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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...
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...
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...
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...
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...
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...

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Related Experiment Video

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Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity
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An automated homology-based approach for identifying transposable elements.

Ryan C Kennedy1, Maria F Unger, Scott Christley

  • 1Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, USA. Ryan.C.Kennedy@alumni.nd.edu

BMC Bioinformatics
|May 4, 2011
PubMed
Summary

We developed TESeeker, an automated homology-based method for identifying transposable elements (TEs) in genomes. This approach successfully identifies high-quality consensus TEs, aiding genome analysis projects.

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Published on: May 19, 2019

Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Transposable elements (TEs) are mobile genetic sequences crucial for genome evolution and gene expression.
  • Accurate identification of TEs is essential for genome projects, but automated methods face challenges due to TE degradation and structural variability.

Purpose of the Study:

  • To develop an automated, homology-based approach for identifying high-quality consensus transposable elements (TEs) in newly sequenced eukaryotic genomes.
  • To create a robust and modular tool for efficient TE detection in large-scale genomic analyses.

Main Methods:

  • A homology-based strategy utilizing a comprehensive library of representative TEs.
  • Implementation via TESeeker, a BLAST-based system incorporating CAP3 assembly, ClustalW2 alignment, and BioPerl scripts.
  • Application to newly sequenced genomes for consensus TE identification.

Main Results:

  • Successful automatic identification of consensus TEs with up to 99% identity to manually annotated sequences.
  • Demonstrated effectiveness in analyzing newly sequenced genomes.
  • Developed a modular system adaptable for various research needs.

Conclusions:

  • Automated TE identification remains an evolving field, with a need for high-quality homology-based approaches.
  • TESeeker provides an automated solution for generating high-quality consensus TE sequences with minimal user input.
  • The TESeeker tool and TE library are available as downloadable resources for the research community.