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Related Concept Videos

Overview of Transposition and Recombination02:13

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...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
DNA-only Transposons02:57

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...
Cis-regulatory Sequences02:02

Cis-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...
Cis-regulatory Sequences02:02

Cis-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...
Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.

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Related Experiment Video

Updated: Jun 4, 2026

Determination of the Optimal Chromosomal Location(s) for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach
11:12

Determination of the Optimal Chromosomal Location(s) for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach

Published on: September 11, 2017

Considering transposable element diversification in de novo annotation approaches.

Timothée Flutre1, Elodie Duprat, Catherine Feuillet

  • 1Unité de Recherche en Génomique-Info, UR 1164, INRA Centre de Versailles-Grignon, Versailles, France.

Plos One
|February 10, 2011
PubMed
Summary

Transposable elements (TEs) are mobile DNA sequences impacting genomes. A new pipeline accurately annotates TE families and studies their diversification, improving genome-wide analysis.

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Novel Sequence Discovery by Subtractive Genomics
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Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity
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Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity

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Last Updated: Jun 4, 2026

Determination of the Optimal Chromosomal Location(s) for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach
11:12

Determination of the Optimal Chromosomal Location(s) for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach

Published on: September 11, 2017

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity
04:04

Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity

Published on: January 20, 2023

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Transposable elements (TEs) are mobile DNA sequences crucial for genome evolution.
  • High-throughput sequencing enables large-scale comparative studies of TE dynamics.
  • Existing de novo TE identification methods vary in their TE family definition steps.

Purpose of the Study:

  • To benchmark algorithms for de novo identification of transposable elements.
  • To develop a robust pipeline for TE family annotation and diversification analysis.
  • To improve the understanding of TE dynamics across diverse species.

Main Methods:

  • Comparative analysis of algorithms for interspersed repeat clustering.
  • Development of a novel procedure for reconciling clustering results and classifying TE sequences.
  • Implementation of an integrated pipeline using the REPET package.

Main Results:

  • A specific combination of clustering algorithms demonstrated high recovery of reference TE families.
  • The developed pipeline successfully annotated TE families and identified structural variations.
  • The approach facilitates simultaneous analysis of TE annotation and diversification.

Conclusions:

  • The combined approach provides accurate de novo identification and annotation of TE families.
  • This method enhances the study of TE dynamics and structural variations at a whole-genome scale.
  • The pipeline is applicable to diverse species, advancing comparative genomics research.