ArticleMobile DNA2019
Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome.
Article in Mobile DNA, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Dynamic and Ongoing De Novo L1 Retrotransposition Contributes to Genome Plasticity and Intrapatient Heterogeneity in Ovarian Cancer.Cancer research · 2026Article
- Rewriting the genome: harnessing R2 retrotransposons for precise DNA insertion.Frontiers in genome editing · 2026Review
- Ultra-sensitive detection of transposon insertions across multiple families by transposable element display sequencing.Genome biology · 2025Article
- Mapping of long interspersed element-1 (L1) insertions by TIPseq provides information about sub chromosomal genetic variation in human embryos.Journal of assisted reproduction and genetics · 2024Article
- Comprehensive profiling of L1 retrotransposons in mouse.Nucleic acids research · 2024Article
- Regulation and function of transposable elements in cancer genomes.Cellular and molecular life sciences : CMLS · 2024Review
- Transposon insertion profiling by sequencing (TIPseq) identifies novel LINE-1 insertions in human sperm.Journal of assisted reproduction and genetics · 2023Article
- TDP-43 safeguards the embryo genome from L1 retrotransposition.Science advances · 2022Article
- Transposable element polymorphisms improve prediction of complex agronomic traits in rice.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Somatic Mobilization: High Somatic Insertion Rate ofInsects · 2022Article
- Intronic LINE-1 insertion in SLCO1B3 as a highly prevalent cause of rotor syndrome in East Asian population.Journal of human genetics · 2022Article
- Transposable elements that have recently been mobile in the human genome.BMC genomics · 2021Article
- Genomic approaches to trace the history of human brain evolution with an emerging opportunity for transposon profiling of ancient humans.Mobile DNA · 2021Review
- Cas9 targeted enrichment of mobile elements using nanopore sequencing.Nature communications · 2021Article
- RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs.Mobile DNA · 2021Article
- The genetics of ductal adenocarcinoma of the pancreas in the year 2020: dramatic progress, but far to go.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2020Review
- TranspoScope: interactive visualization of retrotransposon insertions.Bioinformatics (Oxford, England) · 2020Article
- Human transposon insertion profiling by sequencing (TIPseq) to map LINE-1 insertions in single cells.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Article
- Cell fitness screens reveal a conflict between LINE-1 retrotransposition and DNA replication.Nature structural & molecular biology · 2020Article
- Integrated Mobile Element Scanning (ME-Scan) method for identifying multiple types of polymorphic mobile element insertions.Mobile DNA · 2020Article
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13 authors.
Funding
Abstract
backgroundTransposable elements make up a significant portion of the human genome. Accurately locating these mobile DNAs is vital to understand their role as a source of structural variation and somatic mutation. To this end, laboratories have developed strategies to selectively amplify or otherwise enrich transposable element insertion sites in genomic DNA.
resultsHere we describe a technique, Transposon Insertion Profiling by sequencing (TIPseq), to map Long INterspersed Element 1 (LINE-1, L1) retrotransposon insertions in the human genome. This method uses vectorette PCR to amplify species-specific L1 (L1PA1) insertion sites followed by paired-end Illumina sequencing. In addition to providing a step-by-step molecular biology protocol, we offer users a guide to our pipeline for data analysis, TIPseqHunter. Our recent studies in pancreatic and ovarian cancer demonstrate the ability of TIPseq to identify invariant (fixed), polymorphic (inherited variants), as well as somatically-acquired L1 insertions that distinguish cancer genomes from a patient's constitutional make-up.
conclusionsTIPseq provides an approach for amplifying evolutionarily young, active transposable element insertion sites from genomic DNA. Our rationale and variations on this protocol may be useful to those mapping L1 and other mobile elements in complex genomes.
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