ArticleScience advances2017
Integrating networks and comparative genomics reveals retroelement proliferation dynamics in hominid genomes.
Article in Science advances, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 20 citations in OpenAlex.
- Detection of an anti-angina therapeutic module in the effective population treated by a multi-target drug Danhong injection: a randomized trial.Signal transduction and targeted therapy · 2021Trial
- Genomic profiling of six human somatic histone H1 variants denotes that H1X accumulates at recently incorporated transposable elements.Nucleic acids research · 2024Article
- Review
- The Dfam community resource of transposable element families, sequence models, and genome annotations.Mobile DNA · 2021Article
- Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Frontiers in plant science · 2021Article
- IMCC: A Novel Quantitative Approach Revealing Variation of Global Modular Map and Local Inter-Module Coordination Among Differential Drug's Targeted Cerebral Ischemic Networks.Frontiers in pharmacology · 2021Article
- The effect of hybridization on transposable element accumulation in an undomesticated fungal species.eLife · 2020Article
- Transposon Reactivation in the Germline May Be Useful for Both Transposons and Their Host Genomes.Cells · 2020Review
- Simultaneous TE Analysis of 19 Heliconiine Butterflies Yields Novel Insights into Rapid TE-Based Genome Diversification and Multiple SINE Births and Deaths.Genome biology and evolution · 2019Article
- The Chromosome-Level Genome Assembly of European Grayling Reveals Aspects of a Unique Genome Evolution Process Within Salmonids.G3 (Bethesda, Md.) · 2019Article
- Birth and Death of LTR-Retrotransposons inGenetics · 2018Article
- Phylogenomic analysis reveals splicing as a mechanism of parallel evolution of non-canonical SVAs in hominine primates.Mobile DNA · 2018Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Retroelements (REs) are mobile DNA sequences that multiply and spread throughout genomes by a copy-and-paste mechanism. These parasitic elements are active in diverse genomes, from yeast to humans, where they promote diversity, cause disease, and accelerate evolution. Because of their high copy number and sequence similarity, studying their activity and tracking their proliferation dynamics is a challenge. It is particularly difficult to pinpoint the few REs in a genome that are still active in the haystack of degenerate and suppressed elements. We develop a computational framework based on network theory that tracks the path of RE proliferation throughout evolution. We analyze SVA (SINE-VNTR-Alu), the youngest RE family in human genomes, to understand RE dynamics across hominids. Integrating comparative genomics and network tools enables us to track the course of SVA proliferation, identify yet unknown active communities, and detect tentative "master REs" that played key roles in SVA propagation, providing strong support for the fundamental "master gene" model of RE proliferation. The method is generic and thus can be applied to REs of any of the thousands of available genomes to identify active RE communities and master REs that were pivotal in the evolution of their host genomes.
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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.