Several papers in Nature Methods describe high-throughput yeast one-hybrid screens and their integration with ChIP to characterize transcriptional networks:
Exciting times: bountiful data to facilitate studies of cis-regulatory control
Automated protein-DNA interaction screening of Drosophila regulatory elements
Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping
Yeast one-hybrid assays for gene-centered human gene regulatory network mapping