Sequence motifs at Sp1/Sp3 and Sp2 binding sites in MEFs.

(A) Sequence motifs enriched at Sp1/Sp3 and Sp2 binding sites. Logos were obtained by running MEME-ChIP [48] with 300 bp summits of the top 600 Sp1/Sp3, Sp2, Sp1/Sp3-specific and Sp2-specific ChIP-seq peaks. The numbers next to the logos indicate the occurrence of the motifs, and the statistical significance (E-value). (B) Central motif enrichment analysis of the motifs shown in Fig. 2A. (C) Occurrence of the canonical “CCAAT” sequence at the top 600 Sp1/Sp3, Sp2, Sp1/Sp3-specific and Sp2-specific ChIP-seq peaks. (D) Pairwise distribution of the canonical “CCAAT” sequence at the top 600 Sp1/Sp3, Sp2, Sp1/Sp3-specific and Sp2-specific ChIP-seq peaks. Each short blue line indicates a CCAAT motif. Black lines connect two CCAAT motifs in a promoter if they are located within a distance of 30 to 50 nucleotides.