ArticleNAR genomics and bioinformatics2021
Comprehensive understanding of Tn5 insertion preference improves transcription regulatory element identification.
Article in NAR genomics and bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Transposon-based genome editing of industrial microorganisms: advances, challenges, and prospects.Synthetic and systems biotechnology · 2026Review
- Defining the essential genome of diverse phages with phage Tn-seq.Nature microbiology · 2026Article
- ATAC-seq and MNase-seq Detect Distinct Modes of Chromatin Accessibility.bioRxiv : the preprint server for biology · 2026Article
- Robust footprinting with sample-specific Tn5 bias correction for bulk and single cell ATAC-seq.Nature communications · 2026Article
- ConNIS and labeling instability: New statistical methods for improving the detection of essential genes in TraDIS libraries.PLoS computational biology · 2026Article
- ATAC-seq in Emerging Model Organisms: Challenges and Strategies.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2025Review
- A hierarchical, count-based model highlights challenges in scATAC-seq data analysis and points to opportunities to extract finer-resolution information.Genome biology · 2025Article
- Untargeted CUT&Tag reads are enriched at accessible chromatin and restrict identification of potential G4-forming sequences in G4-targeted CUT&Tag experiments.Nucleic acids research · 2025Article
- KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome.Genome research · 2025Article
- Going beyond cell clustering and feature aggregation: Is there single cell level information in single-cell ATAC-seq data?bioRxiv : the preprint server for biology · 2024Article
- OpenTn5: Open-Source Resource for Robust and Scalable Tn5 Transposase Purification and Characterization.bioRxiv : the preprint server for biology · 2024Article
- Uniform quantification of single-nucleus ATAC-seq data with Paired-Insertion Counting (PIC) and a model-based insertion rate estimator.Nature methods · 2024Article
- Advancements in Focal Amplification Detection in Tumor/Liquid Biopsies and Emerging Clinical Applications.Genes · 2023Review
- Major cell-types in multiomic single-nucleus datasets impact statistical modeling of links between regulatory sequences and target genes.Scientific reports · 2023Article
- Recent advances in genetic tools for engineering probiotic lactic acid bacteria.Bioscience reports · 2023Article
- Investigating chromatin accessibility during development and differentiation by ATAC-sequencing to guide the identification of cis-regulatory elements.Biochemical Society transactions · 2022Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Tn5 transposase, which can efficiently tagment the genome, has been widely adopted as a molecular tool in next-generation sequencing, from short-read sequencing to more complex methods such as assay for transposase-accessible chromatin using sequencing (ATAC-seq). Here, we systematically map Tn5 insertion characteristics across several model organisms, finding critical parameters that affect its insertion. On naked genomic DNA, we found that Tn5 insertion is not uniformly distributed or random. To uncover drivers of these biases, we used a machine learning framework, which revealed that DNA shape cooperatively works with DNA motif to affect Tn5 insertion preference. These intrinsic insertion preferences can be modeled using nucleotide dependence information from DNA sequences, and we developed a computational pipeline to correct for these biases in ATAC-seq data. Using our pipeline, we show that bias correction improves the overall performance of ATAC-seq peak detection, recovering many potential false-negative peaks. Furthermore, we found that these peaks are bound by transcription factors, underscoring the biological relevance of capturing this additional information. These findings highlight the benefits of an improved understanding and precise correction of Tn5 insertion preference.
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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 Socratic graph.