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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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Related Experiment Video

Updated: Jun 13, 2025

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

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

Published on: January 20, 2023

IRescue: uncertainty-aware quantification of transposable elements expression at single cell level.

Benedetto Polimeni^1,2, Federica Marasca¹, Valeria Ranzani¹

¹INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy.

Nucleic Acids Research

|September 13, 2024

Summary

This summary is machine-generated.

Transposable elements (TEs) are mobile DNA sequences. A new tool, IRescue, quantifies TE subfamily expression in single cells, revealing their roles in cellular diversity and disease.

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An Approach to Study Shape-Dependent Transcriptomics at a Single Cell Level

An Approach to Study Shape-Dependent Transcriptomics at a Single Cell Level

Published on: November 2, 2020

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Transposable elements (TEs) are mobile DNA sequences influencing eukaryotic genome evolution.
TEs show tissue-specific transcription, but their role in cellular diversity is hard to study with single-cell RNA sequencing (scRNA-seq).
Challenges include TE ubiquity and genetic similarity, complicating expression analysis.

Purpose of the Study:

To introduce IRescue, a novel software for quantifying transposable element subfamily expression at the single-cell level.
To overcome limitations of scRNA-seq in analyzing TE expression across diverse tissues and conditions.
To link TE expression patterns to cellular heterogeneity and disease states.

Main Methods:

Developed IRescue, a single-cell RNA sequencing analysis tool.
Implemented a unique UMI deduplication algorithm to correct sequencing errors.
Utilized an Expectation-Maximization procedure for accurate multi-mapping read count redistribution.

Main Results:

Demonstrated IRescue's precision using simulated and real scRNA-seq data.
Analyzed data from human colorectal cancer, brain, skin aging, and PBMCs during SARS-CoV-2 infection.
Linked TE expression signatures to specific biological contexts and disease conditions.

Conclusions:

IRescue accurately quantifies transposable element expression in single cells.
TE expression patterns provide insights into cellular heterogeneity.
TE signatures correlate with specific biological contexts and disease progression, highlighting their functional relevance.