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Related Concept Videos

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 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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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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Related Experiment Video

Updated: Dec 31, 2025

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
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Tools and best practices for retrotransposon analysis using high-throughput sequencing data.

Aurélie Teissandier1,2,3,4, Nicolas Servant1,2,3, Emmanuel Barillot1,2,3

  • 11Institut Curie, PSL Research University, 75005 Paris, France.

Mobile DNA
|January 1, 2020
PubMed
Summary
This summary is machine-generated.

Accurate mapping of transposable elements (TEs) in sequencing data is crucial for understanding genome regulation. This study provides recommendations for aligning and quantifying TE reads, improving analysis of TEs in mammalian genomes.

Keywords:
Data analysisHigh-throughput sequencingMappingQuantificationRetrotransposon

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Next-generation sequencing (NGS) provides insights into genome regulation.
  • Mapping sequencing reads to reference genomes is challenging, especially for repetitive sequences like transposable elements (TEs).
  • TEs constitute a significant portion of mammalian genomes, and their reads can cause mapping ambiguities.

Purpose of the Study:

  • To define optimal parameters for aligning TE-derived reads to reference genomes.
  • To compare the efficiency of common read aligners for TE analysis.
  • To evaluate methods for estimating TE representation and mappability.

Main Methods:

  • Utilized simulated sequencing reads from mouse and human genomes.
  • Compared the performance of widely-used sequence aligners.
  • Calculated the mappability of various transposon families across species.

Main Results:

  • Identified optimal alignment parameters for TE-derived reads.
  • Evaluated different methods for quantifying TE abundance.
  • Assessed the mappability of TE families in mouse and human genomes, offering evolutionary insights.

Conclusions:

  • Provided recommendations for aligning and quantifying TEs in sequencing data.
  • Highlighted limitations in detecting young TE families in mouse and human genomes.
  • Aimed to standardize TE analysis procedures and increase awareness of associated challenges.