Genome-Wide and Phase-Specific DNA-Binding Rhythms of BMAL1 Control Circadian Output Functions in Mouse Liver
(A–C) BMAL1 binding profiles (filled symbols, upper panels) in comparison to qPCR measurement on pre-mRNA (open symbols) and mRNA (filled symbols, lower panels). The clock genes are separated into three groups based on the difference of phase of pre-mRNA expression and BMAL1 binding. The data represent the mean ± standard deviation of three experiments. The maximal value was normalized to 1. ZT22 is plotted twice to facilitate visualization. (A) Early targets. Rev-Erbα, Rev-Erbβ, Dbp, Tef, and Dec2 pre-mRNA accumulation coincides with the BMAL1 binding profile. (B) Intermediate targets. Per1, Per2, and Cry2 pre-mRNA accumulation is delayed by a few hours relative to the BMAL1 binding profile. (C) Late targets. For Cry1, Rorγ, and E4bp4, BMAL1 binding does not predict pre-mRNA accumulation. (D) mRNA expression levels in wild-type (WT) and Bmal1−/− mice. Expression levels were measured at ZT6 and ZT18. The clock genes are separated into three groups as in (A–C). Early targets are likely to be controlled directly and only by BMAL1 since their mRNA levels are low both at ZT6 and ZT18 in Bmal1−/− mice. Intermediate and late targets have either intermediate or elevated mRNA levels in Bmal1−/− mice, suggesting more complex transcriptional regulation. The data were analyzed as in (A–C).