2014;12(10):e1001968.
A molecular switch for times of replication stress - Chromatin Assembly Factor 1 helps to protect DNA during recombination-mediated template-switching, favoring the rescue of stalled replication forks by both beneficial and detrimental homologous recombination events.
At blocked replication forks, homologous recombination mediates the nascent strands to switch template in order to ensure replication restart, but faulty template switches underlie genome rearrangements in cancer cells and genomic disorders. Recombination occurs within DNA packaged into chromatin that must first be relaxed and then restored when recombination is completed. The chromatin assembly factor 1, CAF-1, is a histone H3-H4 chaperone involved in DNA synthesis-coupled chromatin assembly during DNA replication and DNA repair. We reveal a novel chromatin factor-dependent step during replication-coupled DNA repair: Fission yeast CAF-1 promotes Rad51-dependent template switches at replication forks, independently of the postreplication repair pathway. We used a physical assay that allows the analysis of the individual steps of template switch, from the recruitment of recombination factors to the formation of joint molecules, combined with a quantitative measure of the resulting rearrangements. We reveal functional and physical interplays between CAF-1 and the RecQ-helicase Rqh1, the BLM homologue, mutations in which cause Bloom's syndrome, a human disease associating genome instability with cancer predisposition. We establish that CAF-1 promotes template switch by counteracting D-loop disassembly by Rqh1. Consequently, the likelihood of faulty template switches is controlled by antagonistic activities of CAF-1 and Rqh1 in the stability of the D-loop. D-loop stabilization requires the ability of CAF-1 to interact with PCNA and is thus linked to the DNA synthesis step. We propose that CAF-1 plays a regulatory role during template switch by assembling chromatin on the D-loop and thereby impacting the resolution of the D-loop.
Author Summary
Obstacles to the progression of DNA replication forks can result in genome rearrangements that are often observed in cancer cells and genomic disorders. Homologous recombination is a mechanism of restarting stalled replication fork that involves synthesis of the new DNA strands switching templates to a second (allelic) copy of the DNA sequence. However, the new strands can also occasionally recombine with nonallelic repeats (distinct regions of the genome that resemble the correct one) and thereby cause the inappropriate fusion of normally distant DNA segments; this is known as faulty template switching. The chromatin assembly factor 1 (CAF-1) is already known to be involved in depositing nucleosomes on DNA during DNA replication and repair. We have found that CAF-1 is also involved in the recombination-mediated template switch pathway in response to replication stress. Using both genetic and physical assays that allow the different steps of template switch to be analyzed, we reveal that CAF-1 protects recombination intermediates from disassembly by the RecQ-type helicase Rqh1, the homologue of BLM (people with mutations that affect BLM have Bloom's syndrome, an inherited predisposition to genome instability and cancer). Consequently, the likelihood of faulty template switch is controlled by the antagonistic activities of CAF-1 and Rqh1. We thus identified an evolutionarily conserved interplay between CAF-1 and RecQ-type helicases that helps to maintain genome stability in the face of replication stress.
doi:10.1371/journal.pbio.1001968
PMCID: PMC4196752  PMID: 25313826
4.  RAD51D- and FANCG-dependent base substitution mutagenesis at the ATP1A1 locus in mammalian cells 
Mutation research  2009;665(1-2):61-66.
Elaborate processes act at the DNA replication fork to minimize the generation of chromatid discontinuity when lesions are encountered. To prevent collapse of stalled replication forks, mutagenic translesion synthesis (TLS) polymerases are recruited temporarily to bypass DNA lesions. When a replication-associated (one-ended) double strand break occurs, homologous recombination repair (HRR) can restore chromatid continuity in what has traditionally been regarded as an “error-free” process. Our previous mutagenesis studies show an important role for HRR in preventing deletions and rearrangements that would otherwise result from error-prone nonhomologous end joining (NHEJ) after fork breakage. An analogous, but distinct, role in minimizing mutations is attributed to the proteins defective in the cancer predisposition disease Fanconi anemia (FA). Cells from FA patients and model systems show an increased proportion of gene-disrupting deletions at the hprt locus as well as decreased mutation rates in the hprt assay, suggesting a role for the FANC proteins in promoting TLS, HRR, and possibly also NHEJ. It remains unclear whether HRR, like the FANC pathway, impacts the rate of base substitution mutagenesis. Therefore, we measured, in isogenic rad51d and fancg CHO mutants, mutation rates at the Na+/K+–ATPase α-subunit (ATP1A1) locus using ouabain resistance, which specifically detects base substitution mutations. Surprisingly, we found that the spontaneous mutation rate was reduced ~2.5-fold in rad51d knockout cells, an even greater extent than observed in fancg cells, when compared with parental and isogenic gene-complemented control lines. A ~2-fold reduction in induced mutations in rad51d cells was seen after treatment with the DNA alkylating agent ethylnitrosurea while a lesser reduction occurred in fancg cells. Should the model ATP1A1 locus be representative of the genome, we conclude that at least 50% of base substitution mutations in this mammalian system arise through error-prone polymerase(s) acting during HRR-mediated restart of broken replication forks.
doi:10.1016/j.mrfmmm.2009.03.001
PMCID: PMC2692916  PMID: 19427512
Fanconi anemia; homologous recombination; translesion synthesis; CHO cells; ouabain resistance
5.  BRCA1 controls homologous recombination at Tus/Ter-stalled mammalian replication forks 
Nature  2014;510(7506):556-559.
