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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

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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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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

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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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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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Evolutionary Relationships through Genome Comparisons

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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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Related Experiment Video

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Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity
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BLAT-based comparative analysis for transposable elements: BLATCAT.

Sangbum Lee1, Sumin Oh2, Keunsoo Kang3

  • 1Department of Computer Science, Dankook University, Cheonan 330-714, Republic of Korea.

Biomed Research International
|June 25, 2014
PubMed
Summary
This summary is machine-generated.

We developed BLATCAT, a new program for comparing transposable elements (TEs) across primate genomes. This tool facilitates efficient analysis of TEs, which significantly impact genome structure and gene regulation.

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Analysis of LINE-1 Retrotransposition at the Single Nucleus Level
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Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Transposable elements (TEs) constitute a substantial portion (~45%) of primate genomes.
  • TEs play critical roles in regulating gene expression and driving genomic fluidity.
  • Comparative genomic analyses are essential for understanding TE evolution and function.

Purpose of the Study:

  • To develop a novel computational tool for the comparative analysis of transposable elements (TEs) in primate genomes.
  • To enable efficient comparison of specific genomic regions across multiple primate species.

Main Methods:

  • Development of the BLAST-like alignment tool (BLAT) based comparative analysis for transposable elements (BLATCAT) program.
  • Utilized BLAT for sequence alignment across six primate genomes (human, chimpanzee, gorilla, orangutan, gibbon, rhesus macaque).
  • Integrated RepeatMasker and Censor functions for TE detection within the BLATCAT framework.

Main Results:

  • BLATCAT allows for simultaneous comparison of TEs across selected primate genomes.
  • The program facilitates the detection and analysis of TEs using established tools like RepeatMasker and Censor.
  • Results are stored in an HTML format for convenient manual inspection of specific genomic loci.

Conclusions:

  • BLATCAT provides a convenient and efficient platform for comparative analysis of transposable elements in primate genomes.
  • This tool aids researchers in investigating the role and evolution of TEs across primate species.
  • The integration of BLAT with TE detection tools enhances comparative genomic studies.