ArticleMobile DNA2021
Transposable element subfamily annotation has a reproducibility problem.
Article in Mobile DNA, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Updated Transposable Element Libraries forbioRxiv : the preprint server for biology · 2026Article
- Diversity and genome engineering applications of R2 non-LTR retrotransposons.RNA (New York, N.Y.) · 2026Review
- Transposable elements impact the human regulatory landscape through cell type specific epigenomic associations.Nature communications · 2026Article
- Boundary-associated propagation of a processed pseudogene dissects pre-existing limitations of genome annotation in the T2T era.Mobile DNA · 2026Article
- ColabCuraTE: an easy-to-use, web-based pipeline for the manual curation of transposable elements.Mobile DNA · 2025Article
- A phylogenetic approach uncovers cryptic endogenous retrovirus subfamilies in the primate lineage.Science advances · 2025Article
- Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding.Genome research · 2025Article
- Characterization of hAT DNA transposon superfamily in the genome of Neotropical fish Apareiodon sp.Molecular genetics and genomics : MGG · 2024Article
- Evolution and subfamilies of HERVL human endogenous retrovirus.Bioinformatics advances · 2024Article
- The good, the bad and the ugly of transposable elements annotation tools.Genetics and molecular biology · 2024Article
- Oncogenic Transformation Drives DNA Methylation Loss and Transcriptional Activation at Transposable Element Loci.Cancer research · 2023Article
- Article
- Genomic Analyses of Non-Coding RNAs Overlapping Transposable Elements and Its Implication to Human Diseases.International journal of molecular sciences · 2022Review
- Revealing Landscapes of Transposable Elements inInsects · 2022Article
- From telomere to telomere: The transcriptional and epigenetic state of human repeat elements.Science (New York, N.Y.) · 2022Article
- An ancestral genomic sequence that serves as a nucleation site for de novo gene birth.PloS one · 2022Article
- The Dfam community resource of transposable element families, sequence models, and genome annotations.Mobile DNA · 2021Article
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Authors and funding
3 authors.
Funding
Abstract
backgroundTransposable element (TE) sequences are classified into families based on the reconstructed history of replication, and into subfamilies based on more fine-grained features that are often intended to capture family history. We evaluate the reliability of annotation with common subfamilies by assessing the extent to which subfamily annotation is reproducible in replicate copies created by segmental duplications in the human genome, and in homologous copies shared by human and chimpanzee.
resultsWe find that standard methods annotate over 10% of replicates as belonging to different subfamilies, despite the fact that they are expected to be annotated as belonging to the same subfamily. Point mutations and homologous recombination appear to be responsible for some of this discordant annotation (particularly in the young Alu family), but are unlikely to fully explain the annotation unreliability.
conclusionsThe surprisingly high level of disagreement in subfamily annotation of homologous sequences highlights a need for further research into definition of TE subfamilies, methods for representing subfamily annotation confidence of TE instances, and approaches to better utilizing such nuanced annotation data in downstream analysis.
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