Genome-Wide Assessment of the Binding Effects of Artificial Transcriptional Activators by High-Throughput Sequencing

One of the major goals in DNA-based personalized medicine is the development of sequence-specific small molecules to target the genome. SAHA-PIPs belong to such class of small molecule. In the context of the complex eukaryotic genome, the differential biological effects of SAHA-PIPs are unclear. This question can be addressed by identifying the binding regions across the genome; however, it is a challenge to enrich small-molecule-bound DNA without chemical crosslinking. Here, we developed a method that employs high-throughput sequencing to map the binding area of small molecules throughout the chromatinized human genome. Analysis of the sequenced data confirmed the presence of specific binding sites for SAHA-PIPs from the enriched sequence reads. Mapping the binding sites and enriched regions on the human genome clarifies the reason for the distinct biological effects of SAHA-PIP. This approach will be useful for identifying the function of other small molecules on a large scale.