Using protein-binding microarrays to study transcription factor specificity: Homologs, isoforms and complexes

Abstract

Protein-DNA bindingis central to specificity in gene regulation, andmethods for characterizing transcription factor (TF)- DNA binding remain crucial to studies of regulatory specificity. High-throughput (HT) technologies have revolutionized our ability to characterize protein-DNA bindingby significantly increasing the number of binding measurements that can beperformed. Protein-binding microarrays (PBMs) are a robust andpowerfulHTplatformfor studying DNA-binding specificityof TFs. Analysis of PBM-determined DNA-binding profiles has provided new insight into the scope and mechanisms of TF binding diversity. In this review, we focus specifically on the PBM technique and discuss its application to the study of TF specificity, in particular, the binding diversity of TF homologs and multi-protein complexes.