Stress related TFBS predictions in Drosophila melanogaster and Humans

Abstract

The dataset consists of the prediction of transcription factor binding sites (ChIP-seq data) and transcription factor binding motifs (Position weight matrices and Transcription factor flexible models) in Drosophila melanogaster and humans.Although transposable elements (TEs) are an important source of regulatory variation, their genome-wide contribution to the transcriptional regulation of stress response genes has not been studied yet. Stress is a major aspect of natural selection in the wild, leading to changes in the transcriptional regulation of a variety of genes that are often triggered by one or a few transcription factors. In this work, we take advantage of the wealth of information available for Drosophila melanogaster and humans to analyze the role of TEs in stress regulatory networks. We used in silico predictions and chromatin immunoprecipitation sequencing (ChIP-seq) data to localize transcription factor binding sites (TFBS) for several stress-response transcription factors involved in six stress regulatory networks: immune, hypoxia, oxidative, xenobiotic, heat shock, and heavymetal stress responses. The predictions at the DNA level were complemented with the analysis of biochemical and genomic features, such as chromatin characteristics and location regarding nearby genes. In addition, we also used population level information to identify a subset of TEs that were more likely to contain functional TFBS. For a representative subset of the most likely candidate TEs, we performed in vivo transgenic reporter assays in different stress conditions. Overall, our results showed that TEs are relevant contributors to the transcriptional regulation of stress response genes.This work was funded by the Ministerio de Economia y Competitividad BFU2014-57779-P, Ministerio de Ciencia, Innovación y Universidades/AEI (BFU2017-82937-P) and the European Commission (H2020-ERC-2014-CoG-647900).Peer reviewe