Genome-Wide DNA-Binding Specificity of PIL5, a Arabidopsis Basic Helix-Loop-Helix (bHLH) Transcription Factor

PIL5 is a member of the bHLH transcription factor super family and plays crucial roles in phytochrome mediated seed germination process in Arabidopsis. While our previous study shows that PIL5 binds to the G-box (CACGTG) motif with high affinity, other attributes must be involved in determining regulatory specificity. In this study we performed a ChIP-chip assay to obtain genome-wide PIL5 binding sites and investigated other attributes which would affect to PIL5 DNA-binding specificity. Our results confirmed that the existence of G-box in promoter region was the most significant binding attribute. Additionally we also found that other attributes such as neighboring motif composition, distance from transcription start site, nucleosome density, DNA methylation and average gene expression were also contributing to PIL5 DNA-binding specificity. The Random Forest classifier using these attributes can classify PIL5 binding sites from non-binding sites with accuracy of 93.05%.