ArticleGenome research2019
Replication timing networks reveal a link between transcription regulatory circuits and replication timing control.
Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
20 citing papers in PubMed, 26 citations in OpenAlex.
- REPLAY: A reproducible and user-friendly application for DNA replication timing analysis from Repli-seq data.bioRxiv : the preprint server for biology · 2026Article
- Parallel analysis of replication timing, gene expression, and copy number with PARTAGE.Genome research · 2026Article
- Transcription elongation can be sufficient, but is not necessary, to advance replication timing.EMBO reports · 2026Article
- DNA methylation and lncRNA control asynchronous DNA replication at specific imprinted gene domains.Nature communications · 2026Article
- PARTAGE: Parallel analysis of replication timing and gene expression.bioRxiv : the preprint server for biology · 2025Article
- Single cell multiomics approach to analyze replication timing and gene expression in mouse preimplantation embryos.Communications biology · 2025Article
- Evolutionarily recent transcription factors partake in human cell cycle regulation.Cell genomics · 2025Article
- Master transcription-factor binding sites constitute the core of early replication control elements.The EMBO journal · 2025Article
- Transcription can be sufficient, but is not necessary, to advance replication timing.bioRxiv : the preprint server for biology · 2025Article
- p63: A Master Regulator at the Crossroads Between Development, Senescence, Aging, and Cancer.Cells · 2025Review
- Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data.Nature communications · 2024Article
- Replication timing and transcriptional control: beyond cause and effect - part IV.Current opinion in genetics & development · 2023Review
- Optimized Repli-seq: improved DNA replication timing analysis by next-generation sequencing.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2022Article
- Mapping Replication Timing in Single Mammalian Cells.Current protocols · 2022Article
- The Fkh1 Forkhead associated domain promotes ORC binding to a subset of DNA replication origins in budding yeast.Nucleic acids research · 2021Article
- Mammalian DNA Replication Timing.Cold Spring Harbor perspectives in biology · 2021Review
- Replication Stress, Genomic Instability, and Replication Timing: A Complex Relationship.International journal of molecular sciences · 2021Review
- Article
- Control of DNA replication timing in the 3D genome.Nature reviews. Molecular cell biology · 2019Review
- Allele-specific control of replication timing and genome organization during development.Genome research · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 4 institutions in 1 country.
Funding
Abstract
DNA replication occurs in a defined temporal order known as the replication timing (RT) program and is regulated during development, coordinated with 3D genome organization and transcriptional activity. However, transcription and RT are not sufficiently coordinated to predict each other, suggesting an indirect relationship. Here, we exploit genome-wide RT profiles from 15 human cell types and intermediate differentiation stages derived from human embryonic stem cells to construct different types of RT regulatory networks. First, we constructed networks based on the coordinated RT changes during cell fate commitment to create highly complex RT networks composed of thousands of interactions that form specific functional subnetwork communities. We also constructed directional regulatory networks based on the order of RT changes within cell lineages, and identified master regulators of differentiation pathways. Finally, we explored relationships between RT networks and transcriptional regulatory networks (TRNs) by combining them into more complex circuitries of composite and bipartite networks. Results identified novel
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Registered trials
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.