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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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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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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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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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Updated: Sep 14, 2025

Analysis of LINE-1 Retrotransposition at the Single Nucleus Level
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Deciphering Complex Interactions Between LTR Retrotransposons and Three Papaver Species Using LTR_Stream.

Tun Xu1,2, Stephen J Bush1, Yizhuo Che1,2

  • 1School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China.

Genomics, Proteomics & Bioinformatics
|July 21, 2025
PubMed
Summary

We developed LTR_Stream for precise clustering of long terminal repeat retrotransposons (LTR-RTs) in plants. This tool reveals complex LTR-RT host genome interactions and their reduction after allopolyploidization in Papaver species.

Keywords:
PapaverHorizontal transferLTR-RT burstLTR-RT clusteringTAD-like structure

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Area of Science:

  • Genomics
  • Plant Biology
  • Molecular Evolution

Background:

  • Long terminal repeat retrotransposons (LTR-RTs) are abundant in plant genomes and understanding their interactions with host DNA is crucial.
  • High-resolution characterization of LTR-RTs is challenging, especially in non-model plant species.

Purpose of the Study:

  • To develop a novel computational tool, LTR_Stream, for precise sub-lineage clustering of LTR-RTs.
  • To investigate the complex interactions between LTR-RTs and the host genome in Papaver species using LTR_Stream.
  • To explore the impact of allopolyploidization on LTR-RT activity and host genome interactions.

Main Methods:

  • Development of LTR_Stream for high-resolution LTR-RT sub-lineage clustering.
  • Application of LTR_Stream to analyze Retand LTR-RTs in three Papaver species.
  • Comparative analysis of LTR-RTs and their genomic interactions pre- and post-allopolyploidization.

Main Results:

  • LTR_Stream provides higher precision in LTR-RT clustering compared to database-based methods.
  • Autonomous Retand elements spread across ancestral subgenomes, enhancing genetic diversity.
  • Truncated LTR-RT fragments containing transcription factor motifs (e.g., TCP, bZIP) contribute to novel topologically associating domain-like (TAD-like) boundaries.
  • Allopolyploidization in Papaver species diminished the observed LTR-RT effects, suggesting a coping mechanism.

Conclusions:

  • LTR_Stream is a valuable tool for studying LTR-RTs in non-model plant species.
  • LTR-RTs play a significant role in shaping plant genome evolution, including genetic diversity and genome architecture.
  • Allopolyploidization may serve as a strategy for plants to manage the impact of LTR-RTs.