ArticleNature communications2016
3D replicon distributions arise from stochastic initiation and domino-like DNA replication progression.
Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- RepliSage: a stochastic graph-based framework for 3D chromatin modeling across the cell cycle.Nucleic acids research · 2026Article
- Spatial organization and dynamics of genome replication: from forks to foci.Nucleic acids research · 2026Review
- ResNet-Powered Multi-Class Identification of Sequence Patterns for Genome Replication Timing Analysis.Interdisciplinary sciences, computational life sciences · 2025Article
- DNA replication and replication stress response in the context of nuclear architecture.Chromosoma · 2024Review
- Unveiling human origins of replication using deep learning: accurate prediction and comprehensive analysis.Briefings in bioinformatics · 2023Article
- Article
- Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths.PLoS computational biology · 2023Article
- The location and development of Replicon Cluster Domains in early replicating DNA.Wellcome open research · 2023Article
- Super-resolution microscopy reveals stochastic initiation of replication in Drosophila polytene chromosomes.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2022Article
- Isoform-specific and ubiquitination dependent recruitment of Tet1 to replicating heterochromatin modulates methylcytosine oxidation.Nature communications · 2022Article
- Convergence of SIRT1 and ATR signaling to modulate replication origin dormancy.Nucleic acids research · 2022Article
- Article
- Preventing excess replication origin activation to ensure genome stability.Trends in genetics : TIG · 2022Review
- Polo-like kinase 1 (Plk1) regulates DNA replication origin firing and interacts with Rif1 in Xenopus.Nucleic acids research · 2021Article
- Organization of DNA Replication Origin Firing inGenes · 2021Article
- Genome-wide mapping of human DNA replication by optical replication mapping supports a stochastic model of eukaryotic replication.Molecular cell · 2021Article
- Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiency.Genome biology · 2021Article
- Mammalian DNA Replication Timing.Cold Spring Harbor perspectives in biology · 2021Review
- Super-resolved live-cell imaging using random illumination microscopy.Cell reports methods · 2021Article
- Developmental differences in genome replication program and origin activation.Nucleic acids research · 2020Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
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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