Fig. 6: Model for GAF-DBD and GAF-FL target search.

a, GAF-DBD uses two search modes to locate its target on chromatin. In the 1D sliding mode, GAF-DBD lands on an off-target location on free DNA and then slides back and forth to locate the cognate motif (GAGAG). It can escape the cognate site to search for the next site nearby. This 1D search mode allows GAF-DBD to invade into the nucleosome edge but no further. Alternatively, GAF-DBD can also directly associate with a solvent-exposed cognate motif in the nucleosome core from 3D space. This 3D search mode allows GAF to effectively target nucleosomal motifs that are inaccessible by 1D sliding. b, GAF-FL uses both 3D and 1D diffusion to locate cognate motif clusters on free DNA. If the motif cluster is inside a nucleosome, GAF-FL can use 3D diffusion for target location. c–h, Hypothetical stepwise model for GAF–remodeler collaboration to mobilize targeted nucleosome for PIC assembly, based on this study and prior literature. c, GAF localizes cognate targets on closed chromatin through a combination of 1D sliding and 3D diffusion. d, Nucleosome-bound GAF multimer may recruit chromatin remodelers, such as NURF and PBAP. e, The recruited ATP-dependent chromatin remodelers shift nucleosomes away from the cognate sites. It is unclear whether GAF dissociates from chromatin during this process. f–h, Once the cognate sites become nucleosome free, GAF multimer rapidly locates the free DNA target through 3D and 1D diffusion (f), enabling downstream PIC recruitment, transcription initiation (g) and binding of other TFs such as HSF (h). HSE, heat shock element; NDR, nucleosome-depleted region.