Intrinsic DNA codes govern distinct modes of nucleosome-transcription factor interactions

The interplay between transcription factors (TFs) and nucleosomes is central to gene regulation, yet most studies adopt a protein-centric perspective that largely overlooks DNA sequence contributions. Here, we identify four distinct nucleosomal DNA classes, including the canonical WW/SS pattern (W = A/T, S = G/C). All four nucleosome types are widespread across the human genome both in vivo and in vitro. Nucleosomes sharing the same pattern are rotationally in phase, whereas different patterns exhibit specific rotational offsets, revealing distinct DNA-encoded codes for nucleosome positioning. Analysis of 747 TFs across eukaryotes shows that the WW/SS and anti-WW/SS patterns are strongly associated with TF binding in chromatin. Differences in the proportions of these two patterns, quantified as {Delta}NPS values, correlate closely with in vitro nucleosome occupancy. Integrating {Delta}NPS with in vivo nucleosome occupancy uncovers four distinct modes of nucleosome-TF interaction and provides new insight into nucleosome-depleted regions around TF binding sites.