Exhaustive search for DNA binding sites of Basillus subtilis transcription factor YsiA by KaScape method

Abstract

Basillus subtilis (B. subtilis) YsiA is also known as FadR is a pre-formed dimeric repressor to regulate fatty acid degradation. However, the knowledge about double-stranded DNA(dsDNA) binding sites of YsiA in the whole genome level is limited so far. In this report, we have applied a newly established high-throughput method, KaScape, to exhaustively study the relative binding sites and energy landscape of YsiA and confirmed the resuls with gel-shift experiments. Weve found that half-binding site is enough for YsiA to bind with dsDNA. Besides detecting the known consensus sequence which is bound by YsiA, we have also detected other minor binding site sequences through the KaScape method. It thus demonstrates that KaScape can be used to study dimeric transcription factors (TFs) in general.