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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 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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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.
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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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TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets.

Ying Jin1, Oliver H Tam1, Eric Paniagua1

  • 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.

Bioinformatics (Oxford, England)
|July 25, 2015
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Summary

This study introduces a new method and software to analyze transposable element (TE) RNA-seq data. The approach improves the accurate quantification of TE transcripts, enhancing differential gene expression analysis.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Standard RNA-seq analysis software struggles with repetitive genomic regions, particularly transposable elements (TEs).
  • TEs constitute a significant portion of eukaryotic genomes (20-80%) and are often excluded from transcriptomic analyses.
  • Accurate analysis of TEs is crucial for understanding genome dynamics and gene regulation.

Purpose of the Study:

  • To develop and present a novel method and software package for incorporating ambiguously mapped reads from both genes and TEs into differential expression analysis.
  • To improve the recovery and quantification of transposable element (TE) transcripts in RNA sequencing data.

Main Methods:

  • Development of a new computational method to handle ambiguously mapped sequencing reads.
  • Implementation of the method into a user-friendly software package.
  • Validation using synthetic datasets and comparison with existing expression analysis methods.

Main Results:

  • The developed method demonstrates superior recovery of TE transcripts compared to other published approaches.
  • The software effectively includes both gene- and TE-associated ambiguously mapped reads in differential expression analysis.
  • Validation with qPCR/NanoString confirmed the improved accuracy of the method on published datasets.

Conclusions:

  • The new method and software significantly enhance the analysis of TE expression from RNA-seq data.
  • This tool provides a more comprehensive understanding of transcriptomic contributions from repetitive genomic elements.
  • The freely available software facilitates broader adoption and improved RNA-seq analyses in the research community.