ArticleCell genomics2024
Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants.
Article in Cell genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 14 citations in OpenAlex.
- Article
- The dynamic genomes of Hydra and the anciently active repeat complement of animal chromosomes.Genome biology · 2025Article
- Article
- Article
- A Concise Guide for the Characterization and Curation of Transposable Elements in Insect Genomes.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Regulatory transposable elements in the encyclopedia of DNA elements.Nature communications · 2024Article
- Jump-starting life: balancing transposable element co-option and genome integrity in the developing mammalian embryo.EMBO reports · 2024Review
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual species, which limits its scope to relatively intact TE sequences. Here, we report a novel approach to uncover previously unannotated degenerate TEs (degTEs) by probing multiple ancestral genomes reconstructed from hundreds of species. We applied this method to the human genome and achieved a 10.8% increase in coverage over the most recent annotation. Further, we discovered that degTEs contribute to various cis-regulatory elements and transcription factor binding sites, including those of a known TE-controlling family, the KRAB zinc-finger proteins. We also report unannotated chimeric transcripts between degTEs and human genes expressed in embryos. This study provides a novel methodology and a freely available resource that will facilitate the investigation of TE co-option events on a full scale.
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