ArticleNucleic acids research2009
Open chromatin encoded in DNA sequence is the signature of 'master' replication origins in human cells.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 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
33 citing papers in PubMed, 58 citations in OpenAlex.
- FANCD2 restrains fork progression and prevents fragility at early origins upon re-replication.Nature communications · 2026Article
- OCT4 enhances the firing efficiency of late DNA replication origins in mouse embryonic stem cells.Nature communications · 2026Article
- DNA replication timing reveals genome-wide features of transcription and fragility.Nature communications · 2025Article
- Genome-wide measurement of DNA replication fork directionality and quantification of DNA replication initiation and termination with Okazaki fragment sequencing.Nature protocols · 2023Review
- Origins of DNA replication in eukaryotes.Molecular cell · 2023Review
- Site-specific decreases in DNA methylation in replicating cells following exposure to oxidative stress.Human molecular genetics · 2023Article
- Surveying mutation density patterns around specific genomic features.Genome research · 2022Article
- Evidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates.Biophysical journal · 2018Article
- Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (The Plant cell · 2017Article
- Evidence of selection for an accessible nucleosomal array in human.BMC genomics · 2016Article
- Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster.Nucleic acids research · 2016Article
- Embryonic stem cell specific "master" replication origins at the heart of the loss of pluripotency.PLoS computational biology · 2015Article
- Peaks cloaked in the mist: the landscape of mammalian replication origins.The Journal of cell biology · 2015Review
- Article
- Profiling of the Chromatin-associated Proteome Identifies HP1BP3 as a Novel Regulator of Cell Cycle Progression.Molecular & cellular proteomics : MCP · 2014Article
- Genetic factors underlying discordance in chromatin accessibility between monozygotic twins.Genome biology · 2014Article
- The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells.PLoS genetics · 2014Article
- Genetic and epigenetic determinants mediate proneness of oncogene breakpoint sites for involvement in TCR translocations.Genes and immunity · 2014Article
- The replication domain model: regulating replicon firing in the context of large-scale chromosome architecture.Journal of molecular biology · 2013Review
- Regulation of the boundaries of accessible chromatin.PLoS genetics · 2013Article
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 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
For years, progress in elucidating the mechanisms underlying replication initiation and its coupling to transcriptional activities and to local chromatin structure has been hampered by the small number (approximately 30) of well-established origins in the human genome and more generally in mammalian genomes. Recent in silico studies of compositional strand asymmetries revealed a high level of organization of human genes around 1000 putative replication origins. Here, by comparing with recently experimentally identified replication origins, we provide further support that these putative origins are active in vivo. We show that regions approximately 300-kb wide surrounding most of these putative replication origins that replicate early in the S phase are hypersensitive to DNase I cleavage, hypomethylated and present a significant enrichment in genomic energy barriers that impair nucleosome formation (nucleosome-free regions). This suggests that these putative replication origins are specified by an open chromatin structure favored by the DNA sequence. We discuss how this distinctive attribute makes these origins, further qualified as 'master' replication origins, priviledged loci for future research to decipher the human spatio-temporal replication program. Finally, we argue that these 'master' origins are likely to play a key role in genome dynamics during evolution and in pathological situations.
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.