Predicting hyperosmolality‐inducible transcription factors using MEME tools

Abstract

Transcriptional regulation is a major mechanism by which organisms are able to adapt to fluctuating environments. Transcriptional regulation depends on the interplay between cis-regulatory elements and trans-acting factors. Euryhaline tilapia (Oreochromis mossambicus) tolerate a wide range of salinity up to 3x seawater and thus, this species is an appropriate model to examine transcriptional regulation mechanisms in response to salinity stress. Using OmB cells (O. mossambicus brain cell line), targeted proteomics analysis revealed 21 proteins that are encoded by genes, which are transcriptionally up-regulated during salinity stress. Potential regulatory regions (including distant and proximal promoter regions and 5’ UTRs) from those genes were isolated to identify common and distinct binding sites for inducible transcription factors. The STREME tool of the MEME suite was used to identify five ungapped motifs that are enriched in the regulatory sequence of all 21 hyperosmolality-responsive tilapia genes. These binding site motifs were analyzed using the TOMTOM and FIMO motif scanning tools. Among the five motifs, the top-ranked two statistically significant motifs were representing binding sites for Forkhead box protein L1 (FoxL1) and metal response element binding transcription factor 1 (Mtf1). The mapping of FoxL1 and Mtf1 motifs in regulatory regions of the 21 hyperosmolality-induced tilapia genes permits their experimental validated via enhancer trapping. Moreover, our results rationalize FoxL1 and Mtf1 genetic manipulation experiments to study their involvement in the osmotic regulation of gene expression.