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Overview of Transposition and Recombination

Overview of Transposition and Recombination

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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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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Transposons

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Related Experiment Video

Updated: May 16, 2026

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

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RetroSeq: transposable element discovery from next-generation sequencing data.

Thomas M Keane¹, Kim Wong, David J Adams

¹Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK. tk2@sanger.ac.uk

Bioinformatics (Oxford, England)

|December 13, 2012

Summary

This summary is machine-generated.

We developed RetroSeq, a tool for identifying transposable element (TE) insertions in genomes using whole-genome sequencing. Our method accurately detects these mobile DNA sequences, crucial for understanding genome evolution.

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Transposable elements (TEs) comprise a substantial portion of eukaryote genomes.
TEs influence gene function and genome evolution.
Detecting non-reference TE insertions is vital for comprehensive genomic analysis.

Purpose of the Study:

To introduce RetroSeq, a novel computational tool.
To enable the detection of non-reference transposable element insertions.
To leverage Illumina paired-end whole-genome sequencing data for TE discovery.

Main Methods:

Development of the RetroSeq algorithm.
Application of RetroSeq to Illumina paired-end whole-genome sequencing data.
Evaluation using a human trio dataset from the 1000 Genomes Project.

Main Results:

RetroSeq successfully identifies non-reference transposable element insertions.
The tool demonstrates high accuracy in TE calling.
Validation performed on a well-characterized human genomic dataset.

Conclusions:

RetroSeq is an effective tool for detecting TE insertions.
The findings highlight the utility of RetroSeq in genomic research.
Accurate TE detection facilitates studies on genome evolution and function.