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Related Concept Videos

Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

13.6K
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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Transposons01:24

Transposons

2.3K
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

17.7K
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...
17.7K
Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

19.8K
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...
19.8K
Retroviruses02:33

Retroviruses

15.1K
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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Related Experiment Video

Updated: Mar 4, 2026

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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LTRtype, an Efficient Tool to Characterize Structurally Complex LTR Retrotransposons and Nested Insertions on

Fan-Chun Zeng1, You-Jie Zhao1, Que-Jie Zhang2,3

  • 1Institution of Genomics and Bioinformatics, South China Agricultural UniversityGuangzhou, China.

Frontiers in Plant Science
|April 20, 2017
PubMed
Summary

A new software, LTRtype, efficiently identifies complex long terminal repeat (LTR) retrotransposons and nested insertions in large genomes. This tool aids in understanding genome evolution and retrotransposon history.

Keywords:
LTR retrotransposonsLTRtypegenome evolutionnested insertionsstructural complexity

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Detection of Retrotransposition Activity of Hot LINE-1s by Long-Distance Inverse PCR
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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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RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

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Detection of Retrotransposition Activity of Hot LINE-1s by Long-Distance Inverse PCR
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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
  • Bioinformatics

Background:

  • Long terminal repeat (LTR) retrotransposons significantly influence genome size, structure, and evolution, particularly in plants.
  • Discovering the structural complexity of LTR retrotransposons and nested insertions is challenging due to vast genomic data.

Purpose of the Study:

  • To develop a novel software, LTRtype, for efficient characterization of structurally complex LTR retrotransposon elements and nested insertions.
  • To provide a tool for analyzing large-scale genomic sequences and understanding retrotransposon evolution.

Main Methods:

  • Development of a novel software tool named LTRtype.
  • Application of LTRtype for scanning and characterizing LTR retrotransposon elements in large genomic datasets.
  • Testing the software on the *Arabidopsis thaliana* genome.

Main Results:

  • LTRtype successfully identifies and characterizes five complex types of LTR retrotransposon elements.
  • The software accurately annotates numerous structurally complex elements and nested insertions.
  • Demonstrated efficiency in analyzing the *Arabidopsis thaliana* genome.

Conclusions:

  • LTRtype is an automatic and efficient tool for analyzing LTR retrotransposon structural complexity.
  • This software facilitates the reconstruction of LTR retrotransposon evolutionary history.
  • LTRtype aids in a deeper understanding of host genome evolution.