Extended Data Fig. 5: MYC-MAX and CLOCK-BMAL1 bind in proximity to nucleosomes.

a, Representative cryo-EM micrograph of 8,841 total, denoised with Janni⁸¹. b, The movies were motion-corrected in RELION and the particles were picked using LoG picking (RELION). Multiple rounds of 2D and 3D classification (RELION) yielded a homogeneous subset of particles used for the final 3D reconstruction. The boxes defined by a dashed line indicate the good models and set of particles used for the following step in the data processing workflow. c, Local-resolution filtered map (MonoRes) for the 3.3 Å resolution map⁹⁰. d, Angular distribution for the particles leading to the 3.3 Å resolution map. e, Gold-standard FSC curve for the final 3.3 Å resolution map. f, Map density around MYC-MAX at position SHL+5.8, contoured at 0.0948 (map postprocessed by LocScale)⁸⁸. g, CLOCK-BMAL1 binds NCP^SHL+5.8 with higher affinity than MYC-MAX. TR-FRET counter-titration of unlabelled CLOCK-BMAL1 or MYC-MAX into the preassembled Eu-NCP^SHL+5.8-His-MYC-MAX complex. Three technical replicates are shown for each condition and three biological replicates were performed with similar results. h, Cross-links between MYC and H2A and H2B lysines (spheres). The cross-linker was DSSO and indicated distances (dashes) are between lysine Cα atoms. i, Position weight matrices (PWMs) of the binding motifs found within the peaks of each ChIP–seq profile as determined by MEME motif discovery (-mod anr -dna -revcom). j–l, Replication correlation analysis for the ChIP–seq samples used in Fig. 4c. The D. melanogaster genome (dm6) was queried for 5,000 hits of the E-box motif CACGTG. Read counts at each motif were normalized, counted for each replicate and replicates were compared in scatter plots. The correlation coefficients are indicated with two-tailed Pearson P values annotated at P < 0.1 (*), 0.05 (**) and 0.01 (***).