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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 Transposons02:57

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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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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.
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...
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MATES: a deep learning-based model for locus-specific quantification of transposable elements in single cell.

Ruohan Wang1,2,3, Yumin Zheng2,3,4, Zijian Zhang5

  • 1School of Computer Science, McGill University, Montreal, Quebec, Canada.

Nature Communications
|October 11, 2024
PubMed
Summary
This summary is machine-generated.

Transposable elements (TEs) are vital for genetic diversity. Our new deep-learning tool, MATES, accurately quantifies TEs at specific loci in single-cell omics data, improving biological insights.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Transposable elements (TEs) significantly contribute to genetic diversity and gene regulation.
  • Current single-cell quantification methods for TEs often lack locus specificity and are limited to transcriptomics data.
  • Accurate, locus-specific TE quantification is essential for understanding their role in biological processes.

Purpose of the Study:

  • To develop a novel deep-learning approach for accurate, locus-specific quantification of transposable elements in single-cell omics data.
  • To overcome limitations of existing methods in handling multi-mapping reads and diverse data modalities.
  • To enhance the exploration of single-cell heterogeneity and gene regulation influenced by TEs.

Main Methods:

  • Introduction of MATES, a deep-learning method for allocating multi-mapping reads to specific transposable element loci.
  • Utilizing context from adjacent read alignments to improve TE locus identification.
  • Application and validation of MATES across diverse single-cell omics datasets.

Main Results:

  • MATES demonstrates superior performance compared to existing methods in TE quantification accuracy.
  • The tool effectively allocates multi-mapping reads to specific TE loci.
  • MATES aids in identifying marker TEs for specific cell populations, revealing cell heterogeneity.

Conclusions:

  • MATES provides an accurate and adaptable tool for transposable element quantification in single-cell genomics.
  • This advancement facilitates deeper exploration of TE functions in gene regulation and cellular diversity.
  • MATES offers a valuable resource for the single-cell genomics community.