title: CLOCK-controlled polyphonic regulation of circadian rhythms through canonical and noncanonical E-boxes.
abstract: In mammalian circadian clockwork, the CLOCK-BMAL1 complex binds to DNA enhancers of target genes and drives circadian oscillation of transcription. Here we identified 7,978 CLOCK-binding sites in mouse liver by chromatin immunoprecipitation-sequencing (ChIP-Seq), and a newly developed bioinformatics method, motif centrality analysis of ChIP-Seq (MOCCS), revealed a genome-wide distribution of previously unappreciated noncanonical E-boxes targeted by CLOCK. In vitro promoter assays showed that CACGNG, CACGTT, and CATG(T/C)G are functional CLOCK-binding motifs. Furthermore, we extensively revealed rhythmically expressed genes by poly(A)-tailed RNA-Seq and identified 1,629 CLOCK target genes within 11,926 genes expressed in the liver. Our analysis also revealed rhythmically expressed genes that have no apparent CLOCK-binding site, indicating the importance of indirect transcriptional and posttranscriptional regulations. Indirect transcriptional regulation is represented by rhythmic expression of CLOCK-regulated transcription factors, such as Krüppel-like factors (KLFs). Indirect posttranscriptional regulation involves rhythmic microRNAs that were identified by small-RNA-Seq. Collectively, CLOCK-dependent direct transactivation through multiple E-boxes and indirect regulations polyphonically orchestrate dynamic circadian outputs.
authors.affiliation: Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
authors.forename: Hikari
authors.initials: H
authors.lastname: Yoshitane
authors.forename: Haruka
authors.initials: H
authors.lastname: Ozaki
authors.forename: Hideki
authors.initials: H
authors.lastname: Terajima
authors.forename: Ngoc-Hien
authors.initials: NH
authors.lastname: Du
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Suzuki
authors.forename: Taihei
authors.initials: T
authors.lastname: Fujimori
authors.forename: Naoki
authors.initials: N
authors.lastname: Kosaka
authors.forename: Shigeki
authors.initials: S
authors.lastname: Shimba
authors.forename: Sumio
authors.initials: S
authors.lastname: Sugano
authors.forename: Toshihisa
authors.initials: T
authors.lastname: Takagi
authors.forename: Wataru
authors.initials: W
authors.lastname: Iwasaki
authors.forename: Yoshitaka
authors.initials: Y
authors.lastname: Fukada
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D056926:CLOCK Proteins / Q000502:physiology*; D002940:Circadian Rhythm; D016384:Consensus Sequence; D024721:E-Box Elements; D057809:HEK293 Cells; D006801:Humans; D051741:Kruppel-Like Transcription Factors / Q000378:metabolism; D008099:Liver; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D018345:Mice, Knockout; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D034622:RNA Interference; D059467:Transcriptome
chemical_list: D051741:Kruppel-Like Transcription Factors; D035683:MicroRNAs; D056926:CLOCK Proteins; C538944:Clock protein, mouse