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3D replicon distributions arise from stochastic initiation and domino-like DNA replication progression.

Löb D, Lengert N, Chagin VO, Reinhart M, Casas-Delucchi CS, Cardoso MC, Drossel B - Nat Commun (2016)

Bottom Line: Critical model features are: spontaneous stochastic firing of individual origins in euchromatin and facultative heterochromatin, inhibition of firing at distances below the size of chromatin loops and a domino-like effect by which replication forks induce firing of nearby origins.The model reproduces the empirical temporal and chromatin-related properties of DNA replication in human cells.We advance the one-dimensional DNA replication model to a spatial model by taking into account chromatin folding in the nucleus, and we are able to reproduce the spatial and temporal characteristics of the replication foci distribution throughout S-phase.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, Institute for Condensed Matter Physics, Technische Universität Darmstadt, 64289 Darmstadt, Germany.

ABSTRACT
DNA replication dynamics in cells from higher eukaryotes follows very complex but highly efficient mechanisms. However, the principles behind initiation of potential replication origins and emergence of typical patterns of nuclear replication sites remain unclear. Here, we propose a comprehensive model of DNA replication in human cells that is based on stochastic, proximity-induced replication initiation. Critical model features are: spontaneous stochastic firing of individual origins in euchromatin and facultative heterochromatin, inhibition of firing at distances below the size of chromatin loops and a domino-like effect by which replication forks induce firing of nearby origins. The model reproduces the empirical temporal and chromatin-related properties of DNA replication in human cells. We advance the one-dimensional DNA replication model to a spatial model by taking into account chromatin folding in the nucleus, and we are able to reproduce the spatial and temporal characteristics of the replication foci distribution throughout S-phase.

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Comparison between the microscopy pattern during replication in experiment and model.(a) Experimental maximum intensity z-projections and middle section images of green fluorescent protein (GFP)-tagged PCNA in HeLa cells during replication (as described by Chagin et al.26 scale bar, 5 μm). (b) The corresponding patterns of the replication model results from a 3D DNA conformation calculated using the random loop model. The fork positions in the simulations were accumulated over 15 min similar to the experimental staining time. A Gaussian blur was applied to imitate the limited experimental voxel sizes of 40 × 40 × 125 nm. In the last row the simulated fork positions are marked depending on the chromatin type (blue, euchromatin; green, facultative heterochromatin; red, constitutive heterochromatin). Images for different parameters and chromatin distributions can be created online at http://sim.bio.tu-darmstadt.de. See also Supplementary Movies 1, 2, 3 for a visualization of the fork movement within the nucleus.
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f4: Comparison between the microscopy pattern during replication in experiment and model.(a) Experimental maximum intensity z-projections and middle section images of green fluorescent protein (GFP)-tagged PCNA in HeLa cells during replication (as described by Chagin et al.26 scale bar, 5 μm). (b) The corresponding patterns of the replication model results from a 3D DNA conformation calculated using the random loop model. The fork positions in the simulations were accumulated over 15 min similar to the experimental staining time. A Gaussian blur was applied to imitate the limited experimental voxel sizes of 40 × 40 × 125 nm. In the last row the simulated fork positions are marked depending on the chromatin type (blue, euchromatin; green, facultative heterochromatin; red, constitutive heterochromatin). Images for different parameters and chromatin distributions can be created online at http://sim.bio.tu-darmstadt.de. See also Supplementary Movies 1, 2, 3 for a visualization of the fork movement within the nucleus.

Mentions: It is known from fluorescence microscopy in fixed2126464748 and living cells4950 that each of the sub-periods of S-phase is characterized by distinct patterns in the three-dimensional (3D) nuclear arrangement as well as by different clustering of RFi. To compare the dynamics of the 1D replication clusters in our model with the experimentally observed 3D characteristics of RFi, we generated in silico microscopy images of our model results (Fig. 4). To this purpose, we created a Monte Carlo simulation based on the random loop model for long polymers by Bohn et al.51, which has already been successfully used to describe folding of chromatin in human cells52.


3D replicon distributions arise from stochastic initiation and domino-like DNA replication progression.

Löb D, Lengert N, Chagin VO, Reinhart M, Casas-Delucchi CS, Cardoso MC, Drossel B - Nat Commun (2016)

Comparison between the microscopy pattern during replication in experiment and model.(a) Experimental maximum intensity z-projections and middle section images of green fluorescent protein (GFP)-tagged PCNA in HeLa cells during replication (as described by Chagin et al.26 scale bar, 5 μm). (b) The corresponding patterns of the replication model results from a 3D DNA conformation calculated using the random loop model. The fork positions in the simulations were accumulated over 15 min similar to the experimental staining time. A Gaussian blur was applied to imitate the limited experimental voxel sizes of 40 × 40 × 125 nm. In the last row the simulated fork positions are marked depending on the chromatin type (blue, euchromatin; green, facultative heterochromatin; red, constitutive heterochromatin). Images for different parameters and chromatin distributions can be created online at http://sim.bio.tu-darmstadt.de. See also Supplementary Movies 1, 2, 3 for a visualization of the fork movement within the nucleus.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4829661&req=5

f4: Comparison between the microscopy pattern during replication in experiment and model.(a) Experimental maximum intensity z-projections and middle section images of green fluorescent protein (GFP)-tagged PCNA in HeLa cells during replication (as described by Chagin et al.26 scale bar, 5 μm). (b) The corresponding patterns of the replication model results from a 3D DNA conformation calculated using the random loop model. The fork positions in the simulations were accumulated over 15 min similar to the experimental staining time. A Gaussian blur was applied to imitate the limited experimental voxel sizes of 40 × 40 × 125 nm. In the last row the simulated fork positions are marked depending on the chromatin type (blue, euchromatin; green, facultative heterochromatin; red, constitutive heterochromatin). Images for different parameters and chromatin distributions can be created online at http://sim.bio.tu-darmstadt.de. See also Supplementary Movies 1, 2, 3 for a visualization of the fork movement within the nucleus.
Mentions: It is known from fluorescence microscopy in fixed2126464748 and living cells4950 that each of the sub-periods of S-phase is characterized by distinct patterns in the three-dimensional (3D) nuclear arrangement as well as by different clustering of RFi. To compare the dynamics of the 1D replication clusters in our model with the experimentally observed 3D characteristics of RFi, we generated in silico microscopy images of our model results (Fig. 4). To this purpose, we created a Monte Carlo simulation based on the random loop model for long polymers by Bohn et al.51, which has already been successfully used to describe folding of chromatin in human cells52.

Bottom Line: Critical model features are: spontaneous stochastic firing of individual origins in euchromatin and facultative heterochromatin, inhibition of firing at distances below the size of chromatin loops and a domino-like effect by which replication forks induce firing of nearby origins.The model reproduces the empirical temporal and chromatin-related properties of DNA replication in human cells.We advance the one-dimensional DNA replication model to a spatial model by taking into account chromatin folding in the nucleus, and we are able to reproduce the spatial and temporal characteristics of the replication foci distribution throughout S-phase.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, Institute for Condensed Matter Physics, Technische Universität Darmstadt, 64289 Darmstadt, Germany.

ABSTRACT
DNA replication dynamics in cells from higher eukaryotes follows very complex but highly efficient mechanisms. However, the principles behind initiation of potential replication origins and emergence of typical patterns of nuclear replication sites remain unclear. Here, we propose a comprehensive model of DNA replication in human cells that is based on stochastic, proximity-induced replication initiation. Critical model features are: spontaneous stochastic firing of individual origins in euchromatin and facultative heterochromatin, inhibition of firing at distances below the size of chromatin loops and a domino-like effect by which replication forks induce firing of nearby origins. The model reproduces the empirical temporal and chromatin-related properties of DNA replication in human cells. We advance the one-dimensional DNA replication model to a spatial model by taking into account chromatin folding in the nucleus, and we are able to reproduce the spatial and temporal characteristics of the replication foci distribution throughout S-phase.

Show MeSH