Genome-Wide Profiling of the Core Clock Protein BMAL1 Targets Reveals a Strict Relationship with Metabolism

Abstract

Circadian rhythms are common to most organisms and govern much of homeostasis and physiology. Since a significant fraction of the mammalian genome is controlled by the clock machinery, understanding the genome-wide signaling and epigenetic basis of circadian gene expression is essential. BMAL1 is a critical circadian transcription factor that regulates genes via E-box elements in their promoters. We used multiple high-throughput approaches, including chromatin immunoprecipitation-based systematic analyses and DNA microarrays combined with bioinformatics, to generate genome-wide profiles of BMAL1 target genes. We reveal that, in addition to E-boxes, the CCAATG element contributes to elicit robust circadian expression. BMAL1 occupancy is found in more than 150 sites, including all known clock genes. Importantly, a significant proportion of BMAL1 targets include genes that encode central regulators of metabolic processes. The database generated in this study constitutes a useful resource to decipher the network of circadian gene control and its intimate links with several fundamental physiological functions.

Reprogramming of the Circadian Clock by Nutritional Challenge

“…Specifically, oscillatory transcripts in the NC-only group showed robust peaks between ZT4-ZT12, while the HFD group showed rather an irregular phase pattern (Figure 2G). The peak of oscillatory transcripts in the NC-only condition is consistent with when the CLOCK:BMAL1 heterodimer is most active and recruited to circadian contacts (Hatanaka et al, 2010; Kondratov et al, 2003; Rey et al, 2011). When comparing the phase of the transcripts and metabolites that oscillated in both liver sets (Figure 2H, left), similar organization was seen, with transcripts and metabolites showing a biphasic pattern and transcript peaks slightly preceding metabolite peaks.…”

Circadian Enhancers Coordinate Multiple Phases of Rhythmic Gene Transcription In Vivo

“…Previous genomic studies of circadian gene regulation have focused primarily on the core clock components BMAL1/CLOCK, which bind DNA with a uniform genome-wide phase peaking at ZT6–9 (Hatanaka et al, 2010; Koike et al, 2012; Menet et al, 2012; Rey et al, 2011; Yoshitane et al, 2014), yet only a small fraction of circadian gene transcription is in this phase. Our data suggest that only the genes with phase ZT6–9 are the true BMAL1/CLOCK targets, while many other genes are bound, but not controlled, by BMAL1/CLOCK possibly due to inactive binding or long distance looping to different genes.…”

CLOCK-Controlled Polyphonic Regulation of Circadian Rhythms through Canonical and Noncanonical E-Boxes

“…High-quality ChIP-Seq data in this study made it possible to quantitatively and comprehensively investigate CLOCK-binding motifs in vivo. MEME is a widely used tool for determining DNA-binding motifs (41), and BMAL1-binding motifs were defined by using MEME in previous studies (20,21). Here we should consider the feature of MEME, which aims at determining representative sequence motifs (Fig.…”

“…Recent works have explored the genome-wide profiling of DNA binding patterns of circadian transcription factors such as REV-ERB␣/␤ (57-59), BMAL1 (20)(21)(22)(23), and CLOCK (22,23; this study). The Takahashi laboratory demonstrated 1,444 genomic sites as common targets of six clock proteins: BMAL1, CLOCK, PER1, PER2, CRY1, and CRY2 (22).…”

“…Here we found in vivo binding sites of CLOCK protein in the mouse liver in a genome-wide manner by chromatin immunoprecipitation-sequencing (ChIP-Seq) analysis. Previous ChIP-Seq studies of circadian clocks confirmed CLOCK-BMAL1 binding to canonical motifs instead of finding all potential binding motifs (20)(21)(22)(23). In this study, significant CLOCK-binding motifs were comprehensively examined by developing a bioinformatics method, MOCCS (motif centrality analysis of ChIP-Seq), which analyzes the frequency distribution of DNA sequences centered at DNA-binding sites found by ChIPSeq analyses.…”