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Related Concept Videos

DNA-only Transposons02:57

DNA-only Transposons

15.3K
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...
485

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qPCRTag Analysis - A High Throughput, Real Time PCR Assay for Sc2.0 Genotyping
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Transposon-Based Tagging In Silico Using FastPCR Software.

Ruslan Kalendar1,2, Dana Kospanova3, Alan H Schulman4,5

  • 1Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland. ruslan.kalendar@helsinki.fi.

Methods in Molecular Biology (Clifton, N.J.)
|April 26, 2021
PubMed
Summary
This summary is machine-generated.

Retrotransposons are valuable molecular genetic tags due to their genome-wide distribution and "copy and paste" replication. This study details in silico methods for retrotransposon fingerprinting using FastPCR software.

Keywords:
Bioinformatic genome analysisDNA fingerprintingDegenerate PCRPCR primer designRetrotransposonTransposon tagging

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Retrotransposons are mobile genetic elements found throughout eukaryotic genomes.
  • Their "copy and paste" replication mechanism creates insertional polymorphisms, making them useful as molecular genetic tags.
  • Existing tagging systems often leverage conserved retrotransposon sequences, such as Long Terminal Repeats (LTRs), and employ PCR-based methods to detect insertion polymorphisms.

Purpose of the Study:

  • To describe in silico protocols for retrotransposon-based fingerprinting.
  • To demonstrate the utility of bioinformatics approaches for predicting retrotransposon insertion outcomes.
  • To present the use of FastPCR software for in silico PCR primer design and analysis in retrotransposon fingerprinting.

Main Methods:

  • Utilizing in silico bioinformatics approaches as a complement to wet lab protocols.
  • Employing the FastPCR software as an integrated tool environment.
  • Designing and analyzing in silico PCR primers for retrotransposon fingerprinting.

Main Results:

  • Development of protocols for in silico retrotransposon-based fingerprinting.
  • Demonstration of FastPCR's capability for primer design and analysis in this context.
  • Prediction of retrotransposon insertion outcomes for unsequenced genomes based on reference genomes.

Conclusions:

  • In silico retrotransposon-based fingerprinting is a viable approach for genomic analysis.
  • FastPCR software provides an effective integrated environment for these analyses.
  • Bioinformatics tools are crucial for complementing experimental methods in studying retrotransposons.