ArticleGenome biology and evolution2015
Sequence Analysis and Characterization of Active Human Alu Subfamilies Based on the 1000 Genomes Pilot Project.
Article in Genome biology and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed, 70 citations in OpenAlex.
- Machine learning reveals sequence and genomic context features underlyingbioRxiv : the preprint server for biology · 2026Article
- Long-read sequencing reveals a hidden Alu-mediated splice defect in CPLANE1, causing orofaciodigital syndrome type VI.European journal of human genetics : EJHG · 2026Article
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- Inverted Alu repeats in loop-out exon skipping across hominoid evolution.Nucleic acids research · 2026Article
- Integrated small and long RNA sequencing reveals piRNA mediated transposon repression during human oogenesis.Nature communications · 2026Article
- Chromatin unfolding via loops can drive clustered transposon insertion.Biophysical journal · 2025Article
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- Long-read sequencing reveals genomic and epigenomic variation in the dark genome of human Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025Article
- Direct identification ofbioRxiv : the preprint server for biology · 2025Article
- Emerging Functions of the Repeat Genome in Nuclear Structure: A View from the Human Karyotype.Annual review of genomics and human genetics · 2025Review
- Adenovirus small E1A directs activation of Alu transcription at YAP/TEAD- and AP-1-bound enhancers through interactions with the EP400 chromatin remodeler.Nucleic acids research · 2024Article
- Long-read sequencing improves the genetic diagnosis of retinitis pigmentosa by identifying an Alu retrotransposon insertion in the EYS gene.Mobile DNA · 2024Article
- DSB profiles in human spermatozoa highlight the role of TMEJ in the male germline.Frontiers in genetics · 2024Article
- SARS-CoV-2 infection severity and mortality is modulated by repeat-mediated regulation of alternative splicing.Microbiology spectrum · 2023Article
- Article
- Owl MonkeyGenes · 2022Article
- Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data.Life (Basel, Switzerland) · 2022Review
- Emerging roles of circular RNAs in retinal diseases.Neural regeneration research · 2022Review
- Article
- A Map of 3' DNA Transduction Variants Mediated by Non-LTR Retroelements on 3202 Human Genomes.Biology · 2022Article
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
Abstract
The goal of the 1000 Genomes Consortium is to characterize human genome structural variation (SV), including forms of copy number variations such as deletions, duplications, and insertions. Mobile element insertions, particularly Alu elements, are major contributors to genomic SV among humans. During the pilot phase of the project we experimentally validated 645 (611 intergenic and 34 exon targeted) polymorphic "young" Alu insertion events, absent from the human reference genome. Here, we report high resolution sequencing of 343 (322 unique) recent Alu insertion events, along with their respective target site duplications, precise genomic breakpoint coordinates, subfamily assignment, percent divergence, and estimated A-rich tail lengths. All the sequenced Alu loci were derived from the AluY lineage with no evidence of retrotransposition activity involving older Alu families (e.g., AluJ and AluS). AluYa5 is currently the most active Alu subfamily in the human lineage, followed by AluYb8, and many others including three newly identified subfamilies we have termed AluYb7a3, AluYb8b1, and AluYa4a1. This report provides the structural details of 322 unique Alu variants from individual human genomes collectively adding about 100 kb of genomic variation. Many Alu subfamilies are currently active in human populations, including a surprising level of AluY retrotransposition. Human Alu subfamilies exhibit continuous evolution with potential drivers sprouting new Alu lineages.
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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.