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Related Concept Videos

Transposons01:24

Transposons

242
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...
242
DNA-only Transposons02:57

DNA-only Transposons

14.9K
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...
14.9K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

19.5K
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.
19.5K
Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

16.3K
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...
16.3K
Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

12.0K
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...
12.0K
LTR Retrotransposons03:08

LTR Retrotransposons

18.0K
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...
18.0K

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Updated: Oct 1, 2025

Identification of Sleeping Beauty Transposon Insertions in Solid Tumors using Linker-mediated PCR
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Identification of Sleeping Beauty Transposon Insertions in Solid Tumors using Linker-mediated PCR

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TransposonUltimate: software for transposon classification, annotation and detection.

Kevin Riehl1, Cristian Riccio1,2, Eric A Miska1,2,3

  • 1Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK.

Nucleic Acids Research
|March 2, 2022
PubMed
Summary
This summary is machine-generated.

TransposonUltimate offers a unified solution for identifying and analyzing transposons, crucial genetic elements involved in evolution and disease. This powerful toolset enhances genomic research by providing standardized classification, annotation, and detection of transposition events.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Evolution

Background:

  • Transposons are mobile genetic elements abundant in genomes, influencing evolution and gene regulation.
  • Transposon activity is linked to various diseases, including cancer and neurodegeneration, making their study clinically relevant.
  • Existing transposon identification methods lack standardization in taxonomy and output formats, hindering comprehensive analysis.

Purpose of the Study:

  • To develop a comprehensive and standardized bioinformatics tool for transposon analysis.
  • To provide modules for transposon classification, annotation, and detection of transposition events.
  • To benchmark the performance of the classification module against existing solutions.

Main Methods:

  • Developed TransposonUltimate, a bundle of three modules: classification, annotation, and detection.
  • Utilized TransposonDB for benchmarking the classification module.
  • Integrated sixteen existing software tools for annotation and detection functionalities.
  • Applied the detection module to identify transposition events in Caenorhabditis elegans genomes.

Main Results:

  • The classification module demonstrated superior performance compared to existing methods on the TransposonDB dataset.
  • Successfully annotated genomes of Caenorhabditis elegans, Rhizophagus irregularis, and Oryza sativa.
  • Discovered 29,554 transposition events in 20 wild type strains of C. elegans.

Conclusions:

  • TransposonUltimate provides a powerful, unified, and standardized platform for transposon research.
  • The toolset facilitates accurate classification, annotation, and detection of transposons and their activity.
  • This resource aids in understanding the role of transposons in genome evolution and disease.