ArticleNature communications2015
3D hotspots of recurrent retroviral insertions reveal long-range interactions with cancer genes.
Article in Nature communications, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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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.
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Who cites it
22 citing papers in PubMed, 39 citations in OpenAlex.
- Emerging magic bullet: subcellular organelle-targeted cancer therapy.Medical review (2021) · 2025Review
- Safer and efficient base editing and prime editing via ribonucleoproteins delivered through optimized lipid-nanoparticle formulations.Nature biomedical engineering · 2025Article
- Integrating Clinical Cancer and PTM Proteomics Data Identifies a Mechanism of ACK1 Kinase Activation.Molecular cancer research : MCR · 2024Article
- InCliniGene enables high-throughput and comprehensive in vivo clonal tracking toward clinical genomics data integration.Database : the journal of biological databases and curation · 2023Article
- When 3D genome technology meets viral infection, including SARS-CoV-2.Journal of medical virology · 2022Review
- The importance of considering regulatory domains in genome-wide analyses - the nearest gene is often wrong!Biology open · 2022Review
- Review
- Integrating molecular profiles into clinical frameworks through the Molecular Oncology Almanac to prospectively guide precision oncology.Nature cancer · 2021Article
- Retroviral integrations contribute to elevated host cancer rates during germline invasion.Nature communications · 2021Article
- Shifting Retroviral Vector Integrations Away from Transcriptional Start Sites via DNA-Binding Protein Domain Insertion into Integrase.Molecular therapy. Methods & clinical development · 2019Article
- A Genome Model to Explain Major Features of Neurodevelopmental Disorders in Newborns.Biomedical informatics insights · 2019Article
- Subclonal mutation selection in mouse lymphomagenesis identifies known cancer loci and suggests novel candidates.Nature communications · 2018Article
- Clinical use of lentiviral vectors.Leukemia · 2018Review
- The human leukemia virus HTLV-1 alters the structure and transcription of host chromatin in cis.eLife · 2018Article
- Interactions between Retroviruses and the Host Cell Genome.Molecular therapy. Methods & clinical development · 2018Review
- Nucleome Analysis Reveals Structure-Function Relationships for Colon Cancer.Molecular cancer research : MCR · 2017Article
- The retrovirus HTLV-1 inserts an ectopic CTCF-binding site into the human genome.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- A Graph Based Framework to Model Virus Integration Sites.Computational and structural biotechnology journal · 2016Article
- Retroviral integration: Site matters: Mechanisms and consequences of retroviral integration site selection.BioEssays : news and reviews in molecular, cellular and developmental biology · 2015Review
- Functional organization of the human 4D Nucleome.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomically distal mutations can contribute to the deregulation of cancer genes by engaging in chromatin interactions. To study this, we overlay viral cancer-causing insertions obtained in a murine retroviral insertional mutagenesis screen with genome-wide chromatin conformation capture data. Here we find that insertions tend to cluster in 3D hotspots within the nucleus. The identified hotspots are significantly enriched for known cancer genes, and bear the expected characteristics of bona fide regulatory interactions, such as enrichment for transcription factor-binding sites. In addition, we observe a striking pattern of mutual exclusive integration. This is an indication that insertions in these loci target the same gene, either in their linear genomic vicinity or in their 3D spatial vicinity. Our findings shed new light on the repertoire of targets obtained from insertional mutagenesis screening and underline the importance of considering the genome as a 3D structure when studying effects of genomic perturbations.
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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.