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Related Concept Videos

Overview of Transposition and Recombination02:13

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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 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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Transposons, or "jumping genes," are small mobile genetic elements (MGEs) that range from 700 to 40,000 base pairs in length. They are found in all organisms and can move within the same chromosome or transfer to different chromosomes. In some cases, transposons can also jump between different host DNA molecules, such as plasmids or viruses, contributing to genetic variability.Barbara McClintock first discovered these mobile genetic elements in the 1940s while studying maize genetics, and she...
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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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piRNA - Piwi-interacting RNAs02:57

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PIWI-interacting RNAs, or piRNAs, are the most abundant short non-coding RNAs. More than 20,000 genes have been found in humans that code for piRNAs while only 2000 genes have been found for miRNAs. piRNAs can act at the transcriptional and post-transcriptional levels and have a vital role in silencing transposable elements present in germ cells. They are also involved in epigenetic silencing and activation. Previously, they were thought to function only in germ cells but new evidence suggests...
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Single Nucleotide Polymorphisms-SNPs01:05

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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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A Pangenome Approach to Detect and Genotype TE Insertion Polymorphisms.

Cristian Groza1, Guillaume Bourque2,3,4,5, Clément Goubert6,7,8

  • 1Quantitative Life Sciences, McGill University, Montreal, QC, Canada. cristian.groza.mcgill@gmail.com.

Methods in Molecular Biology (Clifton, N.J.)
|November 30, 2022
PubMed
Summary

This study introduces a pangenome graph approach to genotype transposable element (TE) variations in human genomes. The method accurately identifies TE insertions and deletions, improving genomic variation analysis.

Keywords:
GenotypingPangenome graphsStructural variationTransposable elements

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Area of Science:

  • Genomics
  • Bioinformatics
  • Population Genetics

Background:

  • Transposable elements (TEs) are mobile genetic sequences contributing to genomic variation.
  • Accurate genotyping of TE polymorphisms, including insertions and deletions, is crucial for understanding genome diversity.
  • Existing methods struggle to comprehensively capture the full spectrum of TE variations within a population.

Purpose of the Study:

  • To develop and validate a pangenome graph-based method for representing and genotyping transposable element (TE) polymorphisms.
  • To integrate reference TE annotations with novel insertions from diverse human genomes.
  • To assess the performance of the pangenome graph approach for TE variant calling.

Main Methods:

  • Construction of a human transposable element pangenome graph incorporating reference and newly identified TEs.
  • Alignment of short-read sequencing data to the pangenome graph.
  • Genotyping of TE insertions and deletions using the pangenome graph structure.

Main Results:

  • A comprehensive TE pangenome was created, comprising approximately 1.2 million reference and 2939 non-reference TEs.
  • The pangenome graph approach achieved a reasonable F1-score of 0.85 for genotyping TE deletions and insertions.
  • Demonstrated specificity and sensitivity in identifying TE variants from sequencing data.

Conclusions:

  • Pangenome graphs provide a flexible and effective framework for analyzing complex transposable element variations.
  • This approach enhances the ability to genotype TE polymorphisms, contributing to a more complete understanding of human genome diversity.
  • The developed method offers a promising tool for population-scale genomic variation studies involving TEs.