Related Experiment Video
Updated: May 9, 2026
04:04
Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity
Published on: January 20, 2023
Evolutionary active transposable elements in the genome of the coelacanth
Domitille Chalopin1, Shaohua Fan, Oleg Simakov
1Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Lyon 1, Lyon, France.
Summary
The coelacanth genome, often deemed a "living fossil," shows significant transposable element (TE) activity, challenging theories of slow genomic evolution. These mobile genetic elements are expressed and have shaped the coelacanth lineage.
Area of Science:
- Genomics
- Evolutionary Biology
- Molecular Biology
Background:
- The coelacanth, a
Purpose of the Study:
- To investigate the activity and abundance of transposable elements (TEs) in the coelacanth genome.
- To assess whether TE activity supports or refutes the hypothesis of slow genomic evolution in coelacanths.
Main Methods:
- Genome-wide analysis of transposable elements in the African coelacanth.
- Identification and quantification of different TE classes, including retrotransposons and DNA transposons.
- Expression analysis of TEs in various coelacanth tissues.
Main Results:
- Transposable elements constitute at least 25% of the coelacanth genome, with non-Long Terminal Repeat (non-LTR) retrotransposons predominating.
- Four major transposition bursts shaped the genome, driven by LINE1, LINE2, CR1, and Deu elements.
- Many TEs are expressed across tissues, indicating potential activity, and the number of TE families is higher than in birds and mammals.
Conclusions:
- The coelacanth genome exhibits substantial transposable element activity, contrary to the notion of slow genomic evolution.
- TEs have played a significant role in shaping the coelacanth lineage.
- The genomic evolution of coelacanths, at least concerning TE activity, does not appear to be particularly slow.
Related Concept Videos
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...
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...
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...
02:02Cis-regulatory Sequences
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
02:02Cis-regulatory Sequences
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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...