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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.
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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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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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Transposable element finder (TEF): finding active transposable elements from next generation sequencing data.

Akio Miyao1, Utako Yamanouchi2

  • 1Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2, Kannondai, Tsukuba, Ibaraki, 305-8518, Japan. miyao@affrc.go.jp.

BMC Bioinformatics
|November 24, 2022
PubMed
Summary

A new algorithm, Transposable Element Finder (TEF), detects transposable element (TE) transpositions, even for unknown TE sequences. This method identifies new TE insertions and their locations, overcoming limitations of previous tools.

Keywords:
Next generation sequenceRetrotransposonTarget site duplicationTos17Transposable element

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Detecting transposable element (TE) transposition events in next-generation sequencing (NGS) data is challenging due to numerous existing TE copies.
  • Previous tools like Transposon Insertion Finder (TIF) require known TE sequences, limiting their application.

Purpose of the Study:

  • To develop a novel algorithm, Transposable Element Finder (TEF), for detecting TE transpositions, including those with unknown sequences.
  • To identify both ends and target site duplications (TSDs) associated with TE transposition events.

Main Methods:

  • Developed TEF, employing two algorithms: one grouping TSDs and comparing k-mers from NGS data, and another using junction mapping of TE end sequence candidates.
  • Validated methods on rice, Arabidopsis, and Drosophila datasets, comparing NGS data between samples.

Main Results:

  • TEF successfully detected both ends and TSDs of known active TEs across multiple species.
  • Identified several novel TE insertions in new genomic locations.
  • PCR confirmed transposition events in rice samples.

Conclusions:

  • TEF effectively detects transposed TEs, their TSDs, sequences, and insertion positions by comparing NGS data.
  • The algorithm's genotype verification and independence from TE libraries make it valuable for discovering unknown TEs.
  • TEF offers a user-friendly solution for identifying TE insertions missed by standard annotation pipelines.