Related Experiment Video
Updated: Jul 15, 2026
11:52
Analysis of LINE-1 Retrotransposition at the Single Nucleus Level
Published on: April 23, 2016
Retrotransposons influence the mouse transcriptome: implication for the divergence of genetic traits
Kyoji Horie1, Ei-Suke Saito, Vincent W Keng
1Research Center for Radiation Emergency Medicine, National Institute of Radiological Sciences, Inage-ku, Chiba 263-8555, Japan. horie@mr-envi.med.osaka-u.ac.jp
Genetics
|April 17, 2007
Summary
Retrotransposons, like Intracisternal A-particle (IAP) elements, can mobilize and alter the mouse transcriptome. This retrotransposon activity drives gene expression and contributes to strain-specific genomic traits.
Area of Science:
- Genomics
- Molecular Biology
- Evolutionary Biology
Background:
- Retrotransposons constitute a significant portion of mammalian genomes, yet their functional roles are often obscured by loss of retrotransposition competency.
- Intracisternal A-particle (IAP) elements, a type of long terminal repeat (LTR) retrotransposon in mice, offer a model system to study retrotransposon-genome interactions due to their potential for mobilization.
Purpose of the Study:
- To investigate whether retrotransposon mobilization, using IAP elements as a model, impacts the mammalian transcriptome.
- To characterize the retrotransposition competency and transcriptional activity of specific IAP elements.
- To explore the contribution of IAP-driven transcription to genetic variation between mouse strains.
Main Methods:
- Retrotransposition assays were performed in cultured cells to assess the mobility of internally deleted IAP elements.
- Transcriptional activity of IAP elements in flanking genomic regions was evaluated.
- Genome-wide transcript analysis was conducted on mouse embryonic stem (ES) cells to identify IAP-induced transcripts and fusion transcripts.
Main Results:
- A subset of internally deleted IAP elements, termed IDelta1, demonstrated efficient retrotransposition when provided with functional IAP proteins.
- The IDelta1 type IAP element exhibited significant transcription-inducing activity in adjacent genomic regions.
- Genome-wide analysis revealed IAP-induced transcripts, including chimeric transcripts formed between IAP sequences and host genes.
- Nearly half of the IAP elements identified in 129 mouse strain ES cells were absent in the C57BL/6 genome, indicating strain-specific retrotransposon presence.
Conclusions:
- Mobilization of retrotransposons, specifically IAP elements, demonstrably alters the mouse transcriptome.
- IAP elements can act as potent transcriptional activators, influencing gene expression in their vicinity.
- Retrotransposon-driven transcription contributes to the genetic diversity observed between mammalian strains, suggesting retrotransposons are key drivers of transcriptome evolution.
Related Concept Videos
03:18Non-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...
02:13Overview 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...
01:24Transposons
Transposons, or "jumping genes," are small mobile genetic elements (MGEs) that range from 700 to 40,000 base pairs in length. They are found in all organisms and can move within the same chromosome or transfer to different chromosomes. In some cases, transposons can also jump between different host DNA molecules, such as plasmids or viruses, contributing to genetic variability.Barbara McClintock first discovered these mobile genetic elements in the 1940s while studying maize genetics, and she...
03:08LTR 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...
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...
02:57DNA-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...
The donor site from where the transposon is excised is either degraded or...
02:32Exon Recombination
The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes.
Exon shuffling follows “splice frame rules.” Each exon has three reading...
Exon shuffling follows “splice frame rules.” Each exon has three reading...