ArticleGenome research2015
Large transcription units unify copy number variants and common fragile sites arising under replication stress.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 113 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
113 citing papers in PubMed, 194 citations in OpenAlex.
- The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts.PLoS genetics · 2016Trial
- Single-cell mapping of chromosome breaks identifies multiple fragile site classes with distinct DNA replication timing landscapes.Nature communications · 2026Article
- Article
- Using the DNA language model, GROVER, to parse effects of sequence, chromatin and regulatory features on genome stability.Bioinformatics (Oxford, England) · 2026Article
- Early replication fragile sites are associated with cancer-related CNVs and SNVs in human embryonic stem cells.Stem cell reports · 2026Article
- High-fidelity rare structural variant detection with HiFiRE3 reduced representation via restriction enzyme ends.bioRxiv : the preprint server for biology · 2026Article
- Recurrent DNA break clusters drive replication-stress-induced copy number variants and genome diversification.Nature communications · 2026Article
- Transcription at an inducible common fragile site reveals replication origin strength hierarchy.Nucleic acids research · 2026Article
- Spontaneous Mutations Occur More in Highly Transcribed Regions in Daphnia.Genome biology and evolution · 2026Article
- Immunofluorescent microscopy to quantify and characterize chromosomal instability (CIN).Methods in cell biology · 2026Article
- The landscape of structural variation in pediatric cancer.bioRxiv : the preprint server for biology · 2025Article
- Template switching during DNA replication is a prevalent source of adaptive gene amplification.eLife · 2025Article
- A new insight into the impact of copy number variations on cell cycle deregulation of luminal-type breast cancer.Oncology reviews · 2025Review
- Analysis of exonic deletions in a large population study provides novel insights into NRXN1 pathology.NPJ genomic medicine · 2024Article
- Review
- Replication stress induces POLQ-mediated structural variant formation throughout common fragile sites after entry into mitosis.Nature communications · 2024Article
- Template switching during DNA replication is a prevalent source of adaptive gene amplification.bioRxiv : the preprint server for biology · 2024Article
- FANCD2 genome binding is nonrandom and is enriched at large transcriptionally active neural genes prone to copy number variation.Functional & integrative genomics · 2024Article
- Mapping recurrent mosaic copy number variation in human neurons.Nature communications · 2024Article
- Linear interaction between replication and transcription shapes DNA break dynamics at recurrent DNA break Clusters.Nature communications · 2024Article
53 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 at 3 institutions in 3 countries.
Funding
Abstract
Copy number variants (CNVs) resulting from genomic deletions and duplications and common fragile sites (CFSs) seen as breaks on metaphase chromosomes are distinct forms of structural chromosome instability precipitated by replication inhibition. Although they share a common induction mechanism, it is not known how CNVs and CFSs are related or why some genomic loci are much more prone to their occurrence. Here we compare large sets of de novo CNVs and CFSs in several experimental cell systems to each other and to overlapping genomic features. We first show that CNV hotpots and CFSs occurred at the same human loci within a given cultured cell line. Bru-seq nascent RNA sequencing further demonstrated that although genomic regions with low CNV frequencies were enriched in transcribed genes, the CNV hotpots that matched CFSs specifically corresponded to the largest active transcription units in both human and mouse cells. Consistently, active transcription units >1 Mb were robust cell-type-specific predictors of induced CNV hotspots and CFS loci. Unlike most transcribed genes, these very large transcription units replicated late and organized deletion and duplication CNVs into their transcribed and flanking regions, respectively, supporting a role for transcription in replication-dependent lesion formation. These results indicate that active large transcription units drive extreme locus- and cell-type-specific genomic instability under replication stress, resulting in both CNVs and CFSs as different manifestations of perturbed replication dynamics.
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.