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[Preprint]. 2024 May 25:2023.07.14.549009. Originally published 2023 Jul 15. [Version 2] doi: 10.1101/2023.07.14.549009

PMC10369947.1; 2023 Jul 15
PMC10369947.2; 2024 May 25

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Extended Data Figure 1. — 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, 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.