Replication fork stalling can promote genomic instability, predisposing to cancer and other diseases1–3. Stalled replication forks may be processed by sister chromatid recombination (SCR), generating error-free or error-prone homologous recombination (HR) outcomes4–8. In mammalian cells, a long-standing hypothesis proposes that the major hereditary breast/ovarian cancer predisposition gene products, BRCA1 and BRCA2, control HR/SCR at stalled replication forks9. Although BRCA1 and BRCA2 affect replication fork processing10–12, direct evidence that BRCA genes regulate HR at stalled chromosomal replication forks is lacking due to a dearth of tools for studying this process. We report that the Escherichia coli Tus/Ter complex13–16 can be engineered to induce site-specific replication fork stalling and chromosomal HR/SCR in mammalian cells. Tus/Ter-induced HR entails processing of bidirectionally arrested forks. We find that the BRCA1 C-terminal tandem BRCT repeat and regions of BRCA1 encoded by exon 11—two BRCA1 elements implicated in tumor suppression—control Tus/Ter-induced HR. Inactivation of either BRCA1 or BRCA2 increases the absolute frequency of “long-tract” gene conversions at Tus/Ter-stalled forks—an outcome not observed in response to a restriction endonuclease-mediated chromosomal double strand break (DSB). Therefore, HR at stalled forks is regulated differently from HR at DSBs arising independently of a fork. We propose that aberrant long-tract HR at stalled replication forks contributes to genomic instability and breast/ovarian cancer predisposition in BRCA mutant cells.
doi:10.1038/nature13295
PMCID: PMC4118467  PMID: 24776801
6.  ruvA Mutants That Resolve Holliday Junctions but Do Not Reverse Replication Forks 
PLoS Genetics  2008;4(3):e1000012.
RuvAB and RuvABC complexes catalyze branch migration and resolution of Holliday junctions (HJs) respectively. In addition to their action in the last steps of homologous recombination, they process HJs made by replication fork reversal, a reaction which occurs at inactivated replication forks by the annealing of blocked leading and lagging strand ends. RuvAB was recently proposed to bind replication forks and directly catalyze their conversion into HJs. We report here the isolation and characterization of two separation-of-function ruvA mutants that resolve HJs, based on their capacity to promote conjugational recombination and recombinational repair of UV and mitomycin C lesions, but have lost the capacity to reverse forks. In vivo and in vitro evidence indicate that the ruvA mutations affect DNA binding and the stimulation of RuvB helicase activity. This work shows that RuvA's actions at forks and at HJs can be genetically separated, and that RuvA mutants compromised for fork reversal remain fully capable of homologous recombination.
Author Summary
DNA replication is the process by which DNA strands are copied to ensure the transmission of the genetic material to daughter cells. Chromosome replication is not a continuous process but is subjected to accidental arrests, owing to the encounter of obstacles or to the dysfunctioning of a replication protein. In bacteria, inactivated replication forks restart but they are most often remodeled before restarting. Interestingly, enzymes involved in homologous recombination, the process that rearranges chromosomes, are also involved in fork-remodeling reactions. The subject of the present study is RuvAB, a highly conserved bacterial complex used as the model enzyme for resolution of recombination intermediates, which we found to also act at blocked forks. We describe here the isolation and characterization of ruvA mutants that have specifically lost the capability to act at inactivated replication forks, although they remain fully capable of homologous recombination. The existence of such ruvA mutants, their properties and those of the purified RuvA mutant proteins, indicate that the action of RuvAB at replication forks is more demanding that its action at recombination intermediates, but have nevertheless been preserved during evolution.
doi:10.1371/journal.pgen.1000012
PMCID: PMC2265524  PMID: 18369438
7.  Rad3ATR Decorates Critical Chromosomal Domains with γH2A to Protect Genome Integrity during S-Phase in Fission Yeast 
PLoS Genetics  2010;6(7):e1001032.
Schizosaccharomyces pombe Rad3 checkpoint kinase and its human ortholog ATR are essential for maintaining genome integrity in cells treated with genotoxins that damage DNA or arrest replication forks. Rad3 and ATR also function during unperturbed growth, although the events triggering their activation and their critical functions are largely unknown. Here, we use ChIP-on-chip analysis to map genomic loci decorated by phosphorylated histone H2A (γH2A), a Rad3 substrate that establishes a chromatin-based recruitment platform for Crb2 and Brc1 DNA repair/checkpoint proteins. Unexpectedly, γH2A marks a diverse array of genomic features during S-phase, including natural replication fork barriers and a fork breakage site, retrotransposons, heterochromatin in the centromeres and telomeres, and ribosomal RNA (rDNA) repeats. γH2A formation at the centromeres and telomeres is associated with heterochromatin establishment by Clr4 histone methyltransferase. We show that γH2A domains recruit Brc1, a factor involved in repair of damaged replication forks. Brc1 C-terminal BRCT domain binding to γH2A is crucial in the absence of Rqh1Sgs1, a RecQ DNA helicase required for rDNA maintenance whose human homologs are mutated in patients with Werner, Bloom, and Rothmund–Thomson syndromes that are characterized by cancer-predisposition or accelerated aging. We conclude that Rad3 phosphorylates histone H2A to mobilize Brc1 to critical genomic domains during S-phase, and this pathway functions in parallel with Rqh1 DNA helicase in maintaining genome integrity.
Author Summary
Eukaryotic genomes, which range in size from ∼107 to ∼1011 base pairs, are replicated with nearly absolute fidelity every cell cycle. This amazing feat happens despite the frequent stalling or collapse of replication forks. The checkpoint kinase ATR is activated by replication fork stalling and phosphorylates histone H2A in nucleosomes surrounding damaged DNA. As the genomic regions triggering ATR activation are largely unknown, we used a whole-genome microarray to map chromosomal domains enriched with phospho-H2A during DNA replication in fission yeast. This analysis identified specific sites, including natural replication fork barriers in ribosomal DNA repeats, retrotransposon elements, and most surprisingly, all heterochromatin regions. Phospho-H2A binds the genome maintenance protein Brc1, and our genetic studies reveal that this molecular pathway becomes crucial in the absence of Rqh1, a conserved DNA helicase that is linked to cancer predisposition. As the fission yeast and human genomes share many similarities, our study reveals genomic landmarks that could similarly trigger ATR activation in human cells and shows that phospho-H2A and Brc1 are a critical part of the network that maintains genome integrity during DNA replication.
doi:10.1371/journal.pgen.1001032
PMCID: PMC2908685  PMID: 20661445
8.  Replication Fork Reversal after Replication–Transcription Collision 
PLoS Genetics  2012;8(4):e1002622.
