ArticleThe EMBO journal2024
Evolutionary insights from profiling LINE-1 activity at allelic resolution in a single human genome.
Article in The EMBO journal, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 7 citations in OpenAlex.
- Active Human Transposable Elements: Long-Read Sequencing Technologies, Computational Analysis, and Implications for Human Disease.Biomolecules · 2026Review
- Transposable Element Activation: A Hallmark of Cancer.Cancer discovery · 2026Review
- Detection of endogenous LINE-1 ORF2p and its potent reverse transcriptase activity in the MCF-7 breast cancer cell line.The FEBS journal · 2026Article
- Pangenome reference assemblies reveal the variation and recent activity of human LINE-1 retrotransposons.bioRxiv : the preprint server for biology · 2026Article
- A phylogenetic estimate of canine retrotransposition rates based on genome assembly comparisons.Mobile DNA · 2026Article
- An Alternative DNA Endonuclease Activity is Associated with the LINE-1 ORF2-encoded Protein.bioRxiv : the preprint server for biology · 2026Article
- High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation.Genome research · 2024Article
- Repetitive Sequence Stability in Embryonic Stem Cells.International journal of molecular sciences · 2024Review
- Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation.medRxiv : the preprint server for health sciences · 2024Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Transposable elements have created the majority of the sequence in many genomes. In mammals, LINE-1 retrotransposons have been expanding for more than 100 million years as distinct, consecutive lineages; however, the drivers of this recurrent lineage emergence and disappearance are unknown. Most human genome assemblies provide a record of this ancient evolution, but fail to resolve ongoing LINE-1 retrotranspositions. Utilizing the human CHM1 long-read-based haploid assembly, we identified and cloned all full-length, intact LINE-1s, and found 29 LINE-1s with measurable in vitro retrotransposition activity. Among individuals, these LINE-1s varied in their presence, their allelic sequences, and their activity. We found that recently retrotransposed LINE-1s tend to be active in vitro and polymorphic in the population relative to more ancient LINE-1s. However, some rare allelic forms of old LINE-1s retain activity, suggesting older lineages can persist longer than expected. Finally, in LINE-1s with in vitro activity and in vivo fitness, we identified mutations that may have increased replication in ancient genomes and may prove promising candidates for mechanistic investigations of the drivers of LINE-1 evolution and which LINE-1 sequences contribute to human disease.
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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 OpenQuestion graph.