Regulatory motifs predicted to be drivers of enhancer activity patterns showed significant enrichment in tissue-specific high-resolution (6bp-40bp) DNase digital genomic footprints (DGF)68 in matching cell types (Extended Data 9b, Table S5b), providing DNA accessibility evidence that the motifs are indeed bound in these cell types. In addition, they showed positional bias relative to both the center of DGF locations, and relative to their boundaries (Extended Data 10), a property not found for shuffled motifs69. These positional biases were highly tissue- and cell type-specific for most activating factors (Extended Data 9c), including POU5F in iPSCs, MEF2D in heart, HNF1B in GI tissues, BHLH in brain, SPI1 in immune cells, and MEF2 in heart and muscle, in each case matching the tissues that showed the highest enrichment. In contrast, for repressive factors and CTCF, positional biases were found in large numbers of tissues, even when the motifs were not enriched in active enhancers. For example, REST (NRSF) was positionally biased in DGF sites in nearly all tissues except brain (Extended Data 9c), even though it was only enriched in active enhancers in brain (Extended Data 9a), consistent with widespread repressive binding in non-brain tissues.
