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      SETD2 is required for DNA double-strand break repair and activation of the p53-mediated checkpoint

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          Abstract

          Histone modifications establish the chromatin states that coordinate the DNA damage response. In this study, we show that SETD2, the enzyme that trimethylates histone H3 lysine 36 (H3K36me3), is required for ATM activation upon DNA double-strand breaks (DSBs). Moreover, we find that SETD2 is necessary for homologous recombination repair of DSBs by promoting the formation of RAD51 presynaptic filaments. In agreement, SETD2-mutant clear cell renal cell carcinoma (ccRCC) cells displayed impaired DNA damage signaling. However, despite the persistence of DNA lesions, SETD2-deficient cells failed to activate p53, a master guardian of the genome rarely mutated in ccRCC and showed decreased cell survival after DNA damage. We propose that this novel SETD2-dependent role provides a chromatin bookmarking instrument that facilitates signaling and repair of DSBs. In ccRCC, loss of SETD2 may afford an alternative mechanism for the inactivation of the p53-mediated checkpoint without the need for additional genetic mutations in TP53.

          DOI: http://dx.doi.org/10.7554/eLife.02482.001

          eLife digest

          Normal wear and tear, exposure to chemicals, and ultraviolet light can all damage DNA, so cells rely on a range of sensors and mechanisms to detect and repair damaged DNA. Cells also package DNA molecules inside structures called histones to protect them against damage.

          Double-strand breaks—one of the most serious forms of DNA damage—are detected by an enzyme called ATM, and can be repaired in two ways. Bringing the broken strands back together is an obvious method, but it is also error prone. Using templates to generate new DNA to repair the damage is less prone to error, but it can only happen at certain times of the cell cycle.

          Some cancers are linked to the faulty repair of double-strand breaks. Moreover, a type of kidney cancer called clear cell renal carcinoma is linked to a lack of activity by a protein called p53, even in individuals who don't have mutations in the gene for this protein. However, many people with this type of cancer have mutations in the gene for a protein called SETD2.

          To investigate the links between SETD2 and DNA repair, Carvalho et al. compared cells with and without mutations in the gene for SETD2. It emerged that SETD2 must be present for DNA repair to take place: the SETD2 modifies the histones so that they can recruit the enzymes that repair the DNA via the template approach (which is relatively error free). SETD2 may be particularly important for repairing damage to genes without introducing errors.

          Carvalho et al. also show that mutations in SETD2 are sufficient to inactivate p53. The gene for this protein, which impedes the proliferation of cells with genomic aberrations, such as double-strand breaks, is mutated in most cancers. Overall the results help to illustrate how histone modifications and the DNA damage repair mechanisms and checkpoints work in concert to suppress cancer.

          DOI: http://dx.doi.org/10.7554/eLife.02482.002

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          Most cited references 29

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          The DNA damage response: ten years after.

          The DNA damage response (DDR), through the action of sensors, transducers, and effectors, orchestrates the appropriate repair of DNA damage and resolution of DNA replication problems, coordinating these processes with ongoing cellular physiology. In the past decade, we have witnessed an explosion in understanding of DNA damage sensing, signaling, and the complex interplay between protein phosphorylation and the ubiquitin pathway employed by the DDR network to execute the response to DNA damage. These findings have important implications for aging and cancer.
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            Human CtIP promotes DNA end resection.

            In the S and G2 phases of the cell cycle, DNA double-strand breaks (DSBs) are processed into single-stranded DNA, triggering ATR-dependent checkpoint signalling and DSB repair by homologous recombination. Previous work has implicated the MRE11 complex in such DSB-processing events. Here, we show that the human CtIP (RBBP8) protein confers resistance to DSB-inducing agents and is recruited to DSBs exclusively in the S and G2 cell-cycle phases. Moreover, we reveal that CtIP is required for DSB resection, and thereby for recruitment of replication protein A (RPA) and the protein kinase ATR to DSBs, and for the ensuing ATR activation. Furthermore, we establish that CtIP physically and functionally interacts with the MRE11 complex, and that both CtIP and MRE11 are required for efficient homologous recombination. Finally, we reveal that CtIP has sequence homology with Sae2, which is involved in MRE11-dependent DSB processing in yeast. These findings establish evolutionarily conserved roles for CtIP-like proteins in controlling DSB resection, checkpoint signalling and homologous recombination.
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              XRCC3 promotes homology-directed repair of DNA damage in mammalian cells.

              Homology-directed repair of DNA damage has recently emerged as a major mechanism for the maintenance of genomic integrity in mammalian cells. The highly conserved strand transferase, Rad51, is expected to be critical for this process. XRCC3 possesses a limited sequence similarity to Rad51 and interacts with it. Using a novel fluorescence-based assay, we demonstrate here that error-free homology-directed repair of DNA double-strand breaks is decreased 25-fold in an XRCC3-deficient hamster cell line and can be restored to wild-type levels through XRCC3 expression. These results establish that XRCC3-mediated homologous recombination can reverse DNA damage that would otherwise be mutagenic or lethal.
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                Author and article information

                Contributors
                URI : http://orcid.org/0000-0002-7774-1355
                Role: Reviewing editor
                Journal
                eLife
                Elife
                eLife
                eLife
                eLife
                eLife Sciences Publications, Ltd
                2050-084X
                06 May 2014
                2014
                : 3
                Affiliations
                [1 ]Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa , Lisboa, Portugal
                Howard Hughes Medical Institute, University of Colorado , United States
                Howard Hughes Medical Institute, University of Colorado , United States
                Author notes
                [†]

                These authors contributed equally to this work.

                Article
                02482
                10.7554/eLife.02482
                4038841
                24843002
                Copyright © 2014, Carvalho et al

                This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

                Product
                Funding
                Funded by: Fundação para a Ciência e Tecnologia, Portugal
                Award ID: PTDC-BIA-BCM-111451-2009
                Award Recipient :
                Funded by: Fundação para a Ciência e Tecnologia, Portugal
                Award ID: PTDC/BIM-ONC/0384-2012
                Award Recipient :
                Funded by: Marie Curie Initial Training Network (RNPnet)
                Award ID: PITN-GA-2011-289007
                Award Recipient :
                Funded by: Fundação para a Ciência e Tecnologia
                Award ID: SFRH/BD/52232/2013
                Award Recipient :
                Funded by: Fundação Calouste Gulbenkian
                Award ID: 96526/2009
                Award Recipient :
                The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
                Categories
                Research Article
                Genes and Chromosomes
                Custom metadata
                0.7
                The involvement of SETD2 in an important DNA repair pathway could explain the high frequency of SETD2 mutations in several cancers and may provide an alternative mechanism to evade the p53-mediated checkpoint.

                Life sciences

                cancer, dna damage response, p53-mediated checkpoint, setd2, human

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