Genome-wide expression analysis of mouse liver reveals CLOCK-regulated circadian output genes.
CLOCK is a positive component of a transcription/translation-based negative feedback loop of the central circadian oscillator in the suprachiasmatic nucleus in mammals. To examine CLOCK-regulated circadian transcription in peripheral tissues, we performed microarray analyses using liver RNA isolated from Clock mutant mice. We also compared expression profiles with those of Cryptochromes (Cry1 and Cry2) double knockout mice. We identified more than 100 genes that fluctuated from day to night and of which expression levels were decreased in Clock mutant mice. In Cry-deficient mice, the expression levels of most CLOCK-regulated genes were elevated to the upper range of normal oscillation. Most of the screened genes had a CLOCK/BMAL1 binding site (E box) in the 5'-flanking region. We found that CLOCK was absolutely concerned with the circadian transcription of one type of liver genes (such as DBP, TEF, and Usp2) and partially with another (such as mPer1, mPer2, mDec1, Nocturnin, P450 oxidoreductase, and FKBP51) because the latter were damped but remained rhythmic in the mutant mice. Our results showed that CLOCK and CRY proteins are involved in the transcriptional regulation of many circadian output genes in the mouse liver. In addition to being a core component of the negative feedback loop that drives the circadian oscillator, CLOCK also appears to be involved in various physiological functions such as cell cycle, lipid metabolism, immune functions, and proteolysis in peripheral tissues.
Oishi
Katsutaka
K
Clock Cell Biology Research Group, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
Miyazaki
Koyomi
K
Kadota
Koji
K
Kikuno
Reiko
R
Nagase
Takahiro
T
Atsumi
Gen-ichi
G
Ohkura
Naoki
N
Azama
Takashi
T
Mesaki
Miho
M
Yukimasa
Shima
S
Kobayashi
Hisato
H
Iitaka
Chisato
C
Umehara
Takashi
T
Horikoshi
Masami
M
Kudo
Takashi
T
Shimizu
Yoshihisa
Y
Yano
Masahiko
M
Monden
Morito
M
Machida
Kazuhiko
K
Matsuda
Juzo
J
Horie
Shuichi
S
Todo
Takeshi
T
Ishida
Norio
N
D020816:Amino Acid Motifs; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D015152:Blotting, Northern; D056926:CLOCK Proteins; D002940:Circadian Rhythm; D005227:Fatty Acids / Q000378:metabolism; D016678:Genome; D006801:Humans; D017403:In Situ Hybridization; D050356:Lipid Metabolism; D008099:Liver / Q000378:metabolism; D008297:Male; D051379:Mice; D018345:Mice, Knockout; D008969:Molecular Sequence Data; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D012313:RNA / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012689:Sequence Homology, Nucleic Acid; D013997:Time Factors; D015534:Trans-Activators / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic
D005227:Fatty Acids; D012333:RNA, Messenger; D015534:Trans-Activators; D012313:RNA; D056926:CLOCK Proteins; C538943:CLOCK protein, human; C538944:Clock protein, mouse