Supplementary Figure 1: Aggregated DNase I cleavage patterns for TF recognition sequences reflecting diverse DNA-binding domains.

(a) Heatmaps of per-nucleotide DNase I cleavages and discovered footprints surrounding NRF1 recognition sequences. Left, observed cleavages. Right, the ratio of the observed cleavages to expected cleavages computed by reassigning tags to a hexamer model DNase I cleavage bias. Blue ticks indicate that the recognition sequence has an associated DNase I footprint. Line plots show the aggregate profile of mean per-nucleotide DNase I cleavages at the 20% most (left column) and 20% least (right column) accessible NRF1 recognition sequences. Top row, observed cleavages. Middle, expected cleavages computed using the hexamer model. Bottom, the log₂ ratio of observed to expected. (b-g) The same as (a) for the recognition sequences for (b) SP1, (c) ELK1, (d) USF1, (e) RFX3, (f) NFIB, and (g) CTCF within accessible chromatin. In each case the cleavage patterns at occupied templates (coinciding with de novo TF footprint calls) parallel known structural features of the respective DNA binding domains.