ArticleGenome research2011
Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 60 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
60 citing papers in PubMed.
- Spatial organization and dynamics of genome replication: from forks to foci.Nucleic acids research · 2026Review
- 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
- ORC1 binds to cis-transcribed RNAs for efficient activation of replication origins.Nature communications · 2023Article
- Genome-wide measurement of DNA replication fork directionality and quantification of DNA replication initiation and termination with Okazaki fragment sequencing.Nature protocols · 2023Review
- Detection and characterization of constitutive replication origins defined by DNA polymerase epsilon.BMC biology · 2023Article
- Review
- 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
- DNA molecular combing-based replication fork directionality profiling.Nucleic acids research · 2021Article
- Orc4 spatiotemporally stabilizes centromeric chromatin.Genome research · 2021Article
- Genome-wide analysis of DNA replication and DNA double-strand breaks using TrAEL-seq.PLoS biology · 2021Article
- TRF2 Mediates Replication Initiation within Human Telomeres to Prevent Telomere Dysfunction.Cell reports · 2020Article
- A predictable conserved DNA base composition signature defines human core DNA replication origins.Nature communications · 2020Article
- Genome duplication ineLife · 2020Article
- Flying High-Muscle-Specific Underreplication inGenes · 2020Article
- Strand-specific Single-stranded DNA Sequencing (4S-seq) ofBio-protocol · 2019Article
- Accelerated Laboratory Evolution Reveals the Influence of Replication on the GC Skew in Escherichia coli.Genome biology and evolution · 2018Article
- Article
- Genome-wide analysis of the spatiotemporal regulation of firing and dormant replication origins in human cells.Nucleic acids research · 2018Article
- A journey through the microscopic ages of DNA replication.Protoplasma · 2017Review
Corrections and comments
- Erratum issued
Authors and funding
6 authors.
Funding
Abstract
We have used a novel bubble-trapping procedure to construct nearly pure and comprehensive human origin libraries from early S- and log-phase HeLa cells, and from log-phase GM06990, a karyotypically normal lymphoblastoid cell line. When hybridized to ENCODE tiling arrays, these libraries illuminated 15.3%, 16.4%, and 21.8% of the genome in the ENCODE regions, respectively. Approximately half of the origin fragments cluster into zones, and their signals are generally higher than those of isolated fragments. Interestingly, initiation events are distributed about equally between genic and intergenic template sequences. While only 13.2% and 14.0% of genes within the ENCODE regions are actually transcribed in HeLa and GM06990 cells, 54.5% and 25.6% of zonal origin fragments overlap transcribed genes, most with activating chromatin marks in their promoters. Our data suggest that cell synchronization activates a significant number of inchoate origins. In addition, HeLa and GM06990 cells activate remarkably different origin populations. Finally, there is only moderate concordance between the log-phase HeLa bubble map and published maps of small nascent strands for this cell line.
Indexed as
Identifiers
What OpenQuestion holds
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.