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Homologous recombination is initiated by the nucleolytic degradation (resection) of DNA double-strand breaks (DSBs). DSB resection is a two-step process. In the short-range step, the MRX (Mre11-Rad50-Xrs2) complex, together with Sae2, incises the 5′-terminated strand at the DSB end and resects back toward the DNA end. Then, the long-range resection nucleases Exo1 and Dna2 further elongate the resected DNA tracts. We found that mutations lowering proteasome functionality bypass the need for Sae2 in DSB resection. In particular, the dysfunction of the proteasome subunit Rpn11 leads to hyper-resection and increases the levels of both Exo1 and Dna2 to such an extent that it allows the bypass of the requirement for either Exo1 or Dna2, but not for both. These observations, along with the finding that Exo1 and Dna2 are ubiquitylated, indicate a role of the proteasome in restraining DSB resection by negatively controlling the abundance of the long-range resection nucleases.

Tel1/ataxia telangiectasia mutated (ATM) kinase plays multiple functions in response to DNA damage, promoting checkpoint-mediated cell-cycle arrest and repair of broken DNA. In addition, Saccharomyces cerevisiae Tel1 stabilizes replication forks that arrest upon the treatment with the topoisomerase poison camptothecin (CPT). We discover that inactivation of the Exo1 nuclease exacerbates the sensitivity of Tel1-deficient cells to CPT and other agents that hamper DNA replication. Furthermore, cells lacking both Exo1 and Tel1 activities exhibit sustained checkpoint activation in the presence of CPT, indicating that Tel1 and Exo1 limit the activation of a Mec1-dependent checkpoint. The absence of Tel1 or its kinase activity enhances recombination between inverted DNA repeats induced by replication fork blockage in an Exo1-dependent manner. Thus, we propose that Exo1 processes intermediates arising at stalled forks in tel1 mutants to promote DNA replication recovery and cell survival.

L'instabilità genomica è una delle caratteristiche delle cellule tumorali e può essere dovuta a difetti nella riparazione dei danni al DNA. Tra le differenti tipologie di danno al DNA, le rotture della doppia elica di DNA sono lesioni citotossiche che devono essere riparate per garantire stabilità genomica ed evitare la morte cellulare. Le cellule eucariotiche affrontano questi danni attivando una risposta con differenti vie molecolari. Tra esse il meccanismo NHEJ lega direttamente le estremità rotte del DNA. Oppure il meccanismo HR utilizza il cromatidio fratello/il cromosoma omologo come templato per riparare la rottura. HR è avviata dalla degradazione nucleolitica (resection) delle estremità 5' del DSB. La resection è un processo a due fasi: la prima fase, short-range, è catalizzata dal complesso MRX/MRN che, insieme a Sae2/CtIP catalizza un taglio endonucleolitico alle estremità 5’ del DNA rotto. Dopo di che, la seconda fase, long-range, prevede l’intervento delle nucleasi Exo1 e Dna2/Sgs1. Esse sono necessarie per generare code di 3’ssDNA. In seguito a una rottura della doppia elica di DNA, le cellule attivano anche un’altra via chiamata checkpoint da danno al DNA, che coordina la riparazione del danno con la progressione del ciclo cellulare. Tra i principali attori del checkpoint ci sono le chinasi Mec1/ATR e Tel1/ATM. Tel1 riconosce le rotture del doppio filamento di DNA non processate, mentre Mec1 è attivato dal DNA a singolo filamento, prodotto dal processo di resection. Una volta stimolate, queste due chinasi apicali attivano per fosforilazione le chinasi effettrici Rad53/CHK2 e Chk1/CHK1. Questa attivazione richiede anche la proteina conservata Rad9/53BP1 la cui associazione al DNA coinvolge diverse vie. Resta da determinare come la short-range resection sia regolata e contribuisca all'attivazione del checkpoint. In questa tesi, ho contribuito a dimostrare che l’inibizione della long-range resection induce una risposta di checkpoint che dipende, Genome instability is one of the hallmarks of cancer cells and can be due to DNA repair defects. Among different types of DNA damage, DNA DSBs are cytotoxic lesions that must be repaired to ensure genomic stability and avoid cell death. Eukaryotic cells deal with DSBs by activating the DNA damage response, that comprises pathways devoted to repair DNA breaks. DSBs can be repaired by NHEJ, which directly ligates the broken DNA ends, or by HR, which uses sister chromatids/homologous chromosomes as a template to repair the DNA break. HR is initiated by nucleolytic degradation (resection) of the 5’-terminated strands at both DSB ends. DSB resection is a two-step process, in which an initial short-range step is catalyzed by Mre11-Rad50-Xrs2/NBS1 (MRX/MRN) complex that, together with Sae2 (CtIP in mammals), catalyzes an endonucleolytic cleavage of the 5’strands. Then, a long-range resection step is carried out by the nucleases Exo1 and Dna2/Sgs1 to generate long 3’ssDNA tails. The DDR comprises also surveillance mechanisms, called DNA damage checkpoint, that couple DSB repair with cell cycle progression. Major checkpoint players include the apical protein kinases Mec1/ATR and Tel1/ATM. Tel1 recognizes unprocessed DSBs, while Mec1 is activated by RPA-coated ssDNA that is generated during the resection process. Once activated, these protein kinases activate by phosphorylation the effector kinases Rad53/CHK2 and Chk1/CHK1. This activation requires the conserved adaptor protein Rad9/53BP1, whose association to chromatin involves multiple pathways. How short-range resection is regulated and contributes to checkpoint activation remains to be determined. In this thesis, I contributed to show that abrogation of long-range resection induces a checkpoint response that depends on the checkpoint complex 9-1-1, which recruits Rad9 at damaged DNA. Furthermore, the 9-1-1 complex, independently of Rad9, restricts short-range resection by negatively regulating Mre11 nuclease. We propose t

Studies performed in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe have led the way in defining the DNA damage checkpoint and in identifying most of the proteins involved in this regulatory network, which turned out to have structural and functional equivalents in humans. Subsequent experiments revealed that the checkpoint is an elaborate signal transduction pathway that has the ability to sense and signal the presence of damaged DNA and transduce this information to influence a multifaceted cellular response that is essential for cancer avoidance. This review focuses on the work that was done in Saccharomyces cerevisiae to articulate the checkpoint concept, to identify its players and the mechanisms of activation and deactivation.

Early work by Muller and McClintock discovered that the physical ends of linear chromosomes, named telomeres, possess an inherent ability to escape unwarranted fusions. Since then, extensive research has shown that this special feature relies on specialized proteins and structural properties that confer identity to the chromosome ends, thus allowing cells to distinguish them from intrachromosomal DNA double-strand breaks. Due to the inability of conventional DNA replication to fully replicate the chromosome ends and the downregulation of telomerase in most somatic human tissues, telomeres shorten as cells divide and lose this protective capacity. Telomere attrition causes the activation of the DNA damage checkpoint that leads to a cell-cycle arrest and the entering of cells into a nondividing state, called replicative senescence, that acts as a barrier against tumorigenesis. However, downregulation of the checkpoint overcomes this barrier and leads to further genomic instability that, if coupled with re-stabilization of telomeres, can drive tumorigenesis. This review focuses on the key experiments that have been performed in the model organism Saccharomyces cerevisiae to uncover the mechanisms that protect the chromosome ends from eliciting a DNA damage response, the conservation of these pathways in mammals, as well as the consequences of their loss in human cancer.

Homologous recombination is triggered by nucleolytic degradation (resection) of DNA double-strand breaks (DSBs). DSB resection requires the Mre11-Rad50-Xrs2 (MRX) complex, which promotes the activity of Exo1 nuclease through a poorly understood mechanism. Here, we describe the Mre11-R10T mutant variant that accelerates DSB resection compared to wild-type Mre11 by potentiating Exo1-mediated processing. This increased Exo1 resection activity leads to a decreased association of the Ku complex to DSBs and an enhanced DSB resection in G1, indicating that Exo1 has a direct function in preventing Ku association with DSBs. Molecular dynamics simulations show that rotation of the Mre11 capping domains is able to induce unwinding of double-strand DNA (dsDNA). The R10T substitution causes altered orientation of the Mre11 capping domain that leads to persistent melting of the dsDNA end. We propose that MRX creates a specific DNA end structure that promotes Exo1 resection activity by facilitating the persistence of this nuclease on the DSB ends, uncovering a novel MRX function in DSB resection