Assembly of Slx4 signaling complexes behind
            <scp>DNA</scp>
            replication forks

Bálint, Attila; Kim, TaeHyung; Gallo, David; Cussiol, José Renato Rosa; Oliveira, Francisco Meirelles Bastos de; Yimit, Askar; Ou, Jiongwen; Nakato, Ryuichiro; Gurevich, Alexey; Shirahige, Katsuhiko; Smolka, Marcus B.; Zhang, Zhaolei; Brown, Grant W.

doi:10.15252/embj.201591190

Cited by 44 publications

(56 citation statements)

References 93 publications

(184 reference statements)

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“…Chromatin immunoprecipitation and deep sequencing (ChIPseq) analysis was performed as previously described (Balint et al 2015). Briefly, cells were synchronously released into 0.04% MMS for 60 min, cross-linked with formaldehyde, and subjected to chromatin immunoprecipitation.…”

Section: Chromatin Immunoprecipitation and Deep Sequencingmentioning

confidence: 99%

Termination of Replication Stress Signaling via Concerted Action of the Slx4 Scaffold and the PP4 Phosphatase

et al. 2015

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In response to replication stress, signaling mediated by DNA damage checkpoint kinases protects genome integrity. However, following repair or bypass of DNA lesions, checkpoint signaling needs to be terminated for continued cell cycle progression and proliferation. In budding yeast, the PP4 phosphatase has been shown to play a key role in preventing hyperactivation of the checkpoint kinase Rad53. In addition, we recently uncovered a phosphatase-independent mechanism for downregulating Rad53 in which the DNA repair scaffold Slx4 decreases engagement of the checkpoint adaptor Rad9 at DNA lesions. Here we reveal that proper termination of checkpoint signaling following the bypass of replication blocks imposed by alkylated DNA adducts requires the concerted action of these two fundamentally distinct mechanisms of checkpoint downregulation. Cells lacking both SLX4 and the PP4-subunit PPH3 display a synergistic increase in Rad53 signaling and are exquisitely sensitive to the DNA alkylating agent methyl methanesulfonate, which induces replication blocks and extensive formation of chromosomal linkages due to template switching mechanisms required for fork bypass. Rad53 hypersignaling in these cells seems to converge to a strong repression of Mus81-Mms4, the endonuclease complex responsible for resolving chromosomal linkages, thus explaining the selective sensitivity of slx4D pph3D cells to alkylation damage. Our results support a model in which Slx4 acts locally to downregulate Rad53 activation following fork bypass, while PP4 acts on pools of active Rad53 that have diffused from the site of lesions. We propose that the proper spatial coordination of the Slx4 scaffold and PP4 action is crucial to allow timely activation of Mus81-Mms4 and, therefore, proper chromosome segregation.

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Section: Chromatin Immunoprecipitation and Deep Sequencingmentioning

confidence: 99%

Termination of Replication Stress Signaling via Concerted Action of the Slx4 Scaffold and the PP4 Phosphatase

et al. 2015

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“…2). 59,[64][65][66] A similar role may also apply to PTIP, which has been detected at sites of DNA breaks and is required for complete genome replication. 61,67,68 The more N-terminally located BRCT1-4 domains of Rtt107, Brc1, and PTIP appear to be more divergent from each other, though all lack the conserved residues for phospho-peptide binding.…”

Section: Rtt107-like Proteins Interact With Histones and Distinct Setmentioning

confidence: 91%

“…One clue has emerged from studies showing that Dpb11, Slx4 and Rtt107 can uncouple Mec1 activity from that of Rad53. 77,84,65 The Slx4-Rtt107-Dpb11 complex can actually increase Mec1-mediated phosphorylation of Rtt107, H2A and Dpb11, presumably due to the Mec1-activation function of Dpb11 ( Fig. 1 and 3).…”

Section: The Rtt107 and Slx4 Association And Its Functions In Conjuncmentioning

confidence: 95%

“…1 and 3). 65 Such selective increase of Mec1 activity in principle can reduce Rad53 functions, because Rtt107 phosphorylation disfavors Rad53 activation (see above). As such, Slx4-Rtt107-Dpb11 plays a dual role in tuning down Rad53 activity: through dampening Rad9 and through selective activation of Mec1.…”

Section: The Rtt107 and Slx4 Association And Its Functions In Conjuncmentioning

confidence: 99%

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Multi-BRCT scaffolds use distinct strategies to support genome maintenance

2016

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Genome maintenance requires coordinated actions of diverse DNA metabolism processes. Scaffolding proteins, such as those containing multiple BRCT domains, can influence these processes by collaborating with numerous partners. The best-studied examples of multi-BRCT scaffolds are the budding yeast Dpb11 and its homologues in other organisms, which regulate DNA replication, repair, and damage checkpoints. Recent studies have shed light on another group of multi-BRCT scaffolds, including Rtt107 in budding yeast and related proteins in other organisms. These proteins also influence several DNA metabolism pathways, though they use strategies unlike those employed by the Dpb11 family of proteins. Yet, at the same time, these 2 classes of multi-BRCT proteins can collaborate under specific situations. This review summarizes recent advances in our understanding of how these multi-BRCT proteins function in distinct manners and how they collaborate, with a focus on Dpb11 and Rtt107.

