Cry1 Circadian Phase in vitro : Wrapped Up with an E-Box

