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      Replication-Coupled Recruitment of Viral and Cellular Factors to Herpes Simplex Virus Type 1 Replication Forks for the Maintenance and Expression of Viral Genomes

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      PLoS Pathogens
      Public Library of Science

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          Abstract

          Herpes simplex virus type 1 (HSV-1) infects over half the human population. Much of the infectious cycle occurs in the nucleus of cells where the virus has evolved mechanisms to manipulate host processes for the production of virus. The genome of HSV-1 is coordinately expressed, maintained, and replicated such that progeny virions are produced within 4–6 hours post infection. In this study, we selectively purify HSV-1 replication forks and associated proteins from virus-infected cells and identify select viral and cellular replication, repair, and transcription factors that associate with viral replication forks. Pulse chase analyses and imaging studies reveal temporal and spatial dynamics between viral replication forks and associated proteins and demonstrate that several DNA repair complexes and key transcription factors are recruited to or near replication forks. Consistent with these observations we show that the initiation of viral DNA replication is sufficient to license late gene transcription. These data provide insight into mechanisms that couple HSV-1 DNA replication with transcription and repair for the coordinated expression and maintenance of the viral genome.

          Author Summary

          HSV-1 is a ubiquitous human pathogen that causes persistent infections for the lifetime of the infected host. Of major interest are the mechanisms underlying how the virus utilizes cellular resources to rapidly replicate with high fidelity. We show that DNA repair and late transcription are coupled to genome replication by identifying the viral and cellular factors that associate with replicating viral DNA. In addition to transcription and repair, the results also describe how RNA processing and virion packaging are temporally coordinated relative to genome replication.

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          Most cited references53

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          Cancer biology and NuRD: a multifaceted chromatin remodelling complex.

          The nucleosome remodelling and histone deacetylase (NuRD; also known as Mi-2) complex regulates gene expression at the level of chromatin. The NuRD complex has been identified - using both genetic and molecular analyses - as a key determinant of differentiation in mouse embryonic stem cells and during development in various model systems. Similar to other chromatin remodellers, such as SWI/SNF and Polycomb complexes, NuRD has also been implicated in the regulation of transcriptional events that are integral to oncogenesis and cancer progression. Emerging molecular details regarding the recruitment of NuRD to specific loci during development, and the modulation of these events in cancer, are used to illustrate how the inappropriate localization of the complex could contribute to tumour biology.
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            The human CDK8 subcomplex is a molecular switch that controls Mediator coactivator function.

            The human CDK8 subcomplex (CDK8, cyclin C, Med12, and Med13) negatively regulates transcription in ways not completely defined; past studies suggested CDK8 kinase activity was required for its repressive function. Using a reconstituted transcription system together with recombinant or endogenous CDK8 subcomplexes, we demonstrate that, in fact, Med12 and Med13 are critical for subcomplex-dependent repression, whereas CDK8 kinase activity is not. A hallmark of activated transcription is efficient reinitiation from promoter-bound scaffold complexes that recruit a series of pol II enzymes to the gene. Notably, the CDK8 submodule strongly represses even reinitiation events, suggesting a means to fine tune transcript levels. Structural and biochemical studies confirm the CDK8 submodule binds the Mediator leg/tail domain via the Med13 subunit, and this submodule-Mediator association precludes pol II recruitment. Collectively, these results reveal the CDK8 subcomplex functions as a simple switch that controls the Mediator-pol II interaction to help regulate transcription initiation and reinitiation events. As Mediator is generally required for expression of protein-coding genes, this may reflect a common mechanism by which activated transcription is shut down in human cells.
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              Mechanisms in eukaryotic mismatch repair.

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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS Pathog
                PLoS Pathog
                plos
                plospath
                PLoS Pathogens
                Public Library of Science (San Francisco, CA USA )
                1553-7366
                1553-7374
                17 January 2017
                January 2017
                : 13
                : 1
                : e1006166
                Affiliations
                [001]Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
                Emory University, UNITED STATES
                Author notes

                The authors have declared that no competing interests exist.

                • Conceptualization: JAD NAD.

                • Data curation: JAD SED.

                • Funding acquisition: NAD.

                • Investigation: JAD SED.

                • Methodology: JAD SED NAD.

                • Writing – original draft: JAD.

                • Writing – review & editing: JAD SED NAD.

                Author information
                http://orcid.org/0000-0003-0968-3090
                http://orcid.org/0000-0001-8381-8577
                Article
                PPATHOGENS-D-16-02487
                10.1371/journal.ppat.1006166
                5271410
                28095497
                f8d2ebdd-7001-46f2-8a49-3b52bf06e85a
                © 2017 Dembowski et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 4 November 2016
                : 3 January 2017
                Page count
                Figures: 6, Tables: 1, Pages: 23
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100000060, National Institute of Allergy and Infectious Diseases;
                Award ID: R01AI030612
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000060, National Institute of Allergy and Infectious Diseases;
                Award ID: R01AI044821
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000060, National Institute of Allergy and Infectious Diseases;
                Award ID: T32AI060525
                Award Recipient :
                Research was supported by grants awarded to NAD from the NIH (R01 AI030612 and R01 AI044821). SED is supported by NIH T32AI060525. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Microbiology
                Virology
                Viral Replication
                Biology and life sciences
                Genetics
                DNA
                DNA replication
                Biology and life sciences
                Biochemistry
                Nucleic acids
                DNA
                DNA replication
                Biology and life sciences
                Genetics
                Gene expression
                DNA transcription
                Biology and life sciences
                Genetics
                DNA
                DNA synthesis
                Biology and life sciences
                Biochemistry
                Nucleic acids
                DNA
                DNA synthesis
                Research and analysis methods
                Chemical synthesis
                Biosynthetic techniques
                Nucleic acid synthesis
                DNA synthesis
                Biology and Life Sciences
                Genetics
                Genomics
                Microbial Genomics
                Viral Genomics
                Viral Genome
                Biology and Life Sciences
                Microbiology
                Microbial Genomics
                Viral Genomics
                Viral Genome
                Biology and Life Sciences
                Microbiology
                Virology
                Viral Genomics
                Viral Genome
                Biology and life sciences
                Biochemistry
                Proteins
                DNA-binding proteins
                Transcription Factors
                Biology and Life Sciences
                Genetics
                Gene Expression
                Gene Regulation
                Transcription Factors
                Biology and Life Sciences
                Biochemistry
                Proteins
                Regulatory Proteins
                Transcription Factors
                Biology and life sciences
                Genetics
                DNA
                DNA repair
                Biology and life sciences
                Biochemistry
                Nucleic acids
                DNA
                DNA repair
                Biology and Life Sciences
                Genetics
                Genomics
                Microbial Genomics
                Viral Genomics
                Biology and Life Sciences
                Microbiology
                Microbial Genomics
                Viral Genomics
                Biology and Life Sciences
                Microbiology
                Virology
                Viral Genomics
                Custom metadata
                vor-update-to-uncorrected-proof
                2017-01-27
                All relevant data are within the paper and its Supporting Information files.

                Infectious disease & Microbiology
                Infectious disease & Microbiology

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