ArticleGenome research2009
Predictable dynamic program of timing of DNA replication in human cells.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
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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.
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Who cites it
74 citing papers in PubMed.
- Replication timing uncovers a two-compartment nuclear architecture of interphase euchromatin.The Plant cell · 2026Article
- DNA methylation and lncRNA control asynchronous DNA replication at specific imprinted gene domains.Nature communications · 2026Article
- 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
- Article
- Genomic patterns of transcription-replication interactions in mouse primary B cells.Nucleic acids research · 2022Article
- Chemically Induced Chromosomal Interaction (CICI) method to study chromosome dynamics and its biological roles.Nature communications · 2022Article
- DNA polymerase zeta contributes to heterochromatin replication to prevent genome instability.The EMBO journal · 2021Article
- Low Replicative Stress Triggers Cell-Type Specific Inheritable Advanced Replication Timing.International journal of molecular sciences · 2021Article
- Loss of histone H3.3 results in DNA replication defects and altered origin dynamics inGenome research · 2020Article
- Mapping replication timing domains genome wide in single mammalian cells with single-cell DNA replication sequencing.Nature protocols · 2020Article
- Efficient, quick and easy-to-use DNA replication timing analysis with START-R suite.NAR genomics and bioinformatics · 2020Article
- High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells.Genome biology · 2020Article
- Genomic methods for measuring DNA replication dynamics.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2020Review
- Control of DNA replication timing in the 3D genome.Nature reviews. Molecular cell biology · 2019Review
- Linking the organization of DNA replication with genome maintenance.Current genetics · 2019Review
- Germline Structural Variations Are Preferential Sites of DNA Replication Timing Plasticity during Development.Genome biology and evolution · 2019Article
- Insights into the Link between the Organization of DNA Replication and the Mutational Landscape.Genes · 2019Review
- Review
- Regulation of the program of DNA replication by CDK: new findings and perspectives.Current genetics · 2019Review
- Germline DNA replication timing shapes mammalian genome composition.Nucleic acids research · 2018Article
14 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
7 authors.
Funding
Abstract
The organization of mammalian DNA replication is poorly understood. We have produced high-resolution dynamic maps of the timing of replication in human erythroid, mesenchymal, and embryonic stem (ES) cells using TimEX, a method that relies on gaussian convolution of massive, highly redundant determinations of DNA copy-number variations during S phase to produce replication timing profiles. We first obtained timing maps of 3% of the genome using high-density oligonucleotide tiling arrays and then extended the TimEX method genome-wide using massively parallel sequencing. We show that in untransformed human cells, timing of replication is highly regulated and highly synchronous, and that many genomic segments are replicated in temporal transition regions devoid of initiation, where replication forks progress unidirectionally from origins that can be hundreds of kilobases away. Absence of initiation in one transition region is shown at the molecular level by single molecule analysis of replicated DNA (SMARD). Comparison of ES and erythroid cells replication patterns revealed that these cells replicate about 20% of their genome in different quarters of S phase. Importantly, we detected a strong inverse relationship between timing of replication and distance to the closest expressed gene. This relationship can be used to predict tissue-specific timing of replication profiles from expression data and genomic annotations. We also provide evidence that early origins of replication are preferentially located near highly expressed genes, that mid-firing origins are located near moderately expressed genes, and that late-firing origins are located far from genes.
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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.