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LTR Retrotransposons

LTR Retrotransposons

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.
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...

Non-LTR Retrotransposons

Non-LTR Retrotransposons

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...

Retroviruses

Retroviruses

Retroviruses and retrotransposons both insert copies of their genetic elements into the genome of the host cell. Thus, the viral genes are passed on when the host genome is replicated or translated. A typical retroviral DNA sequence contains 3-4 genes that encode the different proteins required for its structural assembly and function as a molecular parasite. This DNA is transcribed into a single mRNA, which is very similar in structure to conventional mRNAs, i.e., it is capped at the 5’...

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...

DNA-only Transposons

DNA-only Transposons

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.
The donor site from where the transposon is excised is either degraded or...

Conservative Site-specific Recombination and Phase Variation

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...

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Related Experiment Video

Updated: Jun 11, 2026

Analysis of LINE-1 Retrotransposition at the Single Nucleus Level

Analysis of LINE-1 Retrotransposition at the Single Nucleus Level

Published on: April 23, 2016

Retroposon insertions provide insights into deep lagomorph evolution.

Jan Ole Kriegs, Anja Zemann, Gennady Churakov

Molecular Biology and Evolution

|June 30, 2010

Summary

Phylogenetic relationships in rabbits and hares (Leporidae) were clarified using retroposon insertion sites. This method resolved controversies, supporting nuclear gene data over misleading mitochondrial signals.

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Last Updated: Jun 11, 2026

Analysis of LINE-1 Retrotransposition at the Single Nucleus Level

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Published on: April 23, 2016

Detection of Retrotransposition Activity of Hot LINE-1s by Long-Distance Inverse PCR

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In vivo Application of the REMOTE-control System for the Manipulation of Endogenous Gene Expression

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Area of Science:

Genomics
Molecular Evolution
Phylogenetics

Background:

The mammalian order Lagomorpha, including rabbits and hares (Leporidae), has controversial phylogenetic relationships.
Mitochondrial DNA sequences often yield homoplasious signals, complicating evolutionary analyses.

Discussion:

Genomic orthologous retroposon insertion sites, a nearly homoplasy-free marker, were utilized to resolve phylogenetic disputes.
Analysis of 11 retroposons in eight lagomorphs provided robust evolutionary insights.

Key Insights:

Three retroposons confirmed the monophyly of Leporidae.
Three retroposons supported *Pronolagus* as the sister group to other leporids.
One retroposon supported the monophyly of *Lepus*.

Outlook:

Retroposon insertion site analysis offers a reliable method for resolving deep phylogenetic relationships.
This study refutes misleading mitochondrial data, establishing a clearer evolutionary framework for lagomorphs.