Capturing auxin response factors syntax using DNA binding models (bioRxiv)

Auxin Response Factors (ARFs) are transcription factors that bind to ARF binding sites (ARFbs) to mediate auxin responses. Stigliani et al. analzyed experimentally determined DNA interactions of two ARFs, the repressor ARF2 and the activator MP.  They found that the binding site data are best interpreted using a position weight matrix (PWM). Using this method, they showed small differences in monomeric binding site preferences between the two proteins, but larger differences in how these sites are arranged (e.g., direct repeat, inverted repeat, everted repeat). Their method also enabled them to identify binding sites not found through the use of consensus sequences. (Summary by Mary Williams) bioRxiv