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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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LTR retrotransposons are class I transposable elements with long terminal repeats flanking an internal coding region. These elements are less abundant in mammals compared to other class I transposable elements. About 8 percent of human genomic DNA comprises LTR retrotransposons. Some of the common examples of LTR retrotransposons are Ty elements in yeast and Copia elements in Drosophila.
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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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Related Experiment Video

Updated: Feb 22, 2026

Detection of Retrotransposition Activity of Hot LINE-1s by Long-Distance Inverse PCR
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Population-wide sampling of retrotransposon insertion polymorphisms using deep sequencing and efficient detection.

Qichao Yu1,2, Wei Zhang1,2, Xiaolong Zhang2

  • 1BGI Education Center, UCAS: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.

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|September 24, 2017
PubMed
Summary

This study introduces Specific Insertions Detector (SID), a tool to identify novel human retrotransposon insertion polymorphisms (RIPs). A large dataset of 9342 RIPs, including 8433 new ones, was generated, aiding evolutionary and disease research.

Keywords:
next-generation sequencingretrotransposon insertion polymorphismtransposable elementwhole-genome sequencing

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Area of Science:

  • Genomics
  • Population Genetics
  • Bioinformatics

Background:

  • Active retrotransposons contribute to genetic diversity and disease through polymorphisms.
  • Population-level studies of human retrotransposon insertion polymorphisms (RIPs) are crucial but underexplored.

Purpose of the Study:

  • To develop and validate a computational tool (SID) for detecting non-reference RIPs.
  • To construct a comprehensive RIP database from a large Han Chinese population.
  • To analyze the evolutionary implications and potential applications of RIPs.

Main Methods:

  • Development of the Specific Insertions Detector (SID) tool.
  • Whole-genome deep sequencing of 90 Han Chinese individuals (mean ×68 depth).
  • Comparison of identified RIPs with existing databases (e.g., dbRIP).

Main Results:

  • SID efficiently detects non-reference RIPs in high-depth sequencing data.
  • A novel dataset of 9342 recent RIPs was generated, with 8433 being previously undocumented.
  • Identified RIPs include Alu, L1, SVA, and LTR elements, with some located in gene and protein-coding regions.
  • Analysis revealed weak negative selection on SVA/L1 and neutral selection on Alu elements.

Conclusions:

  • SID is a powerful tool for identifying non-reference RIPs.
  • The generated RIP dataset significantly expands knowledge of human genomic diversity.
  • RIPs hold potential as biomarkers for population evolution, phylogenetic analysis, and disease research.