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Updated: Jun 5, 2025
10:37
Induction and Analysis of Epithelial to Mesenchymal Transition
Published on: August 27, 2013
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Exploring Regulatory Roles of Transposable Elements in EMT and MET through Data-Driven Analysis: Insights from
Doğa Eskier1, Seray Yetkin1, Nazmiye Arslan2
1Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, İzmir 35340, Turkey.
Journal of Molecular Biology
|December 4, 2024
Summary
This study introduces regulaTER, an R library for analyzing transposable element regulation of gene expression. It helps uncover how these elements impact phenotypes, exemplified by epithelial-mesenchymal transition.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Gene expression is controlled by transcriptional, translational, and epigenetic mechanisms.
- Transposable elements (TEs) are known regulators of gene expression, but their full impact is hard to quantify.
- Existing methods lack dedicated approaches to define TE regulatory contributions.
Purpose of the Study:
- To introduce regulaTER, a novel R library designed to analyze the regulatory potential of transposable elements.
- To provide a flexible tool for integrating diverse genomic data and gene expression levels.
- To facilitate the comprehensive assessment of TE roles in specific phenotypes.
Main Methods:
- Development of the regulaTER R library.
- Integration of various genomics data types with gene expression information.
- Validation using a cellular model of epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET).
Main Results:
- regulaTER effectively deciphers the regulatory roles of transposable elements.
- The library demonstrated flexibility in analyzing TE-focused data.
- Insights were gained into MIR and B element subfamilies' roles in EMT/MET via the FoxA transcription factor family.
Conclusions:
- regulaTER is an essential tool for understanding TE-mediated gene expression regulation.
- The library offers high flexibility for diverse TE-centric analyses.
- The study highlights the specific contributions of certain TEs to EMT and MET processes.
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