ArticleBMC genomics2019
Template-switching artifacts resemble alternative polyadenylation.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Review
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Regulation of gene expression by alternative polyadenylation in health and disease.Nature reviews. Genetics · 2026Review
- Multi-platform profiling reveals host- and cell -type-specific pseudorabies virus gene expression.Scientific reports · 2026Article
- Veterinary Herpesviruses: Experimental Tools for Transcriptomics and Neuroscience.Veterinary sciences · 2026Review
- Genomic language model mitigates chimera artifacts in nanopore direct RNA sequencing.Nature communications · 2026Article
- The "cutting edge" of non-canonical RNA splicing.Frontiers in molecular biosciences · 2026Review
- Long-Read Sequencing Reveals RNA Splicing Complexity in Human Diseases.Computational and structural biotechnology journal · 2026Review
- Cross-Species Insights Into Gamma Herpesvirus Transcriptomes: Long-Read and Multi-Omics Perspectives.Journal of medical virology · 2026Review
- Systematic identification and characterization of virus lncRNAs suggests extensive structural mimicry of host lncRNAs.Briefings in bioinformatics · 2025Article
- Comprehensive resolution and classification of the Epstein Barr virus transcriptome.Nature communications · 2025Article
- Morphogenesis, starvation, and light responses in a mushroom-forming fungus revealed by long-read sequencing and extensive expression profiling.Cell genomics · 2025Article
- Long-read transcriptomics of caviid gammaherpesvirus 1: compiling a comprehensive RNA atlas.mSystems · 2025Article
- Temporal transcriptional profiling of host cells infected by a veterinary alphaherpesvirus using nanopore sequencing.Scientific reports · 2025Article
- Mapping the temporal transcriptomic signature of a viral pathogen through CAGE and nanopore sequencing.PloS one · 2025Article
- Long-read Transcriptomics of Caviid Gammaherpesvirus 1: Compiling a Comprehensive RNA Atlas.bioRxiv : the preprint server for biology · 2024Article
- Challenges in identifying mRNA transcript starts and ends from long-read sequencing data.Genome research · 2024Review
- Strategic nucleic acid detection approaches for diagnosing African swine fever (ASF): navigating disease dynamics.Veterinary research · 2024Review
- Exploring the transcriptomic profile of human monkeypox virus via CAGE and native RNA sequencing approaches.mSphere · 2024Article
- Sleep and diurnal alternative polyadenylation sites associated with human APA-linked brain disorders.Research square · 2024Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundAlternative polyadenylation is commonly examined using cDNA sequencing, which is known to be affected by template-switching artifacts. However, the effects of such template-switching artifacts on alternative polyadenylation are generally disregarded, while alternative polyadenylation artifacts are attributed to internal priming.
resultsHere, we analyzed both long-read cDNA sequencing and direct RNA sequencing data of two organisms, generated by different sequencing platforms. We developed a filtering algorithm which takes into consideration that template-switching can be a source of artifactual polyadenylation when filtering out spurious polyadenylation sites. The algorithm outperformed the conventional internal priming filters based on comparison to direct RNA sequencing data. We also showed that the polyadenylation artifacts arise in cDNA sequencing at consecutive stretches of as few as three adenines. There was no substantial difference between the lengths of poly(A) tails at the artifactual and the true transcriptional end sites even though it is expected that internal priming artifacts have shorter poly(A) tails than genuine polyadenylated reads.
conclusionsOur findings suggest that template switching plays an important role in the generation of spurious polyadenylation and support the need for more rigorous filtering of artifactual polyadenylation sites in cDNA data, or that alternative polyadenylation should be annotated using native RNA sequencing.
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