ArticleGenome research2015
Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 109 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
109 citing papers in PubMed, 184 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
- Replication timing uncovers a two-compartment nuclear architecture of interphase euchromatin.The Plant cell · 2026Article
- OCT4 enhances the firing efficiency of late DNA replication origins in mouse embryonic stem cells.Nature communications · 2026Article
- Article
- The long-standing relationship between replication timing, gene expression, and chromatin accessibility is maintained in early mouse embryogenesis.bioRxiv : the preprint server for biology · 2025Article
- HIRA defines early replication initiation zones independently of their genome compartment.Nature communications · 2025Article
- 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
- Comparison of transcriptional activity profiling by metabolic labeling or nuclear RNA sequencing.The Plant journal : for cell and molecular biology · 2025Article
- Specific origin selection and excess functional MCM2-7 loading in ORC-deficient cells.Nucleic acids research · 2025Article
- A comparison of genomic methods to assess DNA replication timing.Scientific reports · 2025Article
- Review
- R-loops acted on by RNase H1 influence DNA replication timing and genome stability in Leishmania.Nature communications · 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
- Review
- Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data.Nature communications · 2024Article
49 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
17 authors at 6 institutions in 1 country.
Funding
Abstract
Duplication of the genome in mammalian cells occurs in a defined temporal order referred to as its replication-timing (RT) program. RT changes dynamically during development, regulated in units of 400-800 kb referred to as replication domains (RDs). Changes in RT are generally coordinated with transcriptional competence and changes in subnuclear position. We generated genome-wide RT profiles for 26 distinct human cell types, including embryonic stem cell (hESC)-derived, primary cells and established cell lines representing intermediate stages of endoderm, mesoderm, ectoderm, and neural crest (NC) development. We identified clusters of RDs that replicate at unique times in each stage (RT signatures) and confirmed global consolidation of the genome into larger synchronously replicating segments during differentiation. Surprisingly, transcriptome data revealed that the well-accepted correlation between early replication and transcriptional activity was restricted to RT-constitutive genes, whereas two-thirds of the genes that switched RT during differentiation were strongly expressed when late replicating in one or more cell types. Closer inspection revealed that transcription of this class of genes was frequently restricted to the lineage in which the RT switch occurred, but was induced prior to a late-to-early RT switch and/or down-regulated after an early-to-late RT switch. Analysis of transcriptional regulatory networks showed that this class of genes contains strong regulators of genes that were only expressed when early replicating. These results provide intriguing new insight into the complex relationship between transcription and RT regulation during human development.
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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.