Genome-wide mapping of Arabidopsis thaliana origins of DNA replication and their associated epigenetic marks
ABSTRACT Genome integrity requires faithful chromosome duplication. Origins of replication, the genomic sites at which DNA replication initiates, are scattered throughout the genome. Their mapping at a genomic scale in multicellular organisms has been challenging. In this study we profiled origins in Arabidopsis thaliana by high-throughput sequencing of newly synthesized DNA and identified ~1,500 putative origins genome-wide. This was supported by chromatin immunoprecipitation and microarray (ChIP-chip) experiments to identify ORC1- and CDC6-binding sites. We validated origin activity independently by measuring the abundance of nascent DNA strands. The midpoints of most A. thaliana origin regions are preferentially located within the 5' half of genes, enriched in G+C, histone H2A.Z, H3K4me2, H3K4me3 and H4K5ac, and depleted in H3K4me1 and H3K9me2. Our data help clarify the epigenetic specification of DNA replication origins in A. thaliana and have implications for other eukaryotes.
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ABSTRACT: DNA replication is a tightly regulated process that initiates from multiple replication origins and leads to the faithful transmission of the genetic material. For proper DNA replication, the chromatin surrounding origins needs to be remodeled. However, remarkably little is known on which epigenetic changes are required to allow the firing of replication origins. Here, we show that the histone demethylase KDM5C/JARID1C is required for proper DNA replication at early origins. JARID1C dictates the assembly of the pre-initiation complex, driving the binding to chromatin of the pre-initiation proteins CDC45 and PCNA, through the demethylation of the histone mark H3K4me3. Fork activation and histone H4 acetylation, additional early events involved in DNA replication, are not affected by JARID1C downregulation. All together, these data point to a prominent role for JARID1C in a specific phase of DNA replication in mammalian cells, through its demethylase activity on H3K4me3. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.Nucleic Acids Research 02/2015; DOI:10.1093/nar/gkv090 · 8.81 Impact Factor
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ABSTRACT: DNA replication, one of the central events in the cell cycle, is the basis of biological inheritance. In order to be duplicated, a DNA double helix must be opened at defined sites, which are called DNA replication origins (ORIs). Unlike in bacteria, where replication initiates from a single replication origin, multiple origins are utilized in the eukaryotic genomes. Among them, the ORIs in budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe have been best characterized. In recent years, advances in DNA microarray and next-generation sequencing technologies have increased the number of yeast species involved in ORIs research dramatically. The ORIs in some non-conventional yeast species such as Kluyveromyces lactis and Pichia pastoris have also been genome-widely identified. Relevant databases of replication origins in yeast were constructed, then the comparative genomic analysis can be carried out. Here, we review several experimental approaches that have been used to map replication origins in yeast and some of the available web resources related to yeast ORIs. We also discuss the sequence characteristics and chromosome structures of ORIs in the four yeast species, which can be utilized to improve yeast replication origins prediction.Frontiers in Microbiology 02/2015; 6:117. DOI:10.3389/fmicb.2015.00117 · 3.94 Impact Factor
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ABSTRACT: The post-embryonic organogenesis in plants requires a continuous production of cells in the organ primordia, their expansion and the coordinated exit to differentiation. Genome replication is one of the most important processes that occur during the cell cycle since maintenance of genomic integrity is of primary relevance for development. Since it is chromatin what must be duplicated, a strict coordination occurs between DNA replication, deposition of new histones, and introduction of histone modifications and variants. In turn, the chromatin landscape affects several stages during genome replication. Thus, chromatin accessibility is crucial for the initial stages and to specify the location of DNA replication origins with different chromatin signatures. The chromatin landscape is also determining the timing of origin activation during S-phase. Genome replication must occur fully but only once during each cell cycle. The re-replication avoidance mechanisms rely primarily on restricting the availability of certain replication factors. However, the presence of specific histone modifications are revealing also as part of the mechanisms to avoid re-replication, in particular for heterochromatin replication. We provide here an update of genome replication mostly focused on data from Arabidopsis, and the advances that genomic approaches are likely to provide in the coming years. Data available, both in plants and animals, point to the relevance of the chromatin landscape in genome replication and require a critical evaluation of the existing views about the nature of replication origins, the mechanisms of origin specification, and the relevance of epigenetic modifications for genome replication. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.The Plant Journal 04/2015; DOI:10.1111/tpj.12847 · 6.82 Impact Factor