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Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

18.8K
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...
18.8K
LTR Retrotransposons03:08

LTR Retrotransposons

19.4K
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...
19.4K
DNA-only Transposons02:57

DNA-only Transposons

17.1K
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...
17.1K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

11.6K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
11.6K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

4.0K
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Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

13.1K
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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Video Experimental Relacionado

Updated: Jan 13, 2026

Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity
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Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity

Published on: January 20, 2023

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Clasificación de secuencias de consenso de elementos transponibles basada en Transformer con TEclass2

Lucas Bickmann1, Matias Rodriguez2, Xiaoyi Jiang1

  • 1Department of Computer Science, University of Münster, 48149 Münster, Germany.

Biology
|January 10, 2026
PubMed
Resumen
Este resumen es generado por máquina.

Los elementos transponibles (TE) son clave para la evolución del genoma pero difíciles de clasificar. El nuevo software, TEclass2, utiliza el aprendizaje profundo para una clasificación precisa de TE, lo que ayuda a la investigación genómica.

Palabras clave:
Clasificación de TEherramienta web bioinformáticaaprendizaje profundoarquitectura Transformerelementos transponibles

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Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms
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Transposon-insertion Sequencing as a Tool to Elucidate Bacterial Colonization Factors in a Burkholderia gladioli Symbiont of Lagria villosa Beetles
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Last Updated: Jan 13, 2026

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Área de la Ciencia:

  • Genómica
  • Bioinformática
  • Biología Computacional

Sus antecedentes:

  • Los elementos transponibles (TE) son abundantes en los genomas eucariotas y son fundamentales para la evolución del genoma.
  • La naturaleza compleja de las secuencias de TE desafía la clasificación precisa y el análisis genómico.
  • Las herramientas actuales de clasificación de TE presentan limitaciones en fiabilidad y alcance.

Objetivo del estudio:

  • Desarrollar una herramienta de software novedosa, precisa y fiable para clasificar secuencias de consenso de elementos transponibles (TE).
  • Mejorar la eficiencia y precisión de la anotación genómica abordando los desafíos en la identificación de TE.
  • Proporcionar una plataforma flexible para la clasificación de TE adaptable a conjuntos de datos personalizados.

Principales métodos:

  • Se desarrolló TEclass2, una herramienta de software que utiliza un enfoque de aprendizaje profundo.
  • Se empleó una arquitectura Transformer lineal con tokenización k-mer y adaptaciones específicas de secuencia.
  • Se implementaron capacidades flexibles de entrenamiento de modelos para conjuntos de datos de TE personalizados.

Principales resultados:

  • TEclass2 logró un rendimiento de clasificación mejorado para secuencias de consenso de TE en dieciséis superfamilias.
  • El software demostró una mayor fiabilidad en comparación con las herramientas de clasificación de TE existentes.
  • Se proporcionó una interfaz web con modelos preentrenados para una clasificación rápida de TE.

Conclusiones:

  • TEclass2 ofrece un avance significativo en la clasificación precisa y rápida de elementos transponibles.
  • La herramienta mejora la precisión de la anotación genómica y apoya la investigación bioinformática futura.
  • TEclass2 proporciona una solución robusta para analizar el complejo panorama de los TE en genomas eucariotas.