Replication fork arrest is a recognized source of genetic instability, and transcription is one of the most prominent causes of replication impediment. We analyze here the requirement for recombination proteins in Escherichia coli when replication–transcription head-on collisions are induced at a specific site by the inversion of a highly expressed ribosomal operon (rrn). RecBC is the only recombination protein required for cell viability under these conditions of increased replication-transcription collisions. In its absence, fork breakage occurs at the site of collision, and the resulting linear DNA is not repaired and is slowly degraded by the RecJ exonuclease. Lethal fork breakage is also observed in cells that lack RecA and RecD, i.e. when both homologous recombination and the potent exonuclease V activity of the RecBCD complex are inactivated, with a slow degradation of the resulting linear DNA by the combined action of the RecBC helicase and the RecJ exonuclease. The sizes of the major linear fragments indicate that DNA degradation is slowed down by the encounter with another rrn operon. The amount of linear DNA decreases nearly two-fold when the Holliday junction resolvase RuvABC is inactivated in recB, as well as in recA recD mutants, indicating that part of the linear DNA is formed by resolution of a Holliday junction. Our results suggest that replication fork reversal occurs after replication–transcription head-on collision, and we propose that it promotes the action of the accessory replicative helicases that dislodge the obstacle.
Author Summary
Genomes are duplicated prior to cell division by DNA replication, and in all organisms replication impairment leads to chromosome instability. In bacteria, replication and transcription take place simultaneously, and in eukaryotes house-keeping genes are expressed during the S-phase; consequently, transcription is susceptible to impair replication progression. Here, we increase head-on replication–transcription collisions on the bacterial chromosome by inversion of a ribosomal operon (rrn). We show that only one recombination protein is required for growth when the rrn genes are highly expressed: the RecBCD complex, an exonuclease/recombinase that promotes degradation and RecA-dependent homologous recombination of linear DNA. In the absence of RecBCD, we observe linear DNA that ends in the collision region. This linear DNA is composed of only the origin-proximal region of the inverted rrn operon, indicating that it results from fork breakage. It is partly RuvABC-dependent (i.e. produced by the E. coli Holliday junction resolvase), indicating that blocked forks are reversed. The linear DNA ends up at the inverted rrn locus only if the RecJ exonuclease is inactivated; otherwise it is degraded, with major products ending in other upstream rrn operons, indicating that DNA degradation is slowed down by ribosomal operon sequences.
doi:10.1371/journal.pgen.1002622
PMCID: PMC3320595  PMID: 22496668
9.  Saccharomyces cerevisiae Rrm3p DNA Helicase Promotes Genome Integrity by Preventing Replication Fork Stalling: Viability of rrm3 Cells Requires the Intra-S-Phase Checkpoint and Fork Restart Activities 
Molecular and Cellular Biology  2004;24(8):3198-3212.
Rrm3p is a 5′-to-3′ DNA helicase that helps replication forks traverse protein-DNA complexes. Its absence leads to increased fork stalling and breakage at over 1,000 specific sites located throughout the Saccharomyces cerevisiae genome. To understand the mechanisms that respond to and repair rrm3-dependent lesions, we carried out a candidate gene deletion analysis to identify genes whose mutation conferred slow growth or lethality on rrm3 cells. Based on synthetic phenotypes, the intra-S-phase checkpoint, the SRS2 inhibitor of recombination, the SGS1/TOP3 replication fork restart pathway, and the MRE11/RAD50/XRS2 (MRX) complex were critical for viability of rrm3 cells. DNA damage checkpoint and homologous recombination genes were important for normal growth of rrm3 cells. However, the MUS81/MMS4 replication fork restart pathway did not affect growth of rrm3 cells. These data suggest a model in which the stalled and broken forks generated in rrm3 cells activate a checkpoint response that provides time for fork repair and restart. Stalled forks are converted by a Rad51p-mediated process to intermediates that are resolved by Sgs1p/Top3p. The rrm3 system provides a unique opportunity to learn the fate of forks whose progress is impaired by natural impediments rather than by exogenous DNA damage.
doi:10.1128/MCB.24.8.3198-3212.2004
PMCID: PMC381616  PMID: 15060144
10.  Minichromosome Maintenance Proteins Interact with Checkpoint and Recombination Proteins To Promote S-Phase Genome Stability▿ †  
Molecular and Cellular Biology  2008;28(5):1724-1738.
The minichromosome maintenance (MCM) complex plays essential, conserved roles throughout DNA synthesis: first, as a component of the prereplication complex at origins and, then, as a helicase associated with replication forks. Here we use fission yeast (Schizosaccharomyces pombe) as a model to demonstrate a role for the MCM complex in protecting replication fork structure and promoting recovery from replication arrest. Loss of MCM function generates lethal double-strand breaks at sites of DNA synthesis during replication elongation, suggesting replication fork collapse. MCM function also maintains the stability of forks stalled by hydroxyurea that activate the replication checkpoint. In cells where the checkpoint is activated, Mcm4 binds the Cds1 kinase and undergoes Cds1-dependent phosphorylation. MCM proteins also interact with proteins involved in homologous recombination, which promotes recovery from arrest by ensuring normal mitosis. We suggest that the MCM complex links replication fork stabilization with checkpoint arrest and recovery through direct interactions with checkpoint and recombination proteins and that this role in S-phase genome stability is conserved from yeast to human cells.
doi:10.1128/MCB.01717-07
PMCID: PMC2258774  PMID: 18180284
11.  Checkpoint-Dependent and -Independent Roles of Swi3 in Replication Fork Recovery and Sister Chromatid Cohesion in Fission Yeast 
PLoS ONE  2010;5(10):e13379.
Multiple genome maintenance processes are coordinated at the replication fork to preserve genomic integrity. How eukaryotic cells accomplish such a coordination is unknown. Swi1 and Swi3 form the replication fork protection complex and are involved in various processes including stabilization of replication forks, activation of the Cds1 checkpoint kinase and establishment of sister chromatid cohesion in fission yeast. However, the mechanisms by which the Swi1–Swi3 complex achieves and coordinates these tasks are not well understood. Here, we describe the identification of separation-of-function mutants of Swi3, aimed at dissecting the molecular pathways that require Swi1–Swi3. Unlike swi3 deletion mutants, the separation-of-function mutants were not sensitive to agents that stall replication forks. However, they were highly sensitive to camptothecin that induces replication fork breakage. In addition, these mutants were defective in replication fork regeneration and sister chromatid cohesion. Interestingly, unlike swi3-deleted cell, the separation-of-functions mutants were proficient in the activation of the replication checkpoint, but their fork regeneration defects were more severe than those of checkpoint mutants including cds1Δ, chk1Δ and rad3Δ. These results suggest that, while Swi3 mediates full activation of the replication checkpoint in response to stalled replication forks, Swi3 activates a checkpoint-independent pathway to facilitate recovery of collapsed replication forks and the establishment of sister chromatid cohesion. Thus, our separation-of-function alleles provide new insight into understanding the multiple roles of Swi1-Swi3 in fork protection during DNA replication, and into understanding how replication forks are maintained in response to different genotoxic agents.
doi:10.1371/journal.pone.0013379
PMCID: PMC2953522  PMID: 20967229
12.  Swi1 Prevents Replication Fork Collapse and Controls Checkpoint Kinase Cds1 
Molecular and Cellular Biology  2003;23(21):7861-7874.
