Application of mRNA Display for In Vitro Selection of DNA-Binding Transcription Factor Complexes

Comprehensive analysis of DNA–protein interactions is important for mapping transcriptional regulatory networks at the genome-wide level. Here, we present a new application of mRNA display, using the in vitro virus (IVV) technology, for in vitro selection of DNA-binding protein complexes. Under optimal selection conditions using bait DNAs, many kinds of DNA-binding protein complexes can be successfully selected from an mRNA display library constructed from poly A⁺ RNA after several rounds of selection. This mRNA display selection system can identify a variety of DNA-binding protein complexes in a single experiment. Remarkably, this system can also select DNA-binding protein heterooligomeric complexes. Since almost all transcription factors form heterooligomeric complexes to bind with their target DNA, this method should be broadly useful to identify DNA-binding transcription factor complexes.