Regulatory elements have been extensively studied in both the biochemical and genomic fields, but the governing principles behind their role in rewiring cellular systems under stress remain unidentified. This study provides insight into the conservation of cis-regulatory elements in the osmotic stress response of seven ascomycetes. Gene expression profiles under osmotic stress were measured for each species, their genes clustered and compared across species using a novel criterion of similar expression behavior. The programming tool ModuleDigger was used to identify potential cis-regulatory modules (CRMs), each composed of a set of co-occurring cis-regulatory elements, or motifs, in the promoter sequences of the genes in the cluster. Only the most induced and most repressed set of genes were processed using ModuleDigger. Then, we evaluated conservation of motif pairs in CRMs across clades. Then motif pairs for the transcription factors RCS1 and SIP4 were conserved in the most induced and most repressed cluster in pre-whole genome duplication species and in the fungal pathogens present in the set. The post-whole genome duplication species shared three motif pair combinations (MIG1, MSN2/MSN4; MIG1, ADR1 and ADR1, MSN2/MSN4). These co-occurring transcription factors correspond to stress-responsive elements and carbon-responsive elements; which suggests an interesting biological interaction between the pathways.
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