The replication checkpoint is a dedicated sensor-response system activated by impeded replication forks. It stabilizes stalled forks and arrests division, thereby preserving genome integrity and promoting cell survival. In budding yeast, Tof1 is thought to act as a specific mediator of the replication checkpoint signal that activates the effector kinase Rad53. Here we report studies of fission yeast Swi1, a Tof1-related protein required for a programmed fork-pausing event necessary for mating type switching. Our studies have shown that Swi1 is vital for proficient activation of the Rad53-like checkpoint kinase Cds1. Together they are required to prevent fork collapse in the ribosomal DNA repeats, and they also prevent irreversible fork arrest at a newly identified hydroxyurea pause site. Swi1 also has Cds1-independent functions. Rad22 DNA repair foci form during S phase in swi1 mutants and to a lesser extent in cds1 mutants, indicative of fork collapse. Mus81, a DNA endonuclease required for recovery from collapsed forks, is vital in swi1 but not cds1 mutants. Swi1 is recruited to chromatin during S phase. We propose that Swi1 stabilizes replication forks in a configuration that is recognized by replication checkpoint sensors.
doi:10.1128/MCB.23.21.7861-7874.2003
PMCID: PMC207622  PMID: 14560029
13.  Break-Induced Replication Is Highly Inaccurate 
PLoS Biology  2011;9(2):e1000594.
DNA replication initiated by one-ended homologous recombination at a double-strand break is highly inaccurate, as it greatly stimulates frameshift mutations over the entire path of the replication fork.
DNA must be synthesized for purposes of genome duplication and DNA repair. While the former is a highly accurate process, short-patch synthesis associated with repair of DNA damage is often error-prone. Break-induced replication (BIR) is a unique cellular process that mimics normal DNA replication in its processivity, rate, and capacity to duplicate hundreds of kilobases, but is initiated at double-strand breaks (DSBs) rather than at replication origins. Here we employed a series of frameshift reporters to measure mutagenesis associated with BIR in Saccharomyces cerevisiae. We demonstrate that BIR DNA synthesis is intrinsically inaccurate over the entire path of the replication fork, as the rate of frameshift mutagenesis during BIR is up to 2,800-fold higher than during normal replication. Importantly, this high rate of mutagenesis was observed not only close to the DSB where BIR is less stable, but also far from the DSB where the BIR replication fork is fast and stabilized. We established that polymerase proofreading and mismatch repair correct BIR errors. Also, dNTP levels were elevated during BIR, and this contributed to BIR-related mutagenesis. We propose that a high level of DNA polymerase errors that is not fully compensated by error-correction mechanisms is largely responsible for mutagenesis during BIR, with Pol δ generating many of the mutagenic errors. We further postulate that activation of BIR in eukaryotic cells may significantly contribute to accumulation of mutations that fuel cancer and evolution.
Author Summary
Accurate transmission of genetic information requires the precise replication of parental DNA. Mutations (which can be beneficial or deleterious) arise from errors that remain uncorrected. DNA replication occurs during S-phase of the cell cycle and is extremely accurate due to highly selective DNA polymerases coupled with effective error-correction mechanisms. In contrast, DNA synthesis associated with short-patch DNA repair is often error-prone. Break-induced replication (BIR) presents an interesting case of large-scale DNA duplication that occurs in the context of DNA repair. In this study we employed a yeast-based system to investigate the level of mutagenesis associated with BIR compared to mutagenesis during normal DNA replication. We report that frameshifts, which are the most deleterious kind of point mutation, are much more frequent during BIR than during normal DNA replication. Surprisingly, we observed that the majority of mutations associated with BIR were created by polymerases responsible for normal DNA replication, which are assumed to be highly precise. Overall, we propose that BIR is a novel source of mutagenesis that may contribute to disease genesis and evolution.
doi:10.1371/journal.pbio.1000594
PMCID: PMC3039667  PMID: 21347245
14.  Swi1 and Swi3 Are Components of a Replication Fork Protection Complex in Fission Yeast 
Molecular and Cellular Biology  2004;24(19):8342-8355.
Swi1 is required for programmed pausing of replication forks near the mat1 locus in the fission yeast Schizosaccharomyces pombe. This fork pausing is required to initiate a recombination event that switches mating type. Swi1 is also needed for the replication checkpoint that arrests division in response to fork arrest. How Swi1 accomplishes these tasks is unknown. Here we report that Swi1 copurifies with a 181-amino-acid protein encoded by swi3+. The Swi1-Swi3 complex is required for survival of fork arrest and for activation of the replication checkpoint kinase Cds1. Association of Swi1 and Swi3 with chromatin during DNA replication correlated with movement of the replication fork. swi1Δ and swi3Δ mutants accumulated Rad22 (Rad52 homolog) DNA repair foci during replication. These foci correlated with the Rad22-dependent appearance of Holliday junction (HJ)-like structures in cells lacking Mus81-Eme1 HJ resolvase. Rhp51 and Rhp54 homologous recombination proteins were not required for viability in swi1Δ or swi3Δ cells, indicating that the HJ-like structures arise from single-strand DNA gaps or rearranged forks instead of broken forks. We propose that Swi1 and Swi3 define a fork protection complex that coordinates leading- and lagging-strand synthesis and stabilizes stalled replication forks.
doi:10.1128/MCB.24.19.8342-8355.2004
PMCID: PMC516732  PMID: 15367656
15.  Hydroxyurea-Stalled Replication Forks Become Progressively Inactivated and Require Two Different RAD51-Mediated Pathways for Restart and Repair 
Molecular Cell  2010;37(4):492-502.
