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      The Histone Chaperone FACT Coordinates H2A.X-Dependent Signaling and Repair of DNA Damage

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          Summary

          Safeguarding cell function and identity following a genotoxic stress challenge entails a tight coordination of DNA damage signaling and repair with chromatin maintenance. How this coordination is achieved and with what impact on chromatin integrity remains elusive. Here, we address these questions by investigating the mechanisms governing the distribution in mammalian chromatin of the histone variant H2A.X, a central player in damage signaling. We reveal that H2A.X is deposited de novo at sites of DNA damage in a repair-coupled manner, whereas the H2A.Z variant is evicted, thus reshaping the chromatin landscape at repair sites. Our mechanistic studies further identify the histone chaperone FACT (facilitates chromatin transcription) as responsible for the deposition of newly synthesized H2A.X. Functionally, we demonstrate that FACT potentiates H2A.X-dependent signaling of DNA damage. We propose that new H2A.X deposition in chromatin reflects DNA damage experience and may help tailor DNA damage signaling to repair progression.

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          Highlights

          • H2A.X is deposited de novo at sites of DNA damage repair, whereas H2A.Z is evicted

          • FACT promotes new H2A.X deposition coupled to repair synthesis

          • FACT stimulates H2A.X-dependent signaling of DNA damage

          • H2A.X is not only a starting point of damage signaling but also an output of repair

          Abstract

          Histone variants convey epigenetic information and define functional chromatin states. Piquet et al. describe a reshaping of histone variant patterns at sites of UVC damage repair with H2A.Z removal followed by de novo deposition of H2A.X. The H2A.X deposition machinery provides a means for fine-tuning DNA damage signaling.

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          Most cited references48

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          Inhibiting eukaryotic transcription: Which compound to choose? How to evaluate its activity?

          This review first discusses ways in which we can evaluate transcription inhibition, describe changes in nuclear structure due to transcription inhibition, and report on genes that are paradoxically stimulated by transcription inhibition. Next, it summarizes the characteristics and mechanisms of commonly used inhibitors: α-amanitin is highly selective for RNAP II and RNAP III but its action is slow, actinomycin D is fast but its selectivity is poor, CDK9 inhibitors such as DRB and flavopiridol are fast and reversible but many genes escape transcription inhibition. New compounds, such as triptolide, are fast and selective and able to completely arrest transcription by triggering rapid degradation of RNAP II.
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            Two distinct modes for propagation of histone PTMs across the cell cycle

            Epigenetic states defined by chromatin can be maintained through mitotic cell division. Alabert et al. tracked histone modifications and histone variants during DNA replication and across the cell cycle and found that post-translational modifications (PTMs) are transmitted with parental histones to newly replicated DNA. Di- and tri-methylation marks are diluted two-fold upon DNA replication, but within one cell cycle all PTMs are restored. H3K9me3 and H3K27me3 are propagated by continuous modification of parental and new histones, because the establishment of these marks extends over several cell generations.
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              Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components.

              To maintain genome function and stability, DNA sequence and its organization into chromatin must be duplicated during cell division. Understanding how entire chromosomes are copied remains a major challenge. Here, we use nascent chromatin capture (NCC) to profile chromatin proteome dynamics during replication in human cells. NCC relies on biotin-dUTP labelling of replicating DNA, affinity purification and quantitative proteomics. Comparing nascent chromatin with mature post-replicative chromatin, we provide association dynamics for 3,995 proteins. The replication machinery and 485 chromatin factors such as CAF-1, DNMT1 and SUV39h1 are enriched in nascent chromatin, whereas 170 factors including histone H1, DNMT3, MBD1-3 and PRC1 show delayed association. This correlates with H4K5K12diAc removal and H3K9me1 accumulation, whereas H3K27me3 and H3K9me3 remain unchanged. Finally, we combine NCC enrichment with experimentally derived chromatin probabilities to predict a function in nascent chromatin for 93 uncharacterized proteins, and identify FAM111A as a replication factor required for PCNA loading. Together, this provides an extensive resource to understand genome and epigenome maintenance.
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                Author and article information

                Contributors
                Journal
                Mol Cell
                Mol. Cell
                Molecular Cell
                Cell Press
                1097-2765
                1097-4164
                06 December 2018
                06 December 2018
                : 72
                : 5
                : 888-901.e7
                Affiliations
                [1 ]Epigenome Integrity Group, Epigenetics & Cell Fate Centre, UMR7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, 75013 Paris, France
                Author notes
                []Corresponding author sophie.polo@ 123456univ-paris-diderot.fr
                [2]

                Present address: Endocytic Trafficking and Intracellular Delivery Group, UMR3666 CNRS/U1143 INSERM, Institut Curie, PSL Research University, 75005 Paris, France

                [3]

                Present address: Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada

                [4]

                Lead Contact

                Article
                S1097-2765(18)30757-3
                10.1016/j.molcel.2018.09.010
                6292839
                30344095
                8ba17704-38d8-4af6-803f-b0f0fa330845
                © 2018 The Author(s)

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                : 25 April 2018
                : 27 July 2018
                : 7 September 2018
                Categories
                Article

                Molecular biology
                anp32e,chromatin,dna damage signaling,dna repair,fact,histone chaperones,histone variants,h2a.x,h2a.z,uv damage

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