Extended Data Fig. 9: Non-pioneer MYC binding with OSK and GET to nucleosome arrays follow distinct mechanism.

a, MYC binding to closed chromatin is markedly different in the four TF combinations. Read density heatmaps showing TF ChIP-seq signal (blue) and ATAC-seq signal (red) spanning ±1 kb of MYC peak summits within closed chromatin in the indicated early reprogramming condition. The numbers (n) of MYC bound sites in each condition are indicated. Colour scale bars (RPGC) are indicated below. E-box motifs identified by de novo motif analysis from each group are indicated. b, Closed chromatin sites proximal to MYC display more opening in early reprogramming. Average chromatin accessibility (ATAC-seq) around ±1 kb of OSK, GET and GETR sites distal versus proximal to MYC sites before and after 72 h ectopic TF expression. The number of sites (n) is indicated. c, Profile plots (top panel) showing E-box motif enrichment on the top (red) and bottom (blue) DNA strands around the near-border (dotted line) of nucleosome arrays bound by OSK and MYC during early reprogramming. MYC ChIP-seq enrichment in early reprogramming is shown in the bottom panel. The average array size highlighted in yellow. d, Same as (c) for OSKM nucleosome arrays corrected for SOX2 motif orientation. e, Same as (c) for GET binding with MYC. f, Cartoon (top panel) and electrostatic surface (bottom panel) representations showing the interaction of MYC/MAX heterodimer with TFAP2C homodimer. The protein surface is coloured according to its electrostatic potential from red (−500 kT, negatively charged) to blue (+500 kT, positively charged). The complex structure was predicted by Alpha-Multimer only considering DBDs of MYC/MAX and TFAP2C. Cartoon representation of DNA (grey) containing TFAP2C site is shown. g, TFAP2C and MYC bind specifically together to Cdx2 enhancer site (TFAP2C target). Super-shift EMSA showing two retarded bands when GETM-48h nuclear lysates were incubated with Cy5-labelled oligonucleotide from Cdx2 enhancer containing TFAP2C site. The two bands correspond to TFAP2C-DNA and MYC/TFAP2C-DNA complexes. The MYC/TFAP2C-DNA band diminished after adding excessive amount of P19 (Cdkn2d promoter) oligonucleotide (MYC target) or MYC antibody as competitors. Both bands diminished after adding TFAP2C antibody, unlike GATA3 and EOMES antibodies. Representative image from n = 2 biological replicates. Uncropped gels are shown in Supplementary Fig. 1. h, Co- immunoprecipitation of TFAP2C and MYC indicating direct protein-protein interaction. Immunoprecipitation of TFAP2C, but not IgG, allows the detection of MYC by western blot in the presence of absence of DNase. Band representing MYC is indicated by an arrowhead. Molecular weight marker (KDa) is indicated. Representative image from n = 2 biological replicates. Raw blots are shown in Supplementary Fig. 1.