Summary
Faithful DNA replication is essential to all life. Hydroxyurea (HU) depletes the cells of dNTPs, which initially results in stalled replication forks that, after prolonged treatment, collapse into DSBs. Here, we report that stalled replication forks are efficiently restarted in a RAD51-dependent process that does not trigger homologous recombination (HR). The XRCC3 protein, which is required for RAD51 foci formation, is also required for replication restart of HU-stalled forks, suggesting that RAD51-mediated strand invasion supports fork restart. In contrast, replication forks collapsed by prolonged replication blocks do not restart, and global replication is rescued by new origin firing. We find that RAD51-dependent HR is triggered for repair of collapsed replication forks, without apparent restart. In conclusion, our data suggest that restart of stalled replication forks and HR repair of collapsed replication forks require two distinct RAD51-mediated pathways.
Graphical Abstract
Highlights
► RAD51 promotes replication fork restart after short hydroxyurea (HU) blocks ► RAD51-mediated fork restart does not create homologous recombination (HR) products ► Long HU blocks lead to fork collapse; replication is restarted by new origin firing ► Collapsed replication forks are repaired by classical RAD51-dependent HR
doi:10.1016/j.molcel.2010.01.021
PMCID: PMC2958316  PMID: 20188668
DNA
16.  UV stalled replication forks restart by re-priming in human fibroblasts 
Nucleic Acids Research  2011;39(16):7049-7057.
Restarting stalled replication forks is vital to avoid fatal replication errors. Previously, it was demonstrated that hydroxyurea-stalled replication forks rescue replication either by an active restart mechanism or by new origin firing. To our surprise, using the DNA fibre assay, we only detect a slightly reduced fork speed on a UV-damaged template during the first hour after UV exposure, and no evidence for persistent replication fork arrest. Interestingly, no evidence for persistent UV-induced fork stalling was observed even in translesion synthesis defective, Polηmut cells. In contrast, using an assay to measure DNA molecule elongation at the fork, we observe that continuous DNA elongation is severely blocked by UV irradiation, particularly in UV-damaged Polηmut cells. In conclusion, our data suggest that UV-blocked replication forks restart effectively through re-priming past the lesion, leaving only a small gap opposite the lesion. This allows continuation of replication on damaged DNA. If left unfilled, the gaps may collapse into DNA double-strand breaks that are repaired by a recombination pathway, similar to the fate of replication forks collapsed after hydroxyurea treatment.
doi:10.1093/nar/gkr420
PMCID: PMC3167624  PMID: 21646340
17.  Single-Stranded Annealing Induced by Re-Initiation of Replication Origins Provides a Novel and Efficient Mechanism for Generating Copy Number Expansion via Non-Allelic Homologous Recombination 
PLoS Genetics  2013;9(1):e1003192.
Copy number expansions such as amplifications and duplications contribute to human phenotypic variation, promote molecular diversification during evolution, and drive the initiation and/or progression of various cancers. The mechanisms underlying these copy number changes are still incompletely understood, however. We recently demonstrated that transient, limited re-replication from a single origin in Saccharomyces cerevisiae efficiently induces segmental amplification of the re-replicated region. Structural analyses of such re-replication induced gene amplifications (RRIGA) suggested that RRIGA could provide a new mechanism for generating copy number variation by non-allelic homologous recombination (NAHR). Here we elucidate this new mechanism and provide insight into why it is so efficient. We establish that sequence homology is both necessary and sufficient for repetitive elements to participate in RRIGA and show that their recombination occurs by a single-strand annealing (SSA) mechanism. We also find that re-replication forks are prone to breakage, accounting for the widespread DNA damage associated with deregulation of replication proteins. These breaks appear to stimulate NAHR between re-replicated repeat sequences flanking a re-initiating replication origin. Our results support a RRIGA model where the expansion of a re-replication bubble beyond flanking homologous sequences followed by breakage at both forks in trans provides an ideal structural context for SSA–mediated NAHR to form a head-to-tail duplication. Given the remarkable efficiency of RRIGA, we suggest it may be an unappreciated contributor to copy number expansions in both disease and evolution.
Author Summary
Duplications and amplifications of chromosomal segments are frequently observed in eukaryotic genomes, including both normal and cancerous human genomes. These copy number variations contribute to the phenotypic variation upon which natural selection acts. For example, the amplification of genes whose excessive copy number facilitates uncontrolled cell division is often selected for during tumor development. Copy number variations can often arise when repetitive sequence elements, which are dispersed throughout eukaryotic genomes, undergo a rearrangement called non-allelic homologous recombination. Exactly how these rearrangements occur is poorly understood. Here, using budding yeast to model this class of copy number variation, we uncover a new and highly efficient mechanism by which these variations can be generated. The precipitating event is the aberrant re-initiation of DNA replication at a replication origin. Normally the hundreds to thousands of origins scattered throughout a eukaryotic genome are tightly controlled such that each is permitted to initiate only once per cell cycle. However, disruptions in these controls can allow origins to re-initiate, and we show how the resulting DNA re-replication structure can be readily converted into a tandem duplication via non-allelic homologous recombination. Hence, the re-initiation of DNA replication is a potential source of copy number variation both in disease and during evolution.
doi:10.1371/journal.pgen.1003192
PMCID: PMC3536649  PMID: 23300490
18.  Caenorhabditis elegans HIM-18/SLX-4 Interacts with SLX-1 and XPF-1 and Maintains Genomic Integrity in the Germline by Processing Recombination Intermediates 
PLoS Genetics  2009;5(11):e1000735.
Homologous recombination (HR) is essential for the repair of blocked or collapsed replication forks and for the production of crossovers between homologs that promote accurate meiotic chromosome segregation. Here, we identify HIM-18, an ortholog of MUS312/Slx4, as a critical player required in vivo for processing late HR intermediates in Caenorhabditis elegans. DNA damage sensitivity and an accumulation of HR intermediates (RAD-51 foci) during premeiotic entry suggest that HIM-18 is required for HR–mediated repair at stalled replication forks. A reduction in crossover recombination frequencies—accompanied by an increase in HR intermediates during meiosis, germ cell apoptosis, unstable bivalent attachments, and subsequent chromosome nondisjunction—support a role for HIM-18 in converting HR intermediates into crossover products. Such a role is suggested by physical interaction of HIM-18 with the nucleases SLX-1 and XPF-1 and by the synthetic lethality of him-18 with him-6, the C. elegans BLM homolog. We propose that HIM-18 facilitates processing of HR intermediates resulting from replication fork collapse and programmed meiotic DSBs in the C. elegans germline.
