Interaction between protein complexes and the genome mediates essential functions including gene regulation, genome integrity, and chromatin organization. Recent advances in chromatin immunoprecipitaion (ChIP)-chip and ChIP-Seq technologies have enabled genome-wide identification of occupancy of transcription factors and modified histones that is critical for uncovering gene regulatory networks. This review discusses ChIP-chip and ChIP-Seq technology, their pitfalls, insights from genome-wide occupancy studies, and applications pertaining to vertebrate retina.