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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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Updated: Oct 7, 2025

The Zebrafish Tol2 System: A Modular and Flexible Gateway-Based Transgenesis Approach

The Zebrafish Tol2 System: A Modular and Flexible Gateway-Based Transgenesis Approach

Published on: November 30, 2022

Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental

Ni-Chen Chang¹, Quirze Rovira², Jonathan Wells¹

¹Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA.

Genome Research

|January 6, 2022

Summary

Zebrafish transposable elements (TEs) show dynamic genomic distribution and varied expression during embryogenesis. This study characterizes nearly 2000 TE families, providing a resource for understanding TE impacts on vertebrate development.

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Area of Science:

Genomics
Developmental Biology
Molecular Evolution

Background:

Transposable elements (TEs) are of significant interest for their role in embryonic development.
Mammalian studies are limited by experimental challenges and low abundance of active TEs.
Zebrafish offer a powerful model for vertebrate development, with TEs comprising over half its genome.

Purpose of the Study:

To characterize the demography, genomic distribution, and expression of zebrafish transposable elements (TEs).
To utilize bulk and single-cell RNA sequencing data for comprehensive analysis.
To establish zebrafish as a model for studying TE impact on vertebrate development.

Main Methods:

Analysis of bulk and single-cell RNA sequencing data from zebrafish embryos.
Characterization of TE demography, including copy number variation and age distribution.
Genomic mapping of TEs relative to genes and intergenic regions.
Locus-specific mapping of TE expression patterns throughout embryogenesis.

Main Results:

Identification of nearly 2000 distinct TE families with wide variations in copy number and age.
Differential genomic distribution: retroelements in intergenic regions, SINEs and DNA transposons near/within genes.
Extensive TE transcription during development, with stage- and tissue-specific patterns observed in self-regulated TEs.
Specific temporal activity: LTR retroelements post-zygotic genome activation, DNA transposons later in development.
Single-cell analysis revealed endogenous retroviruses in specific somatic cell lineages.

Conclusions:

Zebrafish possess a dynamic genomic ecosystem of transposable elements.
TEs exhibit distinct genomic localization and temporally regulated expression during embryogenesis.
This study provides a foundational resource for investigating the functional roles of TEs in vertebrate development using zebrafish.