Author Summary
Homologous recombination (HR) is a process that provides for the accurate and efficient repair of DNA double-strand breaks (DSBs) incurred by cells, thereby maintaining genomic integrity. Proper processing of HR intermediates is critical for biological processes ranging from replication fork restart to the accurate partitioning of chromosomes during meiotic cell divisions. This is further emphasized by the fact that impaired processing of HR intermediates in both mitotic and meiotic cells can result in tumorigenesis and congenital defects. Therefore, the identification of components involved in HR is essential to understand the molecular mechanism of HR. Here, we identify HIM-18/SLX-4 in C. elegans, a protein conserved from yeast to humans that interacts with the nucleases SLX-1 and XPF-1 and is required for DSB repair in the germline. Impaired HIM-18 function results in increased DNA damage sensitivity, the accumulation of recombination intermediates, decreased meiotic crossover frequencies, altered late meiotic chromosome remodeling, the formation of fragile connections between homologs, and an increased chromosome nondisjunction. Finally, HIM-18 is localized to both mitotic and meiotic nuclei in wild-type germlines. We propose that HIM-18 function is required during the processing of late HR intermediates resulting from replication fork collapse and meiotic DSBs.
doi:10.1371/journal.pgen.1000735
PMCID: PMC2770170  PMID: 19936019
19.  A New Role for Translation Initiation Factor 2 in Maintaining Genome Integrity 
PLoS Genetics  2012;8(4):e1002648.
Escherichia coli translation initiation factor 2 (IF2) performs the unexpected function of promoting transition from recombination to replication during bacteriophage Mu transposition in vitro, leading to initiation by replication restart proteins. This function has suggested a role of IF2 in engaging cellular restart mechanisms and regulating the maintenance of genome integrity. To examine the potential effect of IF2 on restart mechanisms, we characterized its influence on cellular recovery following DNA damage by methyl methanesulfonate (MMS) and UV damage. Mutations that prevent expression of full-length IF2-1 or truncated IF2-2 and IF2-3 isoforms affected cellular growth or recovery following DNA damage differently, influencing different restart mechanisms. A deletion mutant (del1) expressing only IF2-2/3 was severely sensitive to growth in the presence of DNA-damaging agent MMS. Proficient as wild type in repairing DNA lesions and promoting replication restart upon removal of MMS, this mutant was nevertheless unable to sustain cell growth in the presence of MMS; however, growth in MMS could be partly restored by disruption of sulA, which encodes a cell division inhibitor induced during replication fork arrest. Moreover, such characteristics of del1 MMS sensitivity were shared by restart mutant priA300, which encodes a helicase-deficient restart protein. Epistasis analysis indicated that del1 in combination with priA300 had no further effects on cellular recovery from MMS and UV treatment; however, the del2/3 mutation, which allows expression of only IF2-1, synergistically increased UV sensitivity in combination with priA300. The results indicate that full-length IF2, in a function distinct from truncated forms, influences the engagement or activity of restart functions dependent on PriA helicase, allowing cellular growth when a DNA–damaging agent is present.
Author Summary
Translation Initiation Factor 2 (IF2) is a bacterial protein that plays an essential role in the initiation of protein synthesis. As such, it not only has an important influence on cellular growth but also is subject to regulation in response to physiological conditions such as nutritional deprivation. Biochemical characterization of IF2's function in replicating movable genetic elements has suggested a new role in the maintenance of genome integrity, potentially regulating replication restart. The parasitic elements exploit the cellular replication restart system to duplicate themselves as they transpose to new positions of the chromosome. In this process, IF2 makes way for action of restart proteins, which assemble replication enzymes for initiation of DNA synthesis. For the bacterial cell, the restart system is the means by which it copes with accidents that result in arrest of chromosomal replication, promoting resumption of replication. We present evidence for an IF2 function associated with restart proteins, allowing chromosomal replication in the presence of DNA–damaging agents. As the IF2 function is a highly conserved one found in all organisms, the findings have implications for understanding the maintenance of genome integrity with respect to physiological status, which can be sensed by the translation apparatus.
doi:10.1371/journal.pgen.1002648
PMCID: PMC3334882  PMID: 22536160
20.  Stepwise Activation of the ATR Signaling Pathway upon Increasing Replication Stress Impacts Fragile Site Integrity 
PLoS Genetics  2013;9(7):e1003643.
Breaks at common fragile sites (CFS) are a recognized source of genome instability in pre-neoplastic lesions, but how such checkpoint-proficient cells escape surveillance and continue cycling is unknown. Here we show, in lymphocytes and fibroblasts, that moderate replication stresses like those inducing breaks at CFSs trigger chromatin loading of sensors and mediators of the ATR pathway but fail to activate Chk1 or p53. Consistently, we found that cells depleted of ATR, but not of Chk1, accumulate single-stranded DNA upon Mre11-dependent resection of collapsed forks. Partial activation of the pathway under moderate stress thus takes steps against fork disassembly but tolerates S-phase progression and mitotic onset. We show that fork protection by ATR is crucial to CFS integrity, specifically in the cell type where a given site displays paucity in backup replication origins. Tolerance to mitotic entry with under-replicated CFSs therefore results in chromosome breaks, providing a pool of cells committed to further instability.
