Fig. 3: Nucleosome blocks GAF-DBD 1D sliding beyond SHL7.
From: GAGA zinc finger transcription factor searches chromatin by 1D–3D facilitated diffusion
a, Schematics of nucleosome constructs where the nucleosomal Cy7-labeled cognate site (blue) is placed at SHL7, SHL5 or SHL3 and the other Cy5-labeled cognate site (red) is on the linker DNA. The nucleosome is positioned by the Widom 601 sequence flanked by 40-bp linker DNA on both sides (40-N-40). Seq., sequence. b–d, Representative single-molecule trajectories of GAF-DBD binding to linker or nucleosomal sites at SHL7 (b), SHL5 (c) and SHL3 (d). e–g, Binding site rastergrams for GAF-DBD on nucleosome constructs where the Cy7-labeled motif is located at SHL7 (e), SHL5 (f) or SHL3 (g). h, GAF-DBD binding categories for each construct; n = 485 for SHL7, n = 260 for SHL5 and n = 272 for SHL3. i, Categories of binding events on SHL7 construct. Data are represented as the mean values ± s.d. of three independent imaging sessions, with a sum of n = 485 binding events. j, GAF-DBD motif dwell times on SHL7, linker site and nonspecific sites on the SHL7 construct (n = 34 traces). Error bars represent 95% confidence intervals. Nucl., nucleosome.
