Exploring Regulatory Roles of Transposable Elements in EMT and MET through Data-Driven Analysis: Insights from regulaTER

[Display omitted] •Accessible TEs present next to key genes involved in EMT and MET progression.•MIR and B subfamily TEs contribute to the regulation of EMT and MET by binding FoxA TFs.•regulaTER is a genome-independent tool dedicated to studying the contribution of TEs in gene regulation. Gene expr...

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Bibliographic Details
Published in:Journal of molecular biology 2024-12, Vol.437 (2), p.168887, Article 168887
Main Authors: Eskier, Doğa, Yetkin, Seray, Arslan, Nazmiye, Karakülah, Gökhan, Alotaibi, Hani
Format: Article
Language:English
Subjects:
EMT
gene regulation
MET
regulaTER
transposable elements
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Summary:[Display omitted] •Accessible TEs present next to key genes involved in EMT and MET progression.•MIR and B subfamily TEs contribute to the regulation of EMT and MET by binding FoxA TFs.•regulaTER is a genome-independent tool dedicated to studying the contribution of TEs in gene regulation. Gene expression is regulated at the transcriptional and translational levels and a plethora of epigenetic mechanisms. Regulation of gene expression by transposable elements is well documented. However, a comprehensive analysis of their regulatory roles is challenging due to the lack of dedicated approaches to define their contribution. Here, we present regulaTER, a new R library dedicated to deciphering the regulatory potential of transposable elements in a given phenotype. regulaTER utilizes a variety of genomics data of any origin and combines gene expression level information to predict the regulatory roles of transposable elements. We further validated its capabilities using data generated from an epithelial-mesenchymal and mesenchymal-epithelial transition cellular model. regulaTER stands out as an essential asset for uncovering the impact of transposable elements on the regulation of gene expression, with high flexibility to perform a range of transposable element-focused analyses. Our results also provided insights on the contribution of the MIR and B element subfamilies in regulating EMT and MET through the FoxA transcription factor family. regulaTER is publicly available and can be downloaded from https://github.com/karakulahg/regulaTER.
ISSN:0022-2836
1089-8638
1089-8638
DOI:10.1016/j.jmb.2024.168887