Figure 1. The Chd1 DNA-binding domain preferentially binds DNA in a specific orientation and position at the edge of the nucleosome.
(A) Schematic of Chd1 domain architecture.
(B) and (C) Cross-linking of single cysteine variants within the Chd1 DNA-binding domain (DBD) to 80N0 and 0N80 nucleosomes or naked DNA in the presence of ADP∙BeF3. Lower schematics provide a summary of cross-linking positions, with the numbering referring to the distances from the nucleosome edge. Cross-linking sites reported here were observed in six or more independent reactions (n ≥ 6).
(D) Cross-links are consistent with a unique position and orientation of the DBD on DNA. The crystal structure of the Chd1 DBD bound to DNA (PDB code 3TED; (Sharma et al., 2011)) is shown, highlighting positions of cysteine substitutions as colored spheres and the corresponding cross-linked bases as colored sticks.
(E) A model of the Chd1 DBD at the edge of the nucleosome. Ideal B-form DNA (gray) was added to one end of the nucleosome crystal structure (1KX5, (Davey et al., 2002)), and the Chd1 DBD was positioned by docking DNA from the crystal structure (3TED) to match cross-linking as shown in (C).
See also Figure S1.