Junghyun Kima,1, Hyojin Kangb,1, Jeongmoo Parka,1, Woohyun Kima, Janghyun Yooc , Nayoung Leea, Jaewook Kima, Tae-young Yoonc, and Giltsu Choia,2
a Department of Biological Sciences, KAIST, Daejeon 34141, Korea
b Department of Convergence Technology Research, KISTI, Daejeon 34141, Korea
c Department of Physics, KAIST, Daejeon 34141, Korea
1 Contributed equally
2 Corresponding Author
The bHLH transcription factor PHYTOCHROME INTERACTING FACTOR 1 (PIF1) binds G box elements in vitro and inhibits light-dependent germination in Arabidopsis thaliana. A previous genome-wide analysis of PIF1 targeting indicated that PIF1 binds 748 sites in imbibed seeds, only 59% of which possess G-box elements. This suggests the G-box is not the sole determinant of PIF1 targeting. The targeting of PIF1 to specific sites could be stabilized by PIF1-interacting transcription factors (PTFs) that bind other nearby sequence elements. Here, we report PIF1 targeting sites are enriched with not only G-boxes but also with other hexameric sequence elements we named G-box coupling elements (GCEs). One of these GCEs possesses an ACGT core and serves as a binding site for group A bZIP transcription factors including ABSCISIC ACID INSENSITIVE 5 (ABI5), which inhibits seed germination in abscisic acid signaling. PIF1 interacts with ABI5 and other group A bZIP transcription factors and together they target a subset of PIF1 binding sites in vivo. In vitro single molecule fluorescence imaging confirms that ABI5 facilitates PIF1 binding to DNA fragments possessing multiple G-boxes or the GCE alone. Thus, we show in vivo PIF1 targeting to specific binding sites is determined by its interaction with PTFs and their binding to GCEs.