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Related Concept Videos

Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

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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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Transposons01:24

Transposons

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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...
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DNA-only Transposons02:57

DNA-only Transposons

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

Conservative Site-specific Recombination and Phase Variation

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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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Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

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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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LTR Retrotransposons03:08

LTR Retrotransposons

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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...
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Related Experiment Video

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Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library
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Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library

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RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing.

Jinfeng Chen1, Travis R Wrightsman2, Susan R Wessler3

  • 1Department of Plant Pathology & Microbiology, University of California, Riverside, CA, United States; Institute for Integrative Genome Biology, University of California, Riverside, CA, United States; Department of Botany and Plant Sciences, University of California, Riverside, CA, United States.

Peerj
|February 3, 2017
PubMed
Summary

RelocaTE2 accurately identifies transposable element (TE) insertion sites, improving the understanding of genetic variation. This tool offers high sensitivity and specificity for analyzing TE polymorphisms in population genetics.

Keywords:
AnnotationBioinformaticsDiversityParallel processingPopulation genomicsResequencingRiceShort readTransposons

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Determination of the Optimal Chromosomal Locations for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach
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Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis
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Determination of the Optimal Chromosomal Locations for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach
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Determination of the Optimal Chromosomal Locations for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach

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Area of Science:

  • Genomics
  • Population Genetics
  • Bioinformatics

Background:

  • Transposable elements (TEs) are key drivers of genetic variation and evolution.
  • Understanding TE polymorphisms is crucial for population genetics, but their identification is challenging due to repetitive sequences.
  • Advancements in sequencing technology enable whole-genome analysis of genetic variations, including TE insertions.

Purpose of the Study:

  • To develop a sensitive and specific tool for identifying transposable element insertion sites.
  • To overcome the challenges posed by repetitive genomic regions in TE polymorphism analysis.
  • To provide a robust solution for characterizing complete genotypes by identifying TE insertion sites.

Main Methods:

  • Developed RelocaTE2, a tool for identifying TE insertion sites using whole-genome sequencing reads.
  • RelocaTE2 utilizes known TE sequences as seeds to locate transposed regions in the genome.
  • The tool detects target site duplications (TSDs) to precisely report TE polymorphism loci.

Main Results:

  • RelocaTE2 demonstrates high sensitivity and specificity, especially with adequate sequencing coverage.
  • The tool outperforms other methods in balancing sensitivity and specificity for TE insertion site identification.
  • RelocaTE2 accurately predicts TSDs and identifies up to 95% of simulated TE insertions in repetitive regions with low false positive rates.

Conclusions:

  • RelocaTE2 offers a robust solution for identifying TE insertion sites with high precision.
  • The tool is effective even in challenging, highly repetitive genomic areas.
  • RelocaTE2 can be integrated into analysis pipelines for comprehensive genotype description, including TE variations.