PLZF-RARα binds an extended repertoire of RAREs. (A) The frequency of consensus RAREs (PuG(G/T)TCA)(0-20 bp)(PuG(G/T)TCA) in PLZF-RARα–bound promoters (4916 genes) was calculated. The total number of RAREs and genes containing RAREs are shown to the far right. The frequency of spacer lengths corresponding to each RARE was also calculated. (B) The ECHS1 promoter peak contains multiple RAREs (underlined). (C) MATRIXReduce was used to identify consensus motifs in PLZF-RARα–enriched peak sequences (2/3 biologic replicates, FDR < 0.2, differentially expressed > 1.5-fold, P < .05; 1672 genes). The top-scoring motif identified in PLZF-RARα–bound promoters was most similar to nuclear hormone receptor binding sites containing the RARE (A/G)GGTCA half site.