ChIP-chip to determine the regulation of the binding targets of a2 and alpha2 in Lachancea kluyveri

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. Epitope-tagged strains were compared to untagged control strains. The a2 ChIP (C-terminally myc tagged) and its corresponding untagged control were performed in a cells. The alpha2 ChIP (C-terminally myc tagged) and its corresponding untagged control were performed in alpha cells. Two biological replicates were performed for the tagged ChIPs and one replicate was performed for the untagged ChIPs.