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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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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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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

18.2K
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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Transposons01:24

Transposons

320
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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Reporter Genes02:11

Reporter Genes

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Reporter genes are a type of protein-coding gene that are often tagged to a gene of interest. Once inside a target cell, reporter genes usually produce visually identifiable characteristics like fluorescence and luminescence when expressed along with the gene of interest. Thus, reporter genes “report” the presence or absence of genes of interest in an organism, determine the gene expression pattern, or track the physical location of a DNA segment or protein in the cell.
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Related Experiment Video

Updated: Oct 16, 2025

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level
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RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

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Locus-specific expression analysis of transposable elements.

Robert Schwarz1, Philipp Koch2, Jeanne Wilbrandt2

  • 1Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11, 07745 Jena, Germany.

Briefings in Bioinformatics
|October 19, 2021
PubMed
Summary
This summary is machine-generated.

Transposable elements (TEs) regulation is vital for genomic integrity. New methods enable accurate, instance-level TE expression analysis from sequencing data, overcoming previous limitations.

Keywords:
RNA sequencingdifferential expression analysissimulationtool comparisontransposable elements

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Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity
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Analysis of LINE-1 Retrotransposition at the Single Nucleus Level
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RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level
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Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity
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Analysis of LINE-1 Retrotransposition at the Single Nucleus Level
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Analysis of LINE-1 Retrotransposition at the Single Nucleus Level

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Transposable elements (TEs) play significant roles in biological functions, often detrimental.
  • Regulation of TEs, through mechanisms like DNA methylation and histone modifications, is crucial for genomic stability.
  • High-throughput studies of TEs are typically limited to family or consensus levels due to alignment challenges with similar sequences and short reads.

Purpose of the Study:

  • To assess transposable element (TE) expression at the individual instance level.
  • To determine if accurate instance-level TE expression analysis is feasible despite sequence similarities and short read lengths.
  • To adapt existing methods for analyzing differential TE expression from conventional sequencing data.

Main Methods:

  • A simulation study was conducted to evaluate the accuracy of instance-level TE expression analysis.
  • Existing bioinformatics tools, SalmonTE and Telescope, were utilized and slightly modified.
  • Analysis was performed on conventional paired-end sequencing data.

Main Results:

  • The study demonstrates that sequence similarities and short read lengths do not prevent accurate instance-level assessment of TE expression.
  • Modified existing methods successfully enabled the analysis of TE expression at the individual instance level.
  • SalmonTE and Telescope accurately tallied a significant number of TE instances, facilitating differential expression recovery.

Conclusions:

  • Instance-level analysis of transposable element (TE) expression is achievable with current sequencing technologies and modified bioinformatics tools.
  • This approach overcomes previous limitations in studying TE expression, enabling a deeper understanding of their roles.
  • The findings support the accurate recovery of differential TE expression in both model and non-model organisms.