ArticleGenome research2013
Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early- and late-firing origins.
Article in Genome research, 2013. 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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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
63 citing papers in PubMed, 108 citations in OpenAlex.
- Spatial organization and dynamics of genome replication: from forks to foci.Nucleic acids research · 2026Review
- Replication Rate-Information Storage Trade-Off Shapes Genome Architecture Across Domains.Journal of molecular evolution · 2026Article
- Decoding DNA metabolism and its clinical relevance through the lens of high-throughput sequencing assays.Medical review (2021) · 2026Review
- Improved short nascent strand sequencing (iSNS-seq) enhances DNA replication origin detection and reduces non-origin biases.bioRxiv : the preprint server for biology · 2026Article
- Nanopore-based sequencing of active DNA replication reveals key principles of metazoan replication dynamics.Science advances · 2026Article
- Multiplexed TrAEL-seq captures DNA replication dynamics in mammalian cells.Nucleic acids research · 2026Article
- Spatial mapping of DNA synthesis reveals dynamics and geometry of human replication nanostructures.The EMBO journal · 2025Article
- Nanopore-based sequencing of active DNA replication reveals key principles of metazoan replication fork progression, origin and termination sites.bioRxiv : the preprint server for biology · 2025Article
- Most human DNA replication initiation is dispersed throughout the genome with only a minority within previously identified initiation zones.Genome biology · 2025Article
- The double life of mammalian DNA replication origins.Genes & development · 2025Review
- A tale of two strands: Decoding chromatin replication through strand-specific sequencing.Molecular cell · 2025Review
- DeOri 10.0: An Updated Database of Experimentally Identified Eukaryotic Replication Origins.Genomics, proteomics & bioinformatics · 2024Article
- Article
- DNA replication and replication stress response in the context of nuclear architecture.Chromosoma · 2024Review
- Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths.PLoS computational biology · 2023Article
- Detection and characterization of constitutive replication origins defined by DNA polymerase epsilon.BMC biology · 2023Article
- Origins of DNA replication in eukaryotes.Molecular cell · 2023Review
- 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
- 3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells.Nucleic acids research · 2022Article
- Global landscape of replicative DNA polymerase usage in the human genome.Nature communications · 2022Article
3 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
6 authors at 1 institution in 1 country.
Funding
Abstract
We have devised a method for isolating virtually pure and comprehensive libraries of restriction fragments that contained replication initiation sites (bubbles) in vivo. We have now sequenced and mapped the bubble-containing fragments from GM06990, a near-normal EBV-transformed lymphoblastoid cell line, and have compared origin distributions with a comprehensive replication timing study recently published for this cell line. We find that early-firing origins, which represent ∼32% of all origins, overwhelmingly represent zones, associate only marginally with active transcription units, are localized within large domains of open chromatin, and are significantly associated with DNase I hypersensitivity. Origin "density" falls from early- to mid-S-phase, but rises again in late S-phase to levels only 17% lower than in early S-phase. Unexpectedly, late origin density calculated on the 1-Mb scale increases as a function of increasing chromatin compaction. Furthermore, the median efficiency of origins in late-replicating, heterochromatic domains is only 25% lower than in early-replicating euchromatic loci. Thus, the activation of early- and late-firing origins must be regulated by quintessentially different mechanisms. The aggregate data can be unified into a model in which initiation site selection is driven almost entirely by epigenetic factors that fashion both the long-range and local chromatin environments, with underlying DNA sequence and local transcriptional activity playing only minor roles. Importantly, the comprehensive origin map we have prepared for GM06990 overlaps moderately well with origin maps recently reported for the genomes of four different human cell lines based on the distributions of small nascent strands.
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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.