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Related Experiment Video

Updated: Jan 10, 2026

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

TE-Seq: a transposable element annotation and RNA-Seq pipeline.

Maxfield M G Kelsey¹, Radha L Kalekar², John M Sedivy³

¹Center on the Biology of Aging, and Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 225 Dyer Street, RI, 02903, Providence, USA. maxfield_kelsey@brown.edu.

|November 28, 2025

Summary

This summary is machine-generated.

Transposable elements (TEs) are crucial in biology. The TE-Seq pipeline simplifies analyzing TE expression from sequencing data, revealing upregulated elements in senescent human lung cells.

Keywords:

LINE-1 Long interspersed nuclear element Long read DNA-Seq Polymorphic loci RNA-Seq Retrotransposable elements Transposable elements

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Transposable elements (TEs) are increasingly recognized for their significant roles in biological processes.
Analyzing TEs in sequencing data is challenging due to their repetitive nature and the need for specialized tools and annotations.
Existing methods often require complex data curation, limiting general accessibility.

Purpose of the Study:

To develop an accessible computational pipeline for analyzing transposable element (TE) sequences and their expression.
To provide an end-to-end solution for examining both genes and TEs in RNA sequencing data.
To facilitate the study of the 'dark genome' and the functional impact of TEs.

Main Methods:

The TE-Seq pipeline was developed as a Snakemake workflow.
It integrates computational methods specifically designed for TE analysis.
The pipeline supports RNA sequencing data and optionally long-read DNA sequencing for polymorphic loci analysis.

Main Results:

TE-Seq provides a comprehensive analysis of TE expression at individual element and clade levels.
Demonstration analysis on human lung fibroblasts revealed upregulated retrotransposable element clades during senescence.
This included the identification of non-reference, intact, and potentially active elements contributing to senescence.

Conclusions:

TE-Seq enhances the accessibility of transposable element analysis from sequencing data.
The pipeline offers a robust method for studying TE expression across various biological contexts.
The findings highlight the role of specific TE clades in cellular senescence.