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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...
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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.
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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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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...
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.
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Cis-regulatory Sequences02:02

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

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Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity
04:04

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Published on: January 20, 2023

TEnest 2.0: computational annotation and visualization of nested transposable elements.

Brent A Kronmiller1, Roger P Wise

  • 1Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|August 7, 2013
PubMed
Summary
This summary is machine-generated.

Transposable elements (TEs) complicate grass genome assembly and annotation. TEnest v2.0 computationally annotates nested TEs, displaying their chronological structure to improve genomic accuracy.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Grass genomes contain complex, repetitive sequences, primarily transposable elements (TEs).
  • Abundant TEs, especially Long Terminal Repeat (LTR) retrotransposons, pose significant challenges for genome sequencing, assembly, and gene annotation.
  • TEs can contain ancient protein-encoding genes that may interfere with gene identification if not properly masked.

Purpose of the Study:

  • To present TEnest v2.0, a computational tool for annotating and visualizing nested transposable elements in grass genomes.
  • To address the challenges TEs present in accurate genome assembly and gene annotation.
  • To provide a method for reconstructing degraded TEs to their ancestral state using organism-specific databases.

Main Methods:

  • Utilized iterative sequence alignment for repeat annotation.
  • Employed organism-specific TE databases to reconstruct degraded TEs.
  • Developed TEnest v2.0 for computational annotation and chronological display of nested TEs.
  • Generated graphical output illustrating the chronological nesting structure and insertion positions of TEs.

Main Results:

  • TEnest v2.0 successfully annotates nested transposable elements.
  • The software provides a chronological display of TE insertions, revealing their nesting structures.
  • The tool aids in distinguishing ancient TE remnants from functional genes, improving gene annotation accuracy.
  • Graphical output visualizes the complexity and history of TE insertions within grass genomes.

Conclusions:

  • Accurate genome assembly and annotation are critical for understanding grass genetics.
  • TEnest v2.0 offers a robust solution for analyzing complex TE landscapes in grass genomes.
  • The tool enhances the accuracy of gene identification by correctly masking repetitive elements.
  • TEnest v2.0 is available as both a Linux command-line and a web version for broader accessibility.