Fig. 2: Decoding the genomic syntax of cCRE organization.

a, Schematic of footprint-to-object prediction and seq2PRINT models and their applications. b, Observed (top) and predicted multiscale footprints (bottom) in example region chr. 4:39181940–39182739. c, Seq2PRINT sequence attribution scores in the region depicted in b, showing attribution scores calculated with respect to multiscale footprints in the whole region (track 1) or specific footprints (tracks 2–5). d, Bar plot showing median precision of TF binding prediction by different methods. e, Bar plot showing median precision of TF binding prediction by seq2PRINT, ChromBPNet and TOBIAS for different TF clusters, as defined in Extended Data Fig. 2e. f, Left, schematic representation of experimental depletion of degron-tagged CTCF and in silico disruption of CTCF binding sites. Right, observed changes in multiscale footprints at CTCF motif sites following experimental CTCF depletion, and seq2PRINT-predicted multiscale footprint changes following in silico CTCF motif disruption. g, Left, seq2PRINT-predicted changes in multiscale footprints following in silico ablation of motif sites of example TFs. Right, heatmap showing clustering of TFs based on seq2PRINT-predicted changes following in silico motif ablation. h, Representative de novo motifs identified by TF motif discovery from sequence attribution scores (TF-MoDISco) from seq2PRINT-predicted sites, and corresponding predicted changes in multiscale footprints following in silico motif ablation (colour scale as in g). Max., maximum; min., minimum.