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Related Concept Videos

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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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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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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Retroviruses02:33

Retroviruses

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Retroviruses and retrotransposons both insert copies of their genetic elements into the genome of the host cell. Thus, the viral genes are passed on when the host genome is replicated or translated. A typical retroviral DNA sequence contains 3-4 genes that encode the different proteins required for its structural assembly and function as a molecular parasite. This DNA is transcribed into a single mRNA, which is very similar in structure to conventional mRNAs, i.e., it is capped at the 5’...
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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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Transposons01:24

Transposons

2.6K
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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Related Experiment Video

Updated: Mar 9, 2026

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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Simulation-based estimation of branching models for LTR retrotransposons.

Serge Moulin1, Nicolas Seux2, Stéphane Chrétien3

  • 1Département d'Informatique des Systèmes Complexes, FEMTO-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, Besançon, France.

Bioinformatics (Oxford, England)
|December 25, 2016
PubMed
Summary

We developed a branching model to study LTR retrotransposon propagation in genomes, considering copy position and degradation. This model allows duplication rates to vary with degradation levels, aiding in understanding transposable element dynamics.

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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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Area of Science:

  • Genomics
  • Molecular Biology
  • Computational Biology

Background:

  • LTR retrotransposons are mobile genetic elements capable of replicating and integrating within eukaryotic genomes.
  • Understanding their propagation dynamics is crucial for comprehending genome evolution and stability.

Purpose of the Study:

  • To propose a novel branching model for simulating LTR retrotransposon propagation.
  • To incorporate the influence of copy position and degradation levels on retrotransposon spread.
  • To develop a method for parameter estimation within this propagation model.

Main Methods:

  • Development of a branching model accounting for LTR retrotransposon positions and degradation.
  • Implementation of simulation functions and visualization tools.
  • Creation of a parameter estimation method using simulation outputs.

Main Results:

  • The model successfully simulates LTR retrotransposon spread, considering copy position and degradation.
  • A method for evaluating propagation model parameters was developed and applied.
  • The spread of ROO, GYPSY, and DM412 elements in Drosophila melanogaster was studied using the model.

Conclusions:

  • The proposed branching model provides a framework for studying LTR retrotransposon dynamics.
  • The developed methods enable parameter estimation and application to specific transposable elements.
  • This work contributes to understanding the complex behavior of mobile elements in eukaryotic genomes.