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Related Concept Videos

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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Overview of Transposition and Recombination02:13

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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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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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
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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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Related Experiment Video

Updated: May 20, 2025

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level
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LocusMasterTE: integrating long-read RNA sequencing improves locus-specific quantification of transposable element

Sojung Lee1,2, Jayne A Barbour1,2, Yee Man Tam1

  • 1School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China.

Genome Biology
|March 27, 2025
PubMed
Summary

Quantifying transposable elements (TEs) is difficult due to their repetitive nature. LocusMasterTE integrates long and short RNA sequencing reads to accurately measure TE expression, aiding disease research.

Keywords:
Expectation–maximization modelShort-read RNA-seq quantificationTransposable elements

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Highly Efficient Ligation of Small RNA Molecules for MicroRNA Quantitation by High-Throughput Sequencing
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Highly Efficient Ligation of Small RNA Molecules for MicroRNA Quantitation by High-Throughput Sequencing
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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Transposable elements (TEs) are mobile DNA sequences that can impact genome integrity and contribute to human diseases.
  • Accurate quantification of TE expression is crucial for understanding their role in disease but remains challenging due to their repetitive genomic sequences.
  • Existing methods struggle to precisely quantify TE expression from RNA sequencing data.

Purpose of the Study:

  • To develop a novel computational method for accurate quantification of transposable element (TE) expression.
  • To improve the accuracy of short-read RNA sequencing-based TE quantification by integrating long-read data.
  • To provide a tool that facilitates new insights into the functional roles of TEs in biological processes and diseases.

Main Methods:

  • Developed LocusMasterTE, a method integrating long-read and short-read RNA sequencing data.
  • Utilized fractional transcript per million (TPM) values from long-read data within an expectation-maximization algorithm.
  • Implemented a read reassignment strategy for multi-mapped reads to enhance short-read quantification accuracy.

Main Results:

  • LocusMasterTE demonstrated increased accuracy in quantifying transposable element expression.
  • The method effectively reassigns multi-mapped reads, a key challenge in TE quantification.
  • Validation using simulated and human datasets confirmed the method's performance.

Conclusions:

  • LocusMasterTE offers a more precise approach to quantifying transposable element expression.
  • This enhanced accuracy can provide deeper insights into the functional significance of TEs.
  • The method has the potential to advance research into TE-mediated impacts on human health and disease.