Developmental enhancers overlap conserved HCTs. (A) The fraction of enhancers functional in mouse (487) that overlap with at least three sites in HCTs (39.2%, yellow) is significantly higher (P < 8.5 × 10−102) than what is expected by chance (1.5%, black). The fraction increases to above 50% if a lower number of TFBSs in an HCT are allowed for an HCT-enhancer overlap. (B) Coverage of positive enhancers by HCTs shows that HCTs are located toward the center of the enhancer. (C) HCTs of different transcription factors are associated with enhancers that show tissue specific, e.g., heart (A), hindbrain (B), or forebrain (D), or a more ubiquitous expression pattern (C,E) in E11.5 mouse embryos. The shade of gray is proportional to the number of tissue-specific enhancers overlapping HCTs for a specific TF, with the lightest shade of gray indicating one, and black indicating 10 (only observed for NOBOX and forebrain-specific enhancers) overlap instances. The tissues and the corresponding number of enhancers found to be active in them (indicated in parentheses) are: Mesenchyme derived from neural crest (1), facial mesenchyme (6), heart (20), other (22), cranial nerve (25), trigeminal V (ganglion, cranial) (18), dorsal root ganglion (34), limb (79), hindbrain (rhombencephalon) (142), midbrain (mesencephalon) (148), forebrain (156), neural tube (103), branchial arch (22), nose (20), eye (32), melanocytes (3), genital tubercle (3), somite (7), ear (6), and tail (2).
