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Genome-Wide and Phase-Specific DNA-Binding Rhythms of BMAL1 Control Circadian Output Functions in Mouse Liver

Figure 3

Genomic sequence preference of BMAL1 binding sites.

(A) Overrepresented motifs found using MEME [56]. DNA sequences in the window of ±50 bp around each BMAL1 site were used for the sequence analysis. The enrichment of Sp1 sites reflects the proximity of BMAL1 sites to TSSs (Figure 2B). (B) Autocorrelation analysis shows that E-box motifs come in tandem, with a spacing of six or seven nucleotides. Grey dashed lines represent the 95% confidence interval. (C) HMM for the tandem E-box motif (E1-E2 element) converges to one canonical E-box site with threshold at 7.2 bits and a tandem E1-E2 element with threshold at 10.2 bits (Table S5). To train the model, each sequence was given a weight proportional to the number of BMAL1 tags at peak binding. (D) Distribution of distances from E1-E2 positions to peak centers. The E1-E2 elements are sharply located around the inferred binding location. (E) Sites with E1-E2 elements have significantly more tags (left) and show more robust rhythmic binding of BMAL1 (right) than sites without E-boxes (Ø) or with single E-boxes (E1). ***, p<5×10−5, Student's t test. (F) BMAL1 sites are strongly enriched in E1-E2 instances compared to control regions. Control regions were taken 500 bp downstream of each site.

Figure 3