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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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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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LTR Retrotransposons03:08

LTR Retrotransposons

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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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Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

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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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Translesion DNA Polymerases

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Translesion (TLS) polymerases rescue stalled DNA polymerases at sites of damaged bases by replacing the replicative polymerase and installing a nucleotide across the damaged site. Doing so, TLS allows additional time for the cell to repair the damage before resuming regular DNA replication.
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PASTEC: an automatic transposable element classification tool.

Claire Hoede1, Sandie Arnoux2, Mark Moisset3

  • 1INRA, UR1164 URGI - Research Unit in Genomics-Info, Versailles, France; INRA, plateforme Bio-informatique Genotoul, Mathématiques et Informatique Appliquées Toulouse UR875, Castanet-Tolosan, France.

Plos One
|May 3, 2014
PubMed
Summary
This summary is machine-generated.

PASTEC automates transposable element (TE) classification using structural features and HMM profiles, improving accuracy and accessibility for genomic research. This tool aids in understanding TE impact and classifying other repetitive elements.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Transposable element (TE) classification is crucial for understanding their genomic impact.
  • Manual inspection by experts is time-consuming and limits accessibility.
  • The increasing volume of genomic data necessitates automated classification methods.

Purpose of the Study:

  • To introduce PASTEC, a novel automated tool for transposable element (TE) classification.
  • To enhance the efficiency and accessibility of TE analysis for scientists.
  • To provide a comprehensive classification system for TEs and other repetitive elements.

Main Methods:

  • PASTEC utilizes structural features and sequence similarities for TE classification.
  • Incorporates Hidden Markov Model (HMM) profiles to infer classification based on conserved protein domains.
  • Offers an exhaustive classification spectrum up to the order level of the Wicker system.

Main Results:

  • PASTEC demonstrates superior performance compared to existing TE classification software.
  • Successfully classifies unknown TEs by identifying conserved functional domains.
  • Automatically identifies other repetitive elements like Simple Sequence Repeats (SSRs) and rDNA.

Conclusions:

  • PASTEC provides an automated, accurate, and accessible solution for TE classification.
  • Its output facilitates manual curation by presenting supporting evidence for each TE consensus.
  • Enables broader scientific access to TE analysis, advancing genomic research.