GAGA Factor Overcomes 1D Diffusion Barrier by 3D Diffusion in Search of Nucleosomal Targets

The eukaryotic chromatin landscape plays important roles in DNA metabolism and is characterized by positioned nucleosomes near regulatory DNA, nucleosome-depleted regions and supranucleosomal organization. Nucleosome core histones limit DNA accessibility by structurally blocking half of the DNA surface and altering its topology, but how nucleosomes affect target search by sequence-specific transcription factors (TFs) remains enigmatic. Here, we used multi-color smFRET to investigate how Drosophila GAGA Factor (GAF) locates its targets. On free DNA, GAF rapidly diffuses in 1D to a single cognate motif but escapes after subsecond transient association. Nucleosomes effectively block 1D diffusion into its core, but GAF can bind, with surprisingly prolonged residence, at internal cognate sites by direct association from 3D. Our findings demonstrate the occlusive power of nucleosomes to 1D sliding and reveal that a combination of 1D and 3D diffusion by a zinc finger TF enables efficient target search on chromatin.