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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
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Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...
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DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
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Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
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Structural and transduction patterns of human-specific polymorphic SVA insertions.

Ashley E Kirby1,2, Mark Loftus1,2, Emily C Golba1

  • 1Department of Genetics and Biochemistry, College of Science, Clemson University, Clemson, South Carolina, USA.

Mobile DNA
|November 6, 2025
PubMed
Summary
This summary is machine-generated.

SINE variable number tandem repeat Alu elements (SVAs), particularly the SVA_F1 subfamily, are actively expanding in the human genome. These elements drive significant transduction events, mobilizing gene sequences and contributing to genetic diversity.

Keywords:
Genetic variationHuman specificMobile element insertionPolymorphismRetrotransposonSVASource elementStructural variationSubfamilyTransductionTransposable element

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Area of Science:

  • Genomics
  • Molecular Biology
  • Human Evolution

Background:

  • SINE variable number tandem repeat Alu elements (SVAs) are hominid-specific retrotransposons contributing to human genetic diversity, evolution, and disease.
  • Recent studies suggest higher SVA mobilization rates and insertion polymorphism than previously estimated.
  • SVAs can mobilize adjacent sequences via transduction (TD) events.

Purpose of the Study:

  • To investigate features of non-reference SVA elements polymorphic in the human genome.
  • To analyze the contribution of different SVA subfamilies to human genomic expansion.
  • To characterize transduction events associated with SVA elements.

Main Methods:

  • Analysis of a structural variant callset from 35 diverse human genomes.
  • Identification and classification of polymorphic, non-reference SVA insertions.
  • Characterization of sequences mobilized via transduction events.

Main Results:

  • SVA_F1 subfamily is a major contributor (55% of analyzed elements) to SVA expansion.
  • 40% of non-reference SVAs exhibit transduction (TD) events, mobilizing adjacent sequences, including exonic regions.
  • Identified 55 active source elements responsible for 84% of TD-carrying SVAs.

Conclusions:

  • SVA_F1 is a more active driver of SVA expansion than previously recognized.
  • TD events are more frequent (two-fold increase) than estimated, with a bias towards 3' events.
  • Discrepant SVA mobilization rates may stem from inter-individual variation, recent mobilization, or selection pressures.