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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

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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Regulation of Expression at Multiple Steps01:23

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The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
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Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
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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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Updated: Nov 15, 2025

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Identifying transposable element expression dynamics and heterogeneity during development at the single-cell level

Jiangping He1, Isaac A Babarinde2, Li Sun2

  • 1Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.

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Transposable elements (TEs) are dynamically expressed in single cells, revealing their role in cell heterogeneity. Our new pipeline, scTE, uncovers previously hidden TE expression patterns in various cell types and developmental stages.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Cell Biology

Background:

  • Transposable elements (TEs) constitute a significant portion of eukaryotic genomes.
  • Their contribution to cellular heterogeneity remains poorly understood.
  • Current single-cell analysis methods are gene-centric, neglecting TE expression.

Purpose of the Study:

  • To develop a computational pipeline for analyzing transposable element (TE) expression at the single-cell level.
  • To investigate the dynamic regulation and cell-type-specific expression of TEs.
  • To explore the utility of TE expression and chromatin accessibility in cell type discrimination.

Main Methods:

  • Development of the scTE (single-cell Transposable Element) processing pipeline.
  • Application of scTE to diverse single-cell RNA sequencing datasets.
  • Analysis of scTE applied to single-cell ATAC-sequencing data.

Main Results:

  • Identified specific TE types expressed in embryonic stem cell subpopulations.
  • Demonstrated dynamic regulation of TEs during pluripotency reprogramming, differentiation, and embryogenesis.
  • Revealed unexpected TE expression in somatic cells, including disease-associated TEs missed by bulk analysis.
  • Showed that TE chromatin accessibility alone can discriminate cell types using scTE.

Conclusions:

  • scTE provides a novel framework for analyzing single-cell TE expression.
  • TEs are dynamically regulated and contribute significantly to cell heterogeneity.
  • TE expression and accessibility offer new avenues for understanding cell states and diseases.