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      Plant DNA Polymerases

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          Abstract

          Maintenance of genome integrity is a key process in all organisms. DNA polymerases (Pols) are central players in this process as they are in charge of the faithful reproduction of the genetic information, as well as of DNA repair. Interestingly, all eukaryotes possess a large repertoire of polymerases. Three protein complexes, DNA Pol α, δ, and ε, are in charge of nuclear DNA replication. These enzymes have the fidelity and processivity required to replicate long DNA sequences, but DNA lesions can block their progression. Consequently, eukaryotic genomes also encode a variable number of specialized polymerases (between five and 16 depending on the organism) that are involved in the replication of damaged DNA, DNA repair, and organellar DNA replication. This diversity of enzymes likely stems from their ability to bypass specific types of lesions. In the past 10–15 years, our knowledge regarding plant DNA polymerases dramatically increased. In this review, we discuss these recent findings and compare acquired knowledge in plants to data obtained in other eukaryotes. We also discuss the emerging links between genome and epigenome replication.

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          Most cited references 145

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          The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

          A system-wide understanding of cellular function requires knowledge of all functional interactions between the expressed proteins. The STRING database aims to collect and integrate this information, by consolidating known and predicted protein–protein association data for a large number of organisms. The associations in STRING include direct (physical) interactions, as well as indirect (functional) interactions, as long as both are specific and biologically meaningful. Apart from collecting and reassessing available experimental data on protein–protein interactions, and importing known pathways and protein complexes from curated databases, interaction predictions are derived from the following sources: (i) systematic co-expression analysis, (ii) detection of shared selective signals across genomes, (iii) automated text-mining of the scientific literature and (iv) computational transfer of interaction knowledge between organisms based on gene orthology. In the latest version 10.5 of STRING, the biggest changes are concerned with data dissemination: the web frontend has been completely redesigned to reduce dependency on outdated browser technologies, and the database can now also be queried from inside the popular Cytoscape software framework. Further improvements include automated background analysis of user inputs for functional enrichments, and streamlined download options. The STRING resource is available online, at http://string-db.org/.
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            Epigenetic inheritance during the cell cycle.

            Studies that concern the mechanism of DNA replication have provided a major framework for understanding genetic transmission through multiple cell cycles. Recent work has begun to gain insight into possible means to ensure the stable transmission of information beyond just DNA, and has led to the concept of epigenetic inheritance. Considering chromatin-based information, key candidates have arisen as epigenetic marks, including DNA and histone modifications, histone variants, non-histone chromatin proteins, nuclear RNA as well as higher-order chromatin organization. Understanding the dynamics and stability of these marks through the cell cycle is crucial in maintaining a given chromatin state.
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              Chromatin replication and epigenome maintenance.

              Stability and function of eukaryotic genomes are closely linked to chromatin structure and organization. During cell division the entire genome must be accurately replicated and the chromatin landscape reproduced on new DNA. Chromatin and nuclear structure influence where and when DNA replication initiates, whereas the replication process itself disrupts chromatin and challenges established patterns of genome regulation. Specialized replication-coupled mechanisms assemble new DNA into chromatin, but epigenome maintenance is a continuous process taking place throughout the cell cycle. If DNA synthesis is perturbed, cells can suffer loss of both genome and epigenome integrity with severe consequences for the organism.
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                Author and article information

                Journal
                Int J Mol Sci
                Int J Mol Sci
                ijms
                International Journal of Molecular Sciences
                MDPI
                1422-0067
                27 September 2019
                October 2019
                : 20
                : 19
                Affiliations
                [1 ]Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; livey@ 123456psb.vib-ugent.be
                [2 ]VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
                [3 ]Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Bâtiment 630, 91405 Orsay, France; cecile.raynaud@ 123456ips2.universite-paris-saclay.fr
                [4 ]Institute of Plant Sciences Paris-Saclay (IPS2), INRA, Bâtiment 630, 91405 Orsay, France
                [5 ]Institute of Plant Sciences Paris-Saclay (IPS2), Paris-Sud University, Bâtiment 630, 91405 Orsay, France
                [6 ]Institute of Plant Sciences Paris-Saclay (IPS2), Univeristy of Evry, Bâtiment 630, 91405 Orsay, France
                [7 ]Institute of Plant Sciences Paris-Saclay (IPS2), Paris-Diderot University, Batiment 630, 91405 Orsay, France
                [8 ]Institute of Plant Sciences Paris-Saclay (IPS2), Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
                [9 ]Institute of Plant Sciences Paris-Saclay (IPS2), Paris-Saclay Univeristy, Bâtiment 630, 91405 Orsay, France
                Author notes
                ijms-20-04814
                10.3390/ijms20194814
                6801657
                31569730
                © 2019 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                Categories
                Review

                Molecular biology

                dna repair, dna replication

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