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Related Concept Videos

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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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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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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Phylogenetic Trees03:21

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Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
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LTR Retrotransposons03:08

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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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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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Related Experiment Video

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Preparation of Non-overlapping Transposable Elements (TEs) Annotation by Interval Tree.

Shohei Kojima1

  • 1Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan. shohei.kojima@riken.jp.

Methods in Molecular Biology (Clifton, N.J.)
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Summary

Transposable elements (TEs) generate PIWI-interacting RNAs (piRNAs). This study resolves overlapping TE annotations to improve piRNA read counting accuracy for better piRNA biology assessment.

Keywords:
Interval treeMobile genetic elementsRepeatMaskerRepetitive DNATransposon annotation

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Transposable elements (TEs) are significant sources of PIWI-interacting RNAs (piRNAs).
  • Accurate piRNA biology studies require precise mapping of sequencing reads to their originating TEs.
  • Existing TE annotations often have overlapping features, complicating read assignment and potentially excluding valuable data during analysis.

Purpose of the Study:

  • To develop a method for resolving overlapping transposable element (TE) annotations.
  • To generate non-overlapping TE annotations for improved PIWI-interacting RNA (piRNA) read counting.
  • To provide scripts for efficient and accurate TE annotation processing.

Main Methods:

  • A computationally efficient tree algorithm is utilized to resolve overlapping regions within TE annotations.
  • The algorithm assigns overlapping regions to a single, best representative TE feature.
  • The resulting non-overlapping annotations are compatible with standard read counting software.

Main Results:

  • A novel method effectively resolves overlapping TE annotations.
  • Generated non-overlapping TE annotations facilitate accurate piRNA read abundance calculations.
  • The provided scripts enable straightforward implementation of the annotation refinement process.

Conclusions:

  • Resolving TE annotation overlaps is crucial for accurate piRNA quantification.
  • The developed tree algorithm provides an efficient solution for creating non-overlapping TE annotations.
  • This approach enhances the reliability of piRNA biology research by improving data analysis pipelines.