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“…Chromatin immunoprecipitation (IP) was performed using Flagepitope-tagged versions of each indicated protein, as previously described (Roberts et al 2008;Balint et al 2015), with modifications. Cells were grown to midlogarithmic phase in YPR (1% yeast extract, 2% peptone, 3% raffinose) at 28°and then arrested in G2/M with 20 mg/ml nocodazole for 4 hr.…”

Section: Chromatin Immunoprecipitation and Deep Sequencingmentioning

confidence: 99%

MTE1 Functions with MPH1 in Double-Strand Break Repair

et al. 2016

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Double-strand DNA breaks occur upon exposure of cells to ionizing radiation and certain chemical agents or indirectly through replication fork collapse at DNA damage sites. If left unrepaired, double-strand breaks can cause genome instability and cell death, and their repair can result in loss of heterozygosity. In response to DNA damage, proteins involved in double-strand break repair by homologous recombination relocalize into discrete nuclear foci. We identified 29 proteins that colocalize with recombination repair protein Rad52 in response to DNA damage. Of particular interest, Ygr042w/Mte1, a protein of unknown function, showed robust colocalization with Rad52. Mte1 foci fail to form when the DNA helicase gene MPH1 is absent. Mte1 and Mph1 form a complex and are recruited to double-strand breaks in vivo in a mutually dependent manner. MTE1 is important for resolution of Rad52 foci during double-strand break repair and for suppressing break-induced replication. Together our data indicate that Mte1 functions with Mph1 in double-strand break repair.KEYWORDS DNA repair; recombination; double-strand breaks; break-induced replication; loss of heterozygosity; nuclear foci E FFECTIVE repair of double-strand DNA breaks (DSBs) is critical to the preservation of genome stability, yet most modes of DSB repair have significant potential to generate sequence alterations or sequence loss. Repair of DSBs by homologous recombination can result in loss of heterozygosity when resolution of recombination intermediates between homologous chromosomes results in a crossover. As such, cells possess several mechanisms by which crossing over can be suppressed in favor of noncrossover recombination products. Double Holliday junction (dHJ) intermediates that result from invasion of a homologous chromosome by both ends of a resected DSB (Szostak et al. 1983) can be resolved nucleolytically by the action of the Yen1 and Mus81/Mms4 endonucleases (Blanco et al. 2010;Ho et al. 2010) to produce a random distribution of crossover and noncrossover products. By contrast, the same dHJ intermediates can be dissolved by the combined helicase and ssDNA decatenase action of the Bloom/TopIIIa/Rmi1 complex (Sgs1/Top3/Rmi1 in yeast) (Wu et al. 2006;Yang et al. 2010) to yield exclusively noncrossover products (Wu and Hickson 2003). Crossovers can also be prevented if the D-loop structure that results from the first strand invasion by one end of a resected DSB into the homologous chromosome is unwound before capture of the second end to form the dHJ. Unwinding of D-loops is catalyzed in vitro and in vivo by the 39-to-59 DNA helicase Mph1 (Sun et al. 2008;Prakash et al. 2009) to prevent loss of heterozygosity due to crossovers and break-induced replication (BIR) (Luke-Glaser and Luke 2012;Mazon and Symington 2013;Stafa et al. 2014).The Mph1 DNA helicase was first identified as a deletion mutant with an increased mutation frequency (Entian et al. 1999). Subsequent characterization revealed that mph1 mutants are sensitive to the alkylating agent M...

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Assembly of Slx4 signaling complexes behind DNA replication forks

Cited by 44 publications

References 93 publications

Termination of Replication Stress Signaling via Concerted Action of the Slx4 Scaffold and the PP4 Phosphatase

Termination of Replication Stress Signaling via Concerted Action of the Slx4 Scaffold and the PP4 Phosphatase

Multi-BRCT scaffolds use distinct strategies to support genome maintenance

MTE1 Functions with MPH1 in Double-Strand Break Repair

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