Replication Fork Polarity Gradients Revealed by Megabase-Sized U-Shaped Replication Timing Domains in Human Cell Lines

Université de Lyon, Lyon, France.
PLoS Computational Biology (Impact Factor: 4.62). 04/2012; 8(4):e1002443. DOI: 10.1371/journal.pcbi.1002443
Source: PubMed

ABSTRACT In higher eukaryotes, replication program specification in different cell types remains to be fully understood. We show for seven human cell lines that about half of the genome is divided in domains that display a characteristic U-shaped replication timing profile with early initiation zones at borders and late replication at centers. Significant overlap is observed between U-domains of different cell lines and also with germline replication domains exhibiting a N-shaped nucleotide compositional skew. From the demonstration that the average fork polarity is directly reflected by both the compositional skew and the derivative of the replication timing profile, we argue that the fact that this derivative displays a N-shape in U-domains sustains the existence of large-scale gradients of replication fork polarity in somatic and germline cells. Analysis of chromatin interaction (Hi-C) and chromatin marker data reveals that U-domains correspond to high-order chromatin structural units. We discuss possible models for replication origin activation within U/N-domains. The compartmentalization of the genome into replication U/N-domains provides new insights on the organization of the replication program in the human genome.

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Available from: Arach Goldar, Sep 27, 2015
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    • "Recent application of graph theory [57] [86] has confirmed the central position of the MaOris in the chromatin interaction network: they form a set of interconnected hubs of chromatin interactions both within and between different human chromosomes. The additional observation of a remarkable gene organization in U/N-domains with a significant enrichment of expressed genes nearby the bordering MaOris [72] [77] [84] [87] prompted the interpretation of these replication domains as chromatin units of highly coordinated regulation of transcription and replication [14] [53] [57]. The analysis of the spatial proximity of evolutionary breakpoints between human and mouse further showed that some aspects of genome 3D architecture are conserved across very large evolutionary distances [62] [64] [88] [89]. "
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    ABSTRACT: Recent analysis of genome-wide epigenetic modification data, mean replication timing (MRT) profiles and chromosome conformation data in mammals have provided increasing evidence that flexibility in replication origin usage is regulated locally by the epigenetic landscape and over larger genomic distances by the 3D chromatin architecture. Here, we review the recent results establishing some link between replication domains and chromatin structural domains in pluripotent and various differentiated cell types in human. We reconcile the originally proposed dichotomic picture of early and late constant timing regions that replicate by multiple rather synchronous origins in separated nuclear compartments of open and closed chromatins, with the U-shaped MRT domains bordered by "master" replication origins specified by a localized (∼200-300kb) zone of open and transcriptionally active chromatin from which a replication wave likely initiates and propagates toward the domain center via a cascade of origin firing. We discuss the relationships between these MRT domains, topologically associated domains and lamina-associated domains. This review sheds a new light on the epigenetically regulated global chromatin reorganization that underlies the loss of pluripotency and the determination of differentiation properties. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
    FEBS letters 04/2015; DOI:10.1016/j.febslet.2015.04.015 · 3.17 Impact Factor
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    • "Hundreds of megabase-sized domains with a U-shaped timing profile were identified independent of skew analysis (Baker et al., 2012; Audit et al., 2013). Demonstrating that the timing gradient equaled the ratio of fork speed to fork directionality led us to predict an N-shaped fork directionality profile of U domains strikingly similar to skew N domains (Guilbaud et al., 2011; Baker et al., 2012). U domains coincided with chromatin modification seems too abundant (80% of all H4 molecules) to explain origin specificity (Schotta et al., 2008). "
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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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    • "A cascade model of secondary origin firing was recently proposed to account for the gradient of replication fork polarity inside U/N-domains [67, 74]. The U-shape of MRT profiles indicates that the effective replication velocity (which equals the inverse of the MRT derivative [62] [65]) increases from Udomain borders to center [62] [74] as the signature of an increasing origin firing frequency during S-phase [75]. This cascade model involves the superposition of specific and efficient initiation at domain borders with random and less efficient initiations elsewhere, in addition to firing stimulated by propagating forks [67] [74]. "
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    ABSTRACT: Besides their large-scale organization in isochores, mammalian genomes display megabase-sized regions, spanning both genes and intergenes, where the strand nucleotide composition asymmetry decreases linearly, possibly due to replication activity. These so-called skew-N domains cover about a third of the human genome and are bordered by two skew upward jumps that were hypothesized to compose a subset of “master” replication origins active in the germline. Skew-N domains were shown to exhibit a particular gene organization. Genes with CpG-rich promoters likely expressed in the germline are over represented near the master replication origins, with large genes being co-oriented with replication fork progression, which suggests some coordination of replication and transcription. In this study, we describe another skew structure that covers ∼13% of the human genome and that is bordered by putative master replication origins similar to the ones flanking skew-N domains. These skew-split-N domains have a shape reminiscent of a N, but split in half, leaving in the center a region of null skew whose length increases with domain size. These central regions (median size ∼860 kb) have a homogeneous composition, i.e. both a null and constant skew and a constant and low GC content. They correspond to heterochromatin gene deserts found in low-GC isochores with an average gene density of 0.81 promoters/Mb as compared to 7.73 promoters/Mb genome wide. The analysis of epigenetic marks and replication timing data confirms that, in these late replicating heterochomatic regions, the initiation of replication is likely to be random. This contrasts with the transcriptionally active euchromatin state found around the bordering well positioned master replication origins. Altogether skew-N domains and skew-split-N domains cover about 50% of the human genome.
    Computational Biology and Chemistry 08/2014; 53. DOI:10.1016/j.compbiolchem.2014.08.020 · 1.12 Impact Factor
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