ArticleMolecular systems biology2014
A chromatin structure-based model accurately predicts DNA replication timing in human cells.
Article in Molecular systems biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed.
- RepliSage: a stochastic graph-based framework for 3D chromatin modeling across the cell cycle.Nucleic acids research · 2026Article
- Soffritto: a deep learning model for predicting high-resolution replication timing.Bioinformatics (Oxford, England) · 2025Article
- A multiplicative behavioral model of DNA replication initiation in cells.Open life sciences · 2025Article
- A comprehensive review of computational cell cycle models in guiding cancer treatment strategies.NPJ systems biology and applications · 2024Review
- Non-canonical functions of enhancers: regulation of RNA polymerase III transcription, DNA replication, and V(D)J recombination.Trends in genetics : TIG · 2024Article
- Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen.Nature communications · 2024Article
- DNA replication and replication stress response in the context of nuclear architecture.Chromosoma · 2024Review
- Review
- Epigenetic regulation of nuclear processes in fungal plant pathogens.PLoS pathogens · 2023Review
- ATXN3 controls DNA replication and transcription by regulating chromatin structure.Nucleic acids research · 2023Article
- Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths.PLoS computational biology · 2023Article
- DNA replication timing: Biochemical mechanisms and biological significance.BioEssays : news and reviews in molecular, cellular and developmental biology · 2022Article
- Kronos scRT: a uniform framework for single-cell replication timing analysis.Nature communications · 2022Article
- Rif1-Dependent Control of Replication Timing.Genes · 2022Review
- Preventing excess replication origin activation to ensure genome stability.Trends in genetics : TIG · 2022Review
- Review
- Fragile sites, chromosomal lesions, tandem repeats, and disease.Frontiers in genetics · 2022Review
- The genetic architecture of DNA replication timing in human pluripotent stem cells.Nature communications · 2021Observational
- Chromosomal Mcm2-7 distribution and the genome replication program in species from yeast to humans.PLoS genetics · 2021Article
- Organization of DNA Replication Origin Firing inGenes · 2021Article
3 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
The metazoan genome is replicated in precise cell lineage-specific temporal order. However, the mechanism controlling this orchestrated process is poorly understood as no molecular mechanisms have been identified that actively regulate the firing sequence of genome replication. Here, we develop a mechanistic model of genome replication capable of predicting, with accuracy rivaling experimental repeats, observed empirical replication timing program in humans. In our model, replication is initiated in an uncoordinated (time-stochastic) manner at well-defined sites. The model contains, in addition to the choice of the genomic landmark that localizes initiation, only a single adjustable parameter of direct biological relevance: the number of replication forks. We find that DNase-hypersensitive sites are optimal and independent determinants of DNA replication initiation. We demonstrate that the DNA replication timing program in human cells is a robust emergent phenomenon that, by its very nature, does not require a regulatory mechanism determining a proper replication initiation firing sequence.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.