Eskier, D.; Yetkin, S.; Arslan, N.; Karakülah, G.; Alotaibi, H.

Gene expression defines the identity of cells and is achieved following multiple levels of regulation at the transcriptional, translational, and a plethora of profound epigenetic mechanisms. Regulation of gene expression by transposable elements (TEs) is well documented. However, comprehensive analysis of the regulatory role of TEs is challenging due to the lack of dedicated analysis approaches to define their contribution. In this study, we sought to understand the contributions of TEs to the epithelial-to-mesenchymal (EMT) and mesenchymal-to-epithelial transition (MET) processes. To do so, we developed regulaTER, an R library that utilizes multi-omics data to predict the regulatory roles of accessible TEs in a phenotype of interest. Our results revealed novel insights into the intricate networks governing the regulation of EMT and MET and showed novel contributions of the MIR and B element subfamilies to the regulation of EMT and MET by the FoxA family of transcription factors. Our tool provides an essential asset for uncovering the impact of accessible TEs on the regulation of gene expression, with high flexibility to perform a range of other TE-centric analyses. regulaTER is publicly available at https://github.com/karakulahg/regulaTER.