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Related Concept Videos

DNA-only Transposons02:57

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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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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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.
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RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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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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Translesion DNA Polymerases02:10

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.
TLS polymerases are found in all three domains of life - archaea, bacteria, and eukaryotes. Of the different classes of TLS polymerases, members of the Y family are fitted with specialized structures that...
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Related Experiment Video

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Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library
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STEAK: A specific tool for transposable elements and retrovirus detection in high-throughput sequencing data.

Cindy G Santander1, Philippe Gambron2, Emanuele Marchi3

  • 1Department of Zoology, University of Oxford, Oxfordshire, UK.

Virus Evolution
|September 27, 2017
PubMed
Summary

STEAK is a new software that efficiently detects repetitive DNA elements and viral sequences in genomic data. It outperforms existing tools in speed and accuracy for research and clinical applications.

Keywords:
HTSendogenous retrovirusesevolutionmobile elementtransposonsvirus integration

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • High-throughput genomics reveals individual variations and their disease relevance.
  • Existing software struggles with repetitive genomic regions, hindering structural variant analysis.
  • Accurate detection of repetitive elements and viral integrations is crucial for understanding disease.

Purpose of the Study:

  • Introduce STEAK, a massively parallel software for detecting chimeric reads in high-throughput sequencing data.
  • Evaluate STEAK's capability in identifying transposable elements (TEs) and retroviral integrations.
  • Compare STEAK's performance against other tools for TE and virus detection.

Main Methods:

  • STEAK utilizes a massively parallel approach to analyze high-throughput sequencing data.
  • The software is designed to detect chimeric reads, crucial for identifying structural variants.
  • Performance was benchmarked using clinical whole genome projects, target enrichment sequences, and the 1000 Genomes CEU Trio.

Main Results:

  • STEAK demonstrates superior computational efficiency, sensitivity, and specificity compared to existing TE and virus detection tools.
  • The software successfully located HERV-K HML-2 in diverse sequencing datasets.
  • STEAK proves robust for detecting and evaluating TE and retroviral integrations.

Conclusions:

  • STEAK is a powerful and flexible tool for analyzing repetitive elements and viral integrations in genomic data.
  • Its high performance makes it suitable for both research and clinical applications.
  • STEAK advances the analysis of structural variants and their role in disease.