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