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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.
Mobile DNA
|November 28, 2025
Summary
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.
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.
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