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Related Concept Videos

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...
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...
Transposons01:24

Transposons

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...
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
LTR Retrotransposons03:08

LTR 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...
Non-LTR Retrotransposons03:18

Non-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...

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Related Experiment Video

Updated: Jun 12, 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

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery.

Fereydoun Hormozdiari1, Iman Hajirasouliha, Phuong Dao

  • 1School of Computing Science, Simon Fraser University, Burnaby, BC, Canada.

Bioinformatics (Oxford, England)
|June 10, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces a novel algorithm to detect transposon insertions, a key type of structural variant linked to human evolution and disease. The enhanced method significantly improves accuracy and performance over existing tools.

More Related Videos

Generating Transposon Insertion Libraries in Gram-Negative Bacteria for High-Throughput Sequencing
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Generating Transposon Insertion Libraries in Gram-Negative Bacteria for High-Throughput Sequencing

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Creation of a Dense Transposon Insertion Library Using Bacterial Conjugation in Enterobacterial Strains Such As Escherichia Coli or Shigella flexneri
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Creation of a Dense Transposon Insertion Library Using Bacterial Conjugation in Enterobacterial Strains Such As Escherichia Coli or Shigella flexneri

Published on: September 23, 2017

Related Experiment Videos

Last Updated: Jun 12, 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

Generating Transposon Insertion Libraries in Gram-Negative Bacteria for High-Throughput Sequencing
08:19

Generating Transposon Insertion Libraries in Gram-Negative Bacteria for High-Throughput Sequencing

Published on: July 7, 2020

Creation of a Dense Transposon Insertion Library Using Bacterial Conjugation in Enterobacterial Strains Such As Escherichia Coli or Shigella flexneri
11:36

Creation of a Dense Transposon Insertion Library Using Bacterial Conjugation in Enterobacterial Strains Such As Escherichia Coli or Shigella flexneri

Published on: September 23, 2017

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Structural variants (SVs) are increasingly studied for their role in human disease.
  • Next-generation sequencing enables large-scale SV detection, as seen in the 1000 Genomes Project.
  • Existing methods struggle to accurately identify transposon insertions, a critical SV class.

Purpose of the Study:

  • To develop a novel computational method for discovering transposon insertions in high-throughput sequencing data.
  • To improve existing SV detection algorithms by incorporating diploid genome information.
  • To enhance the accuracy and scope of structural variation analysis.

Main Methods:

  • A novel formulation for detecting both the location and type of transposon insertions.
  • Integration of 'conflict resolution' into the VariationHunter algorithm to account for diploid genomes.
  • Testing with simulated data from the Venter genome (HuRef) and real data from a Yoruba individual (NA18507).

Main Results:

  • The new algorithm successfully identifies >85% of transposon insertion events with >90% precision on simulated data.
  • The conflict resolution algorithm (VariationHunter-CR) demonstrates superior performance compared to VariationHunter, BreakDancer, and MoDIL.
  • Accurate detection of transposon insertions and improved SV discovery in diploid genomes.

Conclusions:

  • The developed algorithm provides a robust and accurate method for identifying transposon insertions.
  • VariationHunter-CR represents a significant advancement in structural variant detection, particularly for diploid genomes.
  • This work contributes to a better understanding of structural variations in human evolution and disease.