Author Summary
Accurate genome duplication is crucial at each cell generation to maintain genetic information. However, replication forks routinely face lesions on the DNA template and/or travel through sequences intrinsically difficult to replicate, such as common fragile sites (CFS). To help the fork to proceed, the cells have evolved the DNA damage checkpoint that senses different types of damage and triggers well-adapted cellular responses. We have studied the DNA damage response of human lymphoblastoid cells and normal fibroblasts to various levels of fork slowing. We showed that a two- to ten-fold reduction of fork speed leads to global chromatin recruitment of sensors and mediators of the ATR pathway without substantial activation of Chk1, ATM or p53. Analysis of the phenotype of cells depleted of ATR or Chk1 and submitted to moderate levels of stress shows that ATR, but not Chk1, is crucial to CFS integrity. We propose a model explaining how fork speed thresholds direct fine-tuned checkpoint responses that protect genome integrity without blocking cell cycle progression upon moderate replication fork impediment. Tolerance to mitotic entry with under-replicated CFSs therefore results in chromosome breaks, providing a pool of cells committed to further instability.
doi:10.1371/journal.pgen.1003643
PMCID: PMC3715430  PMID: 23874235
21.  Avoiding chromosome pathology when replication forks collide 
Nature  2013;500(7464):10.1038/nature12312.
Chromosome duplication normally initiates via the assembly of replication fork complexes at defined origins1,2. DNA synthesis by any one fork is thought to cease when it meets another travelling in the opposite direction, at which stage the replication machinery may simply dissociate before the nascent strands are finally ligated. But what actually happens is not clear. Here we present evidence consistent with the idea that every fork collision has the potential to threaten genomic integrity. In Escherichia coli this threat is kept at bay by RecG DNA translocase3 and by single-strand DNA exonucleases. Without RecG, replication initiates where forks meet via a replisome assembly mechanism normally associated with fork repair, replication restart and recombination4,5, establishing new forks with the potential to sustain cell growth and division without an active origin. This potential is realised when roadblocks to fork progression are reduced or eliminated. It relies on the chromosome being circular, reinforcing the idea that replication initiation is triggered repeatedly by fork collision. The results reported raise the question of whether replication fork collisions have pathogenic potential for organisms that exploit multiple origins to replicate each chromosome.
doi:10.1038/nature12312
PMCID: PMC3819906  PMID: 23892781
22.  Def1 Promotes the Degradation of Pol3 for Polymerase Exchange to Occur During DNA-Damage–Induced Mutagenesis in Saccharomyces cerevisiae 
PLoS Biology  2014;12(1):e1001771.
After DNA damage, Def1 triggers degradation of the catalytic subunit of the replicative DNA polymerase at stalled replication forks, allowing special polymerases to take over DNA synthesis.
DNA damages hinder the advance of replication forks because of the inability of the replicative polymerases to synthesize across most DNA lesions. Because stalled replication forks are prone to undergo DNA breakage and recombination that can lead to chromosomal rearrangements and cell death, cells possess different mechanisms to ensure the continuity of replication on damaged templates. Specialized, translesion synthesis (TLS) polymerases can take over synthesis at DNA damage sites. TLS polymerases synthesize DNA with a high error rate and are responsible for damage-induced mutagenesis, so their activity must be strictly regulated. However, the mechanism that allows their replacement of the replicative polymerase is unknown. Here, using protein complex purification and yeast genetic tools, we identify Def1 as a key factor for damage-induced mutagenesis in yeast. In in vivo experiments we demonstrate that upon DNA damage, Def1 promotes the ubiquitylation and subsequent proteasomal degradation of Pol3, the catalytic subunit of the replicative polymerase δ, whereas Pol31 and Pol32, the other two subunits of polymerase δ, are not affected. We also show that purified Pol31 and Pol32 can form a complex with the TLS polymerase Rev1. Our results imply that TLS polymerases carry out DNA lesion bypass only after the Def1-assisted removal of Pol3 from the stalled replication fork.
Author Summary
DNA damages can lead to the stalling of the cellular replication machinery if not repaired on time, inducing DNA strand breaks, recombination that can result in gross chromosomal rearrangements, even cell death. In order to guard against this outcome, cells have evolved several precautionary mechanisms. One of these involves the activity of special DNA polymerases—known as translesion synthesis (TLS) polymerases. In contrast to the replicative polymerases responsible for faithfully duplicating the genome, these can carry out DNA synthesis even on a damaged template. For that to occur, they have to take over synthesis from the replicative polymerase that is stalled at a DNA lesion. Although this mechanism allows DNA synthesis to proceed, TLS polymerases work with a high error rate even on undamaged DNA, leading to alterations of the original sequence that can result in cancer. Consequently, the exchange between replicative and special polymerases has to be highly regulated, and the details of this are largely unknown. Here we identified Def1—a protein involved in the degradation of RNA polymerase II—as a prerequisite for error-prone DNA synthesis in yeast. We showed that after treating the cells with a DNA damaging agent, Def1 promoted the degradation of the catalytic subunit of the replicative DNA polymerase δ, without affecting the other two subunits of the polymerase. Our data suggest that the special polymerases can take over synthesis only after the catalytic subunit of the replicative polymerase is removed from the stalled fork in a regulated manner. We predict that the other two subunits remain at the fork and participate in TLS together with the special polymerases.
doi:10.1371/journal.pbio.1001771
PMCID: PMC3897375  PMID: 24465179
23.  Multiple Rad5 activities mediate sister chromatid recombination to bypass DNA damage at stalled replication forks 
Molecular cell  2010;38(5):649-661.
SUMMARY
DNA damage that blocks replication is bypassed in order to complete chromosome duplication and preserve cell viability and genome stability. Rad5, a PCNA polyubiquitin ligase and DNA-dependent ATPase in yeast, is orthologous to putative tumor suppressors and controls error-free damage bypass by an unknown mechanism. To identify the mechanism in vivo, we investigated the roles of Rad5 and analyzed the DNA structures that form during damage bypass at site-specific stalled forks present at replication origins. Rad5 mediated the formation of recombination-dependent, X-shaped DNA structures containing Holliday junctions between sister chromatids. Mutants lacking these damage-induced chromatid junctions were defective in resolving stalled forks, restarting replication and completing chromosome duplication. Rad5 polyubiquitin ligase and ATPase domains both contributed to replication fork recombination. Our results indicate that multiple activities of Rad5 function coordinately with homologous recombination factors to enable replication template switch events that join sister chromatids at stalled forks and bypass DNA damage.
doi:10.1016/j.molcel.2010.03.020
PMCID: PMC2887677  PMID: 20541998
24.  Initiation of Genome Instability and Preneoplastic Processes through Loss of Fhit Expression 
PLoS Genetics  2012;8(11):e1003077.
