Related to Fig. 1. a, DNA-1 sequence. Two DNA strands are coloured in dark and light blue, canonical core motifs TTGT are coloured in red, TTXT motifs are shown in orange. Only motifs that allow SOX binding to the DNA minor groove are considered. The position of the third nucleotide of each motif in the DNA-1 sequence is indicated. Motifs at SHL+2 and −2 are shown in bold. b, Top views of the nucleosome. H2A, H2B, H3 and H4 are shown in yellow, red, blue and green, respectively, DNA is shown in dark and light blue. SHLs are labelled. c, DNA-1a template sequence. Only one TTGT motif is present (red). d, Structure of SOX2 (PDB code 1O4X) was aligned to each of the motifs present in nucleosome 1 and allowing binding of SOX to the minor groove. The number of clashes was calculated using ‘findclash’ command in Chimera software. SOX2 binding to motifs at SHL +2 and SHL −2 gives rise to the least amount of clashes with DNA and histones compared to other locations. The ideal position (modelled) of the SOX motif on the dyad would result in a comparably low number of clashes.