Evaluating genome-scale approaches to eukaryotic DNA replication

Department of Biological Science, Florida State University, Tallahassee, 32306, USA.
Nature Reviews Genetics (Impact Factor: 36.98). 10/2010; 11(10):673-84. DOI: 10.1038/nrg2830
Source: PubMed


Mechanisms regulating where and when eukaryotic DNA replication initiates remain a mystery. Recently, genome-scale methods have been brought to bear on this problem. The identification of replication origins and their associated proteins in yeasts is a well-integrated investigative tool, but corresponding data sets from multicellular organisms are scarce. By contrast, standardized protocols for evaluating replication timing have generated informative data sets for most eukaryotic systems. Here, I summarize the genome-scale methods that are most frequently used to analyse replication in eukaryotes, the kinds of questions each method can address and the technical hurdles that must be overcome to gain a complete understanding of the nature of eukaryotic replication origins.

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Available from: David M Gilbert, Dec 28, 2013
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    • "Chromatin decondensation right after mitosis allows pre- RC assembly (Gilbert, 2010), although detailed measurements of how long pre-RC loading is allowed during G1 are not available (Figure 1). Pre-RC components are present in Arabidopsis as well as in the rest of plants for which genome sequences are available (Shultz et al., 2007; Sanchez et al., 2012), and are highly conserved with yeast and mammalian proteins (Table 1). "
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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.
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    • "DNA microarrays and massive DNA sequencing have caused an explosion in the number of mammalian genome-wide origin maps (Table 1) and replication timing profiles (Gilbert, 2010, 2012; Rhind and Gilbert, 2013). In general, replication timing was highly reproducible but not resolutive enough to map individual origins, whereas origin maps were more resolutive but less concordant. "
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    ABSTRACT: Replication of mammalian genomes starts at sites termed replication origins, which historically have been difficult to locate as a result of large genome sizes, limited power of genetic identification schemes, and rareness and fragility of initiation intermediates. However, origins are now mapped by the thousands using microarrays and sequencing techniques. Independent studies show modest concordance, suggesting that mammalian origins can form at any DNA sequence but are suppressed by read-through transcription or that they can overlap the 5' end or even the entire gene. These results require a critical reevaluation of whether origins form at specific DNA elements and/or epigenetic signals or require no such determinants. © 2015 Hyrien.
    The Journal of Cell Biology 01/2015; 208(2):147-160. DOI:10.1083/jcb.201407004 · 9.83 Impact Factor
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    • "Different regions of the genome are replicated at different stages of S phase and in a predictable, evolutionarily conserved and cell type specific manner [64,66]; this defines the replication-timing program. However, which particular origins actually fire in a given cell cycle and which origins remain dormant appears to be stochastic [1,21,31,47,65]. This observed stochasticity could be due to the intrinsic inefficiency of origin firing which itself may be a mechanism for regulating dormant origins. "
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    ABSTRACT: The ability of a eukaryotic cell to precisely and accurately replicate its DNA is crucial to maintain genome stability. Here we describe our current understanding of the process by which origins are licensed for DNA replication and review recent work suggesting that fork stalling has exerted a strong selective pressure on the positioning of licensed origins. In light of this, we discuss the complex and disparate phenotypes observed in mouse models and humans patients that arise due to defects in replication licensing proteins.
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