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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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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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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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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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piRNA - Piwi-interacting RNAs02:57

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PIWI-interacting RNAs, or piRNAs, are the most abundant short non-coding RNAs. More than 20,000 genes have been found in humans that code for piRNAs while only 2000 genes have been found for miRNAs. piRNAs can act at the transcriptional and post-transcriptional levels and have a vital role in silencing transposable elements present in germ cells. They are also involved in epigenetic silencing and activation. Previously, they were thought to function only in germ cells but new evidence suggests...
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RNA-seq03:21

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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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Updated: Jun 7, 2025

Detection of Retrotransposition Activity of Hot LINE-1s by Long-Distance Inverse PCR
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Detecting transposable elements in long-read genomes using sTELLeR.

Kristine Bilgrav Saether1,2, Jesper Eisfeldt1,2,3

  • 1Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm 171 76, Sweden.

Bioinformatics (Oxford, England)
|November 19, 2024
PubMed
Summary
This summary is machine-generated.

sTELLeR accurately detects transposable elements (TEs) using long-read genome sequencing. This fast and precise tool improves upon existing methods for analyzing repetitive DNA sequences, crucial for understanding genome function and disease.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Transposable elements (TEs) comprise ~50% of the genome and can cause disease by disrupting gene function.
  • Short-read sequencing struggles to characterize repetitive TEs, hindering accurate analysis.
  • Long-read genome sequencing (lrGS) offers improved resolution for TE detection.

Purpose of the Study:

  • To develop a novel tool for accurate, fast, and effective TE detection using lrGS.
  • To enhance the characterization of repetitive DNA sequences, including disease-associated TEs.
  • To provide a computationally efficient and compatible solution for TE analysis in research and clinical settings.

Main Methods:

  • Developed sTELLeR, a Python-based tool for transposable element detection in long reads.
  • Evaluated sTELLeR's performance against existing TE callers.
  • Ensured haplotype awareness and VCF output for downstream analysis compatibility.

Main Results:

  • sTELLeR demonstrates higher precision and sensitivity for Alu element calling compared to similar tools.
  • The tool is significantly faster (5-48x) and uses less computational resources (<2% CPU hours).
  • Haplotype-aware VCF output facilitates integration into existing variant calling workflows.

Conclusions:

  • sTELLeR is a fast, sensitive, and precise caller for TE detection using lrGS.
  • The tool can be readily implemented into variant calling pipelines for improved genomic analysis.
  • sTELLeR advances the potential for clinical detection of TEs and their associated diseases.