ArticleNature protocols2019
Monitoring early S-phase origin firing and replication fork movement by sequencing nascent DNA from synchronized cells.
Article in Nature protocols, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed, 35 citations in OpenAlex.
- The transcription factor ZmMYB3R targets CYCB1;2 to modulate maize drought tolerance.The Plant journal : for cell and molecular biology · 2026Article
- Decoding DNA metabolism and its clinical relevance through the lens of high-throughput sequencing assays.Medical review (2021) · 2026Review
- RNAs anchoring replication complex control initiation and firing of DNA replication.Nature communications · 2026Article
- OCT4 enhances the firing efficiency of late DNA replication origins in mouse embryonic stem cells.Nature communications · 2026Article
- NPR1 modulates DNA replication in vascular endothelial cells via the transcription factor E2F2.Genes & genomics · 2025Article
- Wnt10b signaling regulates replication stress-induced chromosomal instability in human cancer.Life science alliance · 2025Article
- Mammalian H4K16ac regulates the spatiotemporal order of genome replication rather than gene expression.Nucleic acids research · 2025Article
- Temporal control of human DNA replication licensing by CDK4/6-RB signalling and chemical genetics.Nature communications · 2025Article
- Most human DNA replication initiation is dispersed throughout the genome with only a minority within previously identified initiation zones.Genome biology · 2025Article
- CDK12 controls transcription at damaged genes and prevents MYC-induced transcription-replication conflicts.Nature communications · 2024Article
- RECQL4 is not critical for firing of human DNA replication origins.Scientific reports · 2024Article
- Visualizing the dynamics of DNA replication and repair at the single-molecule level.Methods in cell biology · 2024Article
- Temporal imaging of drug dynamics in live cells using stimulated Raman scattering microscopy and a perfusion cell culture system.RSC chemical biology · 2022Article
- Genomic patterns of transcription-replication interactions in mouse primary B cells.Nucleic acids research · 2022Article
- Clickable Cisplatin Derivatives as Versatile Tools to Probe the DNA Damage Response to Chemotherapy.Frontiers in oncology · 2022Article
- A transcription-based mechanism for oncogenic β-catenin-induced lethality in BRCA1/2-deficient cells.Nature communications · 2021Article
- Nonrandom DNA Segregation Detection under Replication Stress.STAR protocols · 2020Article
- Loss of histone H3.3 results in DNA replication defects and altered origin dynamics inGenome research · 2020Article
- High-resolution mapping of mitotic DNA synthesis regions and common fragile sites in the human genome through direct sequencing.Cell research · 2020Article
- Sonic hedgehog accelerates DNA replication to cause replication stress promoting cancer initiation in medulloblastoma.Nature cancer · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A better understanding of DNA replication initiation in human cells and how this process is altered upon DNA replication stress requires the ability to study origin firing genome wide. Previously described methods of mapping DNA replication origins in higher eukaryotes rely principally on fractionation of DNA fragments based on their size and, optionally, on the presence of ribonucleotides at their 5' end. Here, we describe a protocol for EdUseq-HU, a method for mapping early S-phase replication origins. Cells, synchronized by mitotic shake-off, are released in medium containing 5-ethynyl-2'-deoxyuridine (EdU; to label nascent DNA) and hydroxyurea (HU; to limit fork progression after origin firing). After using click chemistry to tag the EdU label with a biotin conjugate that is cleavable under mild conditions, the nascent DNA is captured on streptavidin beads. One variant of EdUseq-HU allows mapping of DNA replication origins on the genome at a resolution of 10 kb, and a second variant monitors progression of replication forks. Using EdUseq-HU, the spatiotemporal program of DNA replication in human cell lines can be interrogated in <2 weeks. The protocol requires basic cell culture and molecular biology skills, as well as familiarity with the Perl programming language and the Linux operating system.
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.