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Related Concept Videos

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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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

1.0K
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...
1.0K
LTR Retrotransposons03:08

LTR Retrotransposons

19.3K
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

Updated: Dec 28, 2025

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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Human transposon insertion profiling by sequencing (TIPseq) to map LINE-1 insertions in single cells.

Wilson McKerrow1, Zuojian Tang1, Jared P Steranka2

  • 1Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, USA.

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
|February 21, 2020
PubMed
Summary

Researchers developed a single-cell method to map Long Interspersed Element-1 (LINE-1) insertions. This technique overcomes previous barriers, enabling detailed studies of genetic diseases and cancer heterogeneity at the cellular level.

Keywords:
TIPseqmobile genetic elementretrotransposonsomatic mosaicismtumour heterogeneitywhole-genome amplification

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

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Area of Science:

  • Genomics
  • Molecular Biology
  • Epigenetics

Background:

  • Long Interspersed Element-1 (LINE-1) sequences constitute a significant portion of the human genome and are highly active mobile elements.
  • LINE-1 insertions are implicated in genetic diseases and are overexpressed in certain cancers.
  • Genome-wide LINE-1 mapping in single cells is crucial for understanding somatic and germline retrotransposition, tumor heterogeneity, and cellular development.

Purpose of the Study:

  • To optimize and validate a modified transposon insertion profiling by sequencing (TIPseq) protocol for LINE-1 mapping in single cells.
  • To address challenges associated with LINE-1 mapping in single cells, such as chimeric artifacts and repetitive sequence features.

Main Methods:

  • Optimization of a modified TIPseq protocol for single-cell analysis.
  • Utilizing whole-genome amplification via multiple displacement amplification.
  • Employing restriction enzyme digestion, vectorette ligation, and LINE-1-targeted PCR.

Main Results:

  • The optimized single-cell TIPseq protocol demonstrated utility for LINE-1 insertion site mapping in lymphoblastoid cells.
  • Results from single-cell TIPseq experiments showed good correlation with established LINE-1 insertion data from whole-genome sequencing and bulk TIPseq.
  • The selected method, involving multiple displacement amplification and subsequent molecular steps, exhibited superior assay performance.

Conclusions:

  • The developed single-cell TIPseq method provides a robust tool for high-resolution LINE-1 insertion analysis.
  • This advancement facilitates detailed studies on the role of LINE-1 in genetic variation, disease pathogenesis, and cellular evolution.
  • The findings pave the way for deeper investigations into the impact of LINE-1 retrotransposition across various biological contexts.