Genomic instability drives tumorigenesis, but how it is initiated in sporadic neoplasias is unknown. In early preneoplasias, alterations at chromosome fragile sites arise due to DNA replication stress. A frequent, perhaps earliest, genetic alteration in preneoplasias is deletion within the fragile FRA3B/FHIT locus, leading to loss of Fhit protein expression. Because common chromosome fragile sites are exquisitely sensitive to replication stress, it has been proposed that their clonal alterations in cancer cells are due to stress sensitivity rather than to a selective advantage imparted by loss of expression of fragile gene products. Here, we show in normal, transformed, and cancer-derived cell lines that Fhit-depletion causes replication stress-induced DNA double-strand breaks. Using DNA combing, we observed a defect in replication fork progression in Fhit-deficient cells that stemmed primarily from fork stalling and collapse. The likely mechanism for the role of Fhit in replication fork progression is through regulation of Thymidine kinase 1 expression and thymidine triphosphate pool levels; notably, restoration of nucleotide balance rescued DNA replication defects and suppressed DNA breakage in Fhit-deficient cells. Depletion of Fhit did not activate the DNA damage response nor cause cell cycle arrest, allowing continued cell proliferation and ongoing chromosomal instability. This finding was in accord with in vivo studies, as Fhit knockout mouse tissue showed no evidence of cell cycle arrest or senescence yet exhibited numerous somatic DNA copy number aberrations at replication stress-sensitive loci. Furthermore, cells established from Fhit knockout tissue showed rapid immortalization and selection of DNA deletions and amplifications, including amplification of the Mdm2 gene, suggesting that Fhit loss-induced genome instability facilitates transformation. We propose that loss of Fhit expression in precancerous lesions is the first step in the initiation of genomic instability, linking alterations at common fragile sites to the origin of genome instability.
Author Summary
Normal cells have robust mechanisms to maintain the proper sequence of their DNA; in cancer cells these mechanisms are compromised, resulting in complex changes in the DNA of tumors. How this genome instability begins has not been defined, except in cases of familial cancers, which often have mutations in genes called “caretaker” genes, necessary to preserve DNA stability. We have defined a mechanism for genome instability in non-familial tumors that occur sporadically in the population. Certain fragile regions of our DNA are more difficult to duplicate during cell division and are prone to breakage. A fragile region, FRA3B, lies within the FHIT gene, and deletions within FRA3B are common in precancer cells, causing loss of Fhit protein expression. We find that loss of Fhit protein causes defective DNA replication, leading to further DNA breaks. Cells that continue DNA replication in the absence of Fhit develop numerous chromosomal aberrations. Importantly, cells established from tissues of mice that are missing Fhit undergo selection for increasing DNA alterations that can promote immortality, a cancer cell hallmark. Thus, loss of Fhit expression in precancer cells is the first step in the initiation of genomic instability and facilitates cancer development.
doi:10.1371/journal.pgen.1003077
PMCID: PMC3510054  PMID: 23209436
25.  SUMO Modification Regulates BLM and RAD51 Interaction at Damaged Replication Forks 
PLoS Biology  2009;7(12):e1000252.
SUMO modification of BLM controls the switch between BLM's pro- and anti-recombinogenic roles in homologous recombination following DNA damage during replication.
The gene mutated in Bloom's syndrome, BLM, is important in the repair of damaged replication forks, and it has both pro- and anti-recombinogenic roles in homologous recombination (HR). At damaged forks, BLM interacts with RAD51 recombinase, the essential enzyme in HR that catalyzes homology-dependent strand invasion. We have previously shown that defects in BLM modification by the small ubiquitin-related modifier (SUMO) cause increased γ-H2AX foci. Because the increased γ-H2AX could result from defective repair of spontaneous DNA damage, we hypothesized that SUMO modification regulates BLM's function in HR repair at damaged forks. To test this hypothesis, we treated cells that stably expressed a normal BLM (BLM+) or a SUMO-mutant BLM (SM-BLM) with hydroxyurea (HU) and examined the effects of stalled replication forks on RAD51 and its DNA repair functions. HU treatment generated excess γ-H2AX in SM-BLM compared to BLM+ cells, consistent with a defect in replication-fork repair. SM-BLM cells accumulated increased numbers of DNA breaks and were hypersensitive to DNA damage. Importantly, HU treatment failed to induce sister-chromatid exchanges in SM-BLM cells compared to BLM+ cells, indicating a specific defect in HR repair and suggesting that RAD51 function could be compromised. Consistent with this hypothesis, RAD51 localization to HU-induced repair foci was impaired in SM-BLM cells. These data suggested that RAD51 might interact noncovalently with SUMO. We found that in vitro RAD51 interacts noncovalently with SUMO and that it interacts more efficiently with SUMO-modified BLM compared to unmodified BLM. These data suggest that SUMOylation controls the switch between BLM's pro- and anti-recombinogenic roles in HR. In the absence of BLM SUMOylation, BLM perturbs RAD51 localization at damaged replication forks and inhibits fork repair by HR. Conversely, BLM SUMOylation relieves its inhibitory effects on HR, and it promotes RAD51 function.
Author Summary
Replication is the process in which cellular DNA is duplicated. DNA damage incurred during replication is detrimental to the cell. Homologous recombination, in which DNA sequences are exchanged between two similar or identical strands of DNA, plays a pivotal role in correcting replication processes that have failed due to DNA breakage and is tightly regulated, because deficient or excess recombination results in genomic instability. Previous studies have implicated the DNA-processing enzyme BLM in the regulation of homologous recombination; BLM is defective in Bloom's syndrome, which is characterized by excess recombination and cancer susceptibility. Here, we show that modification of BLM by the small protein SUMO controls BLM's function in regulating homologous recombination at sites where DNA replication failed. We showed that cells expressing a SUMO-deficient mutant of BLM accumulated more DNA damage and displayed defects in repair by homologous recombination. An enzyme involved in homologous recombination, RAD51, displayed a defect in localization to sites where DNA replication failed. Our data support a model in which SUMO modification regulates BLM's function in homologous recombination by controlling the localization of RAD51 to failed replication sites.
doi:10.1371/journal.pbio.1000252
PMCID: PMC2779653  PMID: 19956565

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