Gene expression arrays comparing Kluyveromyces lactis wild-type a cells to MATa2 knock-out a cells and wild-type alpha cells to MATalpha2 knock-out alpha cells

We examine how different transcriptional network structures can evolve from a common, ancestral network. We show that regulatory protein modularity, conversion of one cis-regulatory sequence to another, distribution of binding energy among protein-protein and protein-DNA interactions, and exploitation of ancestral network features all contribute to the evolution of a novel mode of regulation at a conserved gene set. The formation of this derived mode of regulation did not disrupt the ancestral mode and thereby created a hybrid regulatory state where both means of transcription regulation (ancestral and derived) contribute to the conserved expression pattern of the network. Finally, we show how this hybrid regulatory state has resolved in different ways in different lineages to generate the diversity of regulatory network structures observed in modern species. a2 KO and alpha2 KO mRNA abundance was measured relative to a WT cell of the same mating type. 2 replicates each. Dye-swaps were performed.