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Related Concept Videos

Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

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...
DNA-only Transposons02:57

DNA-only Transposons

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...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
LTR Retrotransposons03:08

LTR Retrotransposons

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...
Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

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...
Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.

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Related Experiment Video

Updated: May 24, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
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Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

Roadmap for annotating transposable elements in eukaryote genomes.

Emmanuelle Permal1, Timothée Flutre, Hadi Quesneville

  • 1Unité de Recherches en Génomique Info - URGI (UR1164) - INRA - Centre de Versailles, Versailles cedex, France.

Methods in Molecular Biology (Clifton, N.J.)
|February 28, 2012
PubMed
Summary
This summary is machine-generated.

Annotating transposable elements (TEs) is a genome analysis bottleneck. This guide offers a roadmap using combined de novo and knowledge-based methods for comprehensive TE identification and annotation in genome projects.

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Use of Alu Element Containing Minigenes to Analyze Circular RNAs
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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • High-throughput sequencing enables genome analysis of non-model organisms.
  • Transposable element (TE) annotation is a critical bottleneck in genome analysis.
  • Current methods for TE detection require optimization for comprehensive results.

Purpose of the Study:

  • To provide a roadmap for efficient transposable element (TE) annotation in genome projects.
  • To outline tools and best practices for TE identification and copy annotation.
  • To address the bottleneck in genome analysis caused by TE annotation.

Main Methods:

  • Utilizing combined de novo and knowledge-based approaches for TE detection.
  • Implementing a step-by-step process for TE annotation, from family identification to copy annotation.
  • Leveraging a curated set of bioinformatics tools and established good practices.

Main Results:

  • The proposed combined approach enhances the comprehensiveness and sensitivity of TE detection.
  • A clear roadmap facilitates researchers in navigating the complexities of TE annotation.
  • Efficient annotation of TE families and copies is achievable through systematic methodology.

Conclusions:

  • Combined de novo and knowledge-based methods are effective for comprehensive TE annotation.
  • A structured approach with appropriate tools and practices is essential for overcoming annotation bottlenecks.
  • This roadmap empowers researchers to successfully annotate transposable elements in diverse genomes.