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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

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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

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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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RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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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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Updated: Mar 1, 2026

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Identifying transposon insertions and their effects from RNA-sequencing data.

Julian R de Ruiter1,2, Sjors M Kas1, Eva Schut1

  • 1Division of Molecular Pathology and Cancer Genomics Netherlands, Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands.

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Summary

IM-Fusion accurately identifies transposon insertion sites and their target genes using RNA-sequencing data. This method enhances cancer gene discovery by revealing how insertions affect gene expression in mouse models.

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Area of Science:

  • Genomics
  • Cancer Biology
  • Molecular Genetics

Background:

  • Insertional mutagenesis with engineered transposons is a key method for identifying cancer genes in mouse models.
  • Current analysis relies on DNA sequencing and heuristics, lacking direct evidence of target gene impact or transcript alteration.
  • This limits the understanding of how transposon insertions affect gene function in cancer development.

Purpose of the Study:

  • To develop IM-Fusion, a novel approach for identifying transposon insertion sites from gene-transposon fusions in RNA-sequencing data.
  • To accurately identify transposon insertions and their true target genes in complex biological samples.
  • To determine the effect of transposon insertions on target gene expression and prioritize significant alterations.

Main Methods:

  • Developed IM-Fusion, an analysis method utilizing standard single- and paired-end RNA-sequencing data.
  • Applied IM-Fusion to transposon screens from 123 mammary tumors and 20 B-cell acute lymphoblastic leukemias.
  • Integrated insertion site identification with gene expression quantification.

Main Results:

  • IM-Fusion accurately identified transposon insertions and their cognate target genes across diverse cancer types.
  • The method successfully linked specific insertions to significant alterations in target gene expression levels.
  • Prioritization of insertions based on expression impact was achieved, highlighting functionally relevant events.

Conclusions:

  • IM-Fusion significantly enhances the accuracy of cancer gene discovery in forward genetic screens.
  • The approach provides direct insight into the biological effects of transposon insertions on candidate cancer genes.
  • IM-Fusion is expected to improve the identification and validation of genes driving cancer development.