Identification of transcription factor-DNA interactions in vivo

Abstract

Recent technological developments have revolutionized our understanding of transcriptional regulation by providing an unprecedented ability to interrogate in vivo transcription factor binding. The combination of high-throughput sequencing with chromatin precipitation of transcription factors and specifically labeled histones has allowed direct protein-DNA contacts to be visualized across genomes as large and complex as mammals at base-pair resolution. This chapter reviews the developments that led to these insights, with particular focus on examples of early protein-DNA localization experiments using genomic microarrays in mammals and yeast. Four state-of-the-art research directions are highlighted as examples of previously unimaginable frontiers now under active investigation.