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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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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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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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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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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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ClassifyTE: a stacking-based prediction of hierarchical classification of transposable elements.

Manisha Panta1, Avdesh Mishra2, Md Tamjidul Hoque1

  • 1Department of Computer Science, University of New Orleans, New Orleans, LA 70148, USA.

Bioinformatics (Oxford, England)
|March 8, 2021
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Summary

Transposable Elements (TEs) are jumping genes that can alter gene expression and cause mutations. A new machine learning tool, ClassifyTE, accurately classifies TEs hierarchically, improving analysis of their evolutionary roles.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Transposable Elements (TEs), or jumping genes, are mobile DNA sequences influencing genome evolution.
  • TEs can alter gene expression, increase mutation rates, and mediate large-scale genetic rearrangements.
  • Accurate classification of TEs is crucial for understanding their impact on germline and somatic evolution.

Purpose of the Study:

  • To develop an accurate and robust method for the hierarchical classification of Transposable Elements.
  • To evaluate the performance of various machine learning techniques for TE classification.
  • To provide an automated tool for classifying TEs up to the super-family level.

Main Methods:

  • A stacking-based machine learning (ML) approach was employed for hierarchical TE classification.
  • The proposed method, ClassifyTE, was trained and validated on multiple benchmark datasets.
  • Performance was compared against existing state-of-the-art TE classification methods.

Main Results:

  • The ClassifyTE system demonstrated superior performance, achieving significant average percentage improvements in hF measure across datasets.
  • An automated, end-to-end hierarchical classification tool, ClassifyTE, was developed.
  • High concordance was observed when evaluating ClassifyTE on a novel TE library, validating its accuracy at higher taxonomic levels.

Conclusions:

  • ClassifyTE offers a highly accurate and automated solution for hierarchical TE classification.
  • The tool facilitates a more precise analysis of the genetic and evolutionary roles of Transposable Elements.
  • This advancement aids researchers in understanding genome dynamics and evolution driven by TEs.