Feng Xinyu A, Yamadi Maryam, Fu Yiben, Ness Kaitlin M, Liu Celina, Ahmed Ishtiyaq, Bowman Gregory D, Johnson Margaret E, Ha Taekjip, Wu Carl
Department of Biology, Johns Hopkins University, Baltimore, MD, USA.
Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.
Nat Struct Mol Biol. 2025 Aug 5. doi: 10.1038/s41594-025-01643-0.
The search for target sites on chromatin by eukaryotic sequence-specific transcription factors (TFs) is integral to the regulation of gene expression but the mechanism of nuclear exploration has remained obscure. Here we use multicolor single-molecule fluorescence resonance energy transfer and single-particle imaging to track the diffusion of purified Drosophila GAGA factor (GAF) on DNA and nucleosomes. Monomeric GAF DNA-binding domain (DBD) bearing one zinc finger finds its cognate site through one-dimensional (1D) or three-dimensional (3D) diffusion on bare DNA and rapidly slides back and forth between naturally clustered motifs for seconds before dissociation. Multimeric, full-length GAF also finds clustered motifs on DNA through 1D-3D diffusion but remains locked on target for longer periods. Nucleosome architecture effectively blocks GAF-DBD 1D sliding into the histone core but favors retention of GAF-DBD once it has bound to a solvent-exposed motif through 3D diffusion. Despite the occlusive nature of nucleosomes, 1D-3D facilitated diffusion enables GAF to effectively search for clustered cognate motifs in chromatin, providing a mechanism for navigation to nucleosomal and nucleosome-free sites by a member of the zinc finger TF family.
