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

Daniel Löb1♦ , Nicor Lengert1♦* , Vadim Chagin2,3♦ , Marius Reinhart3 , Corella S. Casas-Delucchi3 , M. Cristina Cardoso3 , Barbara Drossel1
♦ equally contribution authors
* Contact: nicor@fkp.physik.tu-darmstadt.de

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.

Take a look at our results below or start your own simulations...

Comparison between the microscopy pattern of GFP-tagged PCNA

Pseudo cell images during early (left), mid (center) and late (right) S-phase were created by combining our 1D replication simulation with a random loop model for the 3D DNA chromatin folding. The simulation is able to create microscopy patters of replication similar to the experimentally observed patterns during early, mid and late S-phase.

Experiment (top: Middle section, bottom: Z-max Projection)

Simulation (top: Middle section, middle: Z-max Projection, bottom: chromatin type)

Euchromatin
Facultative heterochromatin
Constitutive heterochromatin

Number of active forks in the three chromatin zones (and total) during the replication process

During mid S-phase a distinct peak of the fork number in facultative heterochromatin is visible.

Distance distribution between adjacent fired origins

DNA combing data on inter-origin distances for HeLa Kyoto cells indicates a peak close to but below the 200 Kbp mark and a heavy tail extending to the 400 Kbp to 700 Kbp range. The distance distribution obtained from our model calculations does have both of these features.


Replication timing as a function of the giemsa staining: comparison between experiment and simulation

Types of the chromatin zones were derived from human genome Giemsa band data of the UCSC Genome Browser project where zero staining was interpreted as euchromatin, light staining as facultative heterochromatin and dark staining as constitutive heterochromatin. The replication timing of both heterochromatin types in our simulation agrees with the experimental observations, but there are deviations in the timing of euchromatic zones.