TFBS repertoire and position conservation between orthologous human and macaque CREs. (A–C) TFBS repertoire conservation across PDs. Depicted are mean values ± SEM. (A) TFBS repertoire conservation increases with higher PD among promoters and decreases slightly at high PD enhancers. (B) CREs that overlap NPC peaks with conserved openness show higher TFBS repertoire conservation than species-specific NPC peaks.
(C) TFBS repertoire conservation differs across tissues, in which the brain shows the highest conservation at lower PDs. (D) Simplified schematic of the scenarios of repertoire and position conservation. (E) TFBS position conservation versus repertoire conservation across PD categories. Depicted are mean values ± SEM. (F) Standardized scores (z-scores) of sequence (primate phyloP), TFBS repertoire, and binding site conservation between human and cynomolgus macaque.
(G) A schematic depicting how lower sequence conservation might lead to higher TFBS repertoire conservation through compensatory
mechanisms. (H) A summary of the scaled average conservation metric scores across PDs. Sequence, primate phyloP scores; TFBS position, 
; TFBS repertoire, 
; CpG observed/expected, 
; accessibility, 1 − |LFC| of NPC-DA; and downstream expression, 1 − |LFC| of NPC-DE.
