ArticleBMC evolutionary biology2013
Characterisation of the potential function of SVA retrotransposons to modulate gene expression patterns.
Article in BMC evolutionary biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 72 citations in OpenAlex.
- Article
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- The Influence of CG sites on dynamic DNA sequence mutagenesis in the genomic evolution of mammalian lifespan.Nucleic acids research · 2025Article
- Landscape and mutational dynamics of G-quadruplexes in the complete human genome and in haplotypes of diverse ancestry.bioRxiv : the preprint server for biology · 2025Article
- Ribosomal DNA arrays are the most H-DNA rich element in the human genome.NAR genomics and bioinformatics · 2025Article
- The landscape of non-reference SINE-VNTR-Alus in amyotrophic lateral sclerosis.Experimental biology and medicine (Maywood, N.J.) · 2025Article
- Mini-heterochromatin domains constrain the cis-regulatory impact of SVA transposons in human brain development and disease.Nature structural & molecular biology · 2024Article
- Article
- Deciphering the role of a SINE-VNTR-Alu retrotransposon polymorphism as a biomarker of Parkinson's disease progression.Scientific reports · 2024Article
- Exploring SVA Insertion Polymorphisms in Shaping Differential Gene Expressions in the Central Nervous System.Biomolecules · 2024Article
- Transposable Elements: Emerging Therapeutic Targets in Neurodegenerative Diseases.Neurotoxicity research · 2024Review
- A SINE-VNTR-Alu at the LRIG2 locus is associated with proximal and distal gene expression in CRISPR and population models.Scientific reports · 2024Article
- HLA Genetics for the Human Diseases.Advances in experimental medicine and biology · 2024Review
- Regulation of expression quantitative trait loci by SVA retrotransposons within the major histocompatibility complex.Experimental biology and medicine (Maywood, N.J.) · 2023Article
- The landscape of human SVA retrotransposons.Nucleic acids research · 2023Article
- Reference LINE-1 insertion polymorphisms correlate with Parkinson's disease progression and differential transcript expression in the PPMI cohort.Scientific reports · 2023Article
- A Genome-Wide Screen for the Exonisation of Reference SINE-VNTR-Alus and Their Expression in CNS Tissues of Individuals with Amyotrophic Lateral Sclerosis.International journal of molecular sciences · 2023Article
- RDA coupled with deep sequencing detects somatic SVA-retrotranspositions and mosaicism in the human brain.Frontiers in cell and developmental biology · 2023Article
- R-loop landscape in mature human sperm: Regulatory and evolutionary implications.Frontiers in genetics · 2023Article
- The Role of Transposable Elements of the Human Genome in Neuronal Function and Pathology.International journal of molecular sciences · 2022Review
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRetrotransposons are a major component of the human genome constituting as much as 45%. The hominid specific SINE-VNTR-Alus are the youngest of these elements constituting 0.13% of the genome; they are therefore a practical and amenable group for analysis of both their global integration, polymorphic variation and their potential contribution to modulation of genome regulation.
resultsConsistent with insertion into active chromatin we have determined that SVAs are more prevalent in genic regions compared to gene deserts. The consequence of which, is that their integration has greater potential to have affects on gene regulation. The sequences of SVAs show potential for the formation of secondary structure including G-quadruplex DNA. We have shown that the human specific SVA subtypes (E-F1) show the greatest potential for forming G-quadruplexes within the central tandem repeat component in addition to the 5' 'CCCTCT' hexamer. We undertook a detailed analysis of the PARK7 SVA D, located in the promoter of the PARK7 gene (also termed DJ-1), in a HapMap cohort where we identified 2 variable number tandem repeat domains and 1 tandem repeat within this SVA with the 5' CCCTCT element being one of the variable regions. Functionally we were able to demonstrate that this SVA contains multiple regulatory elements that support reporter gene expression in vitro and further show these elements exhibit orientation dependency.
conclusionsOur data supports the hypothesis that SVAs integrate preferentially in to open chromatin where they could modify the existing transcriptional regulatory domains or alter expression patterns by a variety of mechanisms.
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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.