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      The essential kinase ATR: ensuring faithful duplication of a challenging genome

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          Abstract

          One way to preserve a rare book is to lock it away from all potential sources of damage. Of course, an inaccessible book is also of little use, and the paper and ink will continue to degrade with age in any case. Like a book, the information stored in our DNA needs to be read, but it is also subject to continuous assault. In this review, we examine how the replication stress response that is controlled by the kinase ataxia telangiectasia and Rad3-related (ATR) senses and resolves threats to DNA integrity so the DNA remains available to read in all of our cells. We discuss the multiple data that have revealed an elegant yet increasingly complex mechanism of ATR activation. These involve a core set of components that recruit ATR to stressed replication forks, stimulate kinase activity and amplify ATR signaling. We focus on the activities of ATR in control of cell cycle checkpoints, origin firing and replication fork stability, and how proper regulation of these processes is crucial to ensure faithful duplication of a challenging genome.

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          ATR prohibits replication catastrophe by preventing global exhaustion of RPA.

          ATR, activated by replication stress, protects replication forks locally and suppresses origin firing globally. Here, we show that these functions of ATR are mechanistically coupled. Although initially stable, stalled forks in ATR-deficient cells undergo nucleus-wide breakage after unscheduled origin firing generates an excess of single-stranded DNA that exhausts the nuclear pool of RPA. Partial reduction of RPA accelerated fork breakage, and forced elevation of RPA was sufficient to delay such "replication catastrophe" even in the absence of ATR activity. Conversely, unscheduled origin firing induced breakage of stalled forks even in cells with active ATR. Thus, ATR-mediated suppression of dormant origins shields active forks against irreversible breakage via preventing exhaustion of nuclear RPA. This study elucidates how replicating genomes avoid destabilizing DNA damage. Because cancer cells commonly feature intrinsically high replication stress, this study also provides a molecular rationale for their hypersensitivity to ATR inhibitors. Copyright © 2013 Elsevier Inc. All rights reserved.
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            Regulated Eukaryotic DNA Replication Origin Firing with Purified Proteins

            Eukaryotic cells initiate DNA replication from multiple origins, which must be tightly regulated to promote precise genome duplication in every cell cycle. To accomplish this, initiation is partitioned into two temporally discrete steps: a double hexameric MCM complex is first loaded at replication origins during G1 phase, and then converted to the active CMG (Cdc45, MCM, GINS) helicase during S phase. Here we describe the reconstitution of budding yeast DNA replication initiation with 16 purified replication factors, made from 42 polypeptides. Origin-dependent initiation recapitulates regulation seen in vivo. Cyclin dependent kinase (CDK) inhibits MCM loading by phosphorylating the origin recognition complex (ORC) and promotes CMG formation by phosphorylating Sld2 and Sld3. Dbf4 dependent kinase (DDK) promotes replication by phosphorylating MCM, and can act either before or after CDK. These experiments define the minimum complement of proteins, protein kinase substrates and co-factors required for regulated eukaryotic DNA replication.
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              Replication fork reversal in eukaryotes: from dead end to dynamic response.

              The remodelling of replication forks into four-way junctions following replication perturbation, known as fork reversal, was hypothesized to promote DNA damage tolerance and repair during replication. Albeit conceptually attractive, for a long time fork reversal in vivo was found only in prokaryotes and specific yeast mutants, calling its evolutionary conservation and physiological relevance into question. Based on the recent visualization of replication forks in metazoans, fork reversal has emerged as a global, reversible and regulated process, with intriguing implications for replication completion, chromosome integrity and the DNA damage response. The study of the putative in vivo roles of recently identified eukaryotic factors in fork remodelling promises to shed new light on mechanisms of genome maintenance and to provide novel attractive targets for cancer therapy.
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                Author and article information

                Journal
                100962782
                22271
                Nat Rev Mol Cell Biol
                Nat. Rev. Mol. Cell Biol.
                Nature reviews. Molecular cell biology
                1471-0072
                1471-0080
                25 January 2018
                16 August 2017
                October 2017
                01 April 2018
                : 18
                : 10
                : 622-636
                Affiliations
                [a ]Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA
                [b ]Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
                Author notes
                [* ]Corresponding author: cimprich@ 123456stanford.edu
                Article
                PMC5796526 PMC5796526 5796526 nihpa936974
                10.1038/nrm.2017.67
                5796526
                28811666
                38944c3e-f836-4924-b3dc-6ea513b3b432
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