Extended Data Fig. 4: The seq2PRINT framework.

a, Schematic illustration of the seq2PRINT model. b-c, Down-sampling test for seq2PRINT. Showing (b) Pearson correlation coefficient between predicted and ground truth multiscale footprints and (c) median precision of TF binding prediction at top 10% predicted binding sites. Here, ground truth footprints were defined as observed footprints without any down-sampling. d, Waterfall plot showing precision improvement of seq2PRINT over ChromBPNet for individual TFs. e, Observed footprints (40 bp scale) at bound and unbound motif sites for ATF3 and YY1. Bound and unbound motif sites are defined by overlap with ChIP-seq peaks. f, TF binding scores predicted by seq2PRINT at bound and unbound motif sites for ATF3 and YY1. g, Observed changes in multiscale footprints at GR binding sites after dexamethasone treatment to induce relocalization of GR into the nucleus and binding to DNA²⁴. h, seq2PRINT-predicted differences in multiscale footprints at GR motif sites comparing WT GR motif and in silico disruption of GR motif. (Pearson correlation=0.73 with observed changes). i, Observed changes in multiscale footprints at Stat2 binding sites in B cells after IFN treatment²⁵. j, seq2PRINT-predicted differences in multiscale footprints at Stat2 binding sites comparing WT Stat2 motif and in silico disruption of Stat2 motif. (Pearson correlation=0.23 with observed changes). k, Heatmap showing clustering of TFs based on Jaccard similarity of motif matches. Rows and columns are individual TFs.