ArticlePLoS genetics2014
Chromatin landscapes of retroviral and transposon integration profiles.
Article in PLoS genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
- Sleeping Beauty-engineered CAR T cells achieve antileukemic activity without severe toxicities.The Journal of clinical investigation · 2020Trial
- Barcoded Sleeping Beauty Transposons as Mobile Reporters of Chromatin Architecture.International journal of molecular sciences · 2026Article
- Retroviral intasome architecture shapes the dynamics of target DNA search and integration.PLoS pathogens · 2026Article
- Methodological landscape in the field of integration site identification of retroviruses and retroviral vectors.Frontiers in bioengineering and biotechnology · 2025Review
- Current Non-Viral-Based Strategies to Manufacture CAR-T Cells.International journal of molecular sciences · 2024Review
- Engineering of potent CAR NK cells using non-viral Sleeping Beauty transposition from minimalistic DNA vectors.Molecular therapy : the journal of the American Society of Gene Therapy · 2024Article
- Engineering strategies to safely drive CAR T-cells into the future.Frontiers in immunology · 2024Review
- InCliniGene enables high-throughput and comprehensive in vivo clonal tracking toward clinical genomics data integration.Database : the journal of biological databases and curation · 2023Article
- Article
- Optimization of piggyBac Transposon System Electrotransfection in Sheep Fibroblasts.Molecular biotechnology · 2023Article
- High-Throughput Identification, Modeling, and Analysis of Cancer Driver Genes In Vivo.Cold Spring Harbor perspectives in medicine · 2023Review
- Prolonged activity of the transposase helper may raise safety concerns during DNA transposon-based gene therapy.Molecular therapy. Methods & clinical development · 2023Article
- Article
- Transmicron: accurate prediction of insertion probabilities improves detection of cancer driver genes from transposon mutagenesis screens.Nucleic acids research · 2023Article
- Review
- A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution.Nature ecology & evolution · 2022Article
- Engineered Sleeping Beauty transposase redirects transposon integration away from genes.Nucleic acids research · 2022Article
- Genomic context sensitivity of insulator function.Genome research · 2022Article
- The Past, Present, and Future of Non-Viral CAR T Cells.Frontiers in immunology · 2022Review
- Jumping Ahead withViruses · 2021Review
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The ability of retroviruses and transposons to insert their genetic material into host DNA makes them widely used tools in molecular biology, cancer research and gene therapy. However, these systems have biases that may strongly affect research outcomes. To address this issue, we generated very large datasets consisting of ~ 120,000 to ~ 180,000 unselected integrations in the mouse genome for the Sleeping Beauty (SB) and piggyBac (PB) transposons, and the Mouse Mammary Tumor Virus (MMTV). We analyzed ~ 80 (epi)genomic features to generate bias maps at both local and genome-wide scales. MMTV showed a remarkably uniform distribution of integrations across the genome. More distinct preferences were observed for the two transposons, with PB showing remarkable resemblance to bias profiles of the Murine Leukemia Virus. Furthermore, we present a model where target site selection is directed at multiple scales. At a large scale, target site selection is similar across systems, and defined by domain-oriented features, namely expression of proximal genes, proximity to CpG islands and to genic features, chromatin compaction and replication timing. Notable differences between the systems are mainly observed at smaller scales, and are directed by a diverse range of features. To study the effect of these biases on integration sites occupied under selective pressure, we turned to insertional mutagenesis (IM) screens. In IM screens, putative cancer genes are identified by finding frequently targeted genomic regions, or Common Integration Sites (CISs). Within three recently completed IM screens, we identified 7%-33% putative false positive CISs, which are likely not the result of the oncogenic selection process. Moreover, results indicate that PB, compared to SB, is more suited to tag oncogenes.
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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.