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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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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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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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Epistasis Analysis01:09

Epistasis Analysis

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Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
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Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Updated: Jun 10, 2025

Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library
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A unified framework to analyze transposable element insertion polymorphisms using graph genomes.

Cristian Groza1, Xun Chen2, Travis J Wheeler3

  • 1Quantitative Life Sciences, McGill University, Montréal, QC, Canada.

Nature Communications
|October 16, 2024
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Summary
This summary is machine-generated.

GraffiTE is a new pipeline for analyzing mobile DNA insertions, called transposable elements, which contribute to genomic diversity. This tool helps researchers easily study these elements across various species and sequencing types.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Transposable elements (TEs) are mobile DNA sequences that drive genomic diversity through insertion polymorphisms.
  • Analyzing polymorphic TEs is crucial for understanding genome evolution and variation.
  • Existing methods may lack flexibility or ease of use for comprehensive TE insertion analysis.

Purpose of the Study:

  • To introduce GraffiTE, a flexible computational pipeline for the identification and genotyping of polymorphic transposable element insertions.
  • To enable non-expert users to perform detailed analyses of TE landscapes across diverse species and datasets.
  • To leverage graph genomes and advanced structural variant detection for improved TE analysis.

Main Methods:

  • Integration of state-of-the-art structural variant detection algorithms with graph genome approaches.
  • Identification of polymorphic mobile element insertions from genomic assemblies or long-read sequencing data.
  • Genotyping of TE variants using both short and long read sequencing datasets.

Main Results:

  • Benchmarking on simulated and real datasets demonstrated high precision and recall rates for GraffiTE.
  • GraffiTE successfully analyzed human, Drosophila melanogaster, maize, and Cannabis sativa pangenome data, showcasing its versatility.
  • The pipeline revealed detailed landscapes of polymorphic TEs and their frequency variations across different individuals and cultivars.

Conclusions:

  • GraffiTE provides a robust and user-friendly solution for analyzing polymorphic transposable element insertions.
  • The pipeline is compatible with various sequencing technologies and adaptable to species with limited prior TE knowledge.
  • GraffiTE facilitates comprehensive studies of genomic diversity driven by mobile DNA across a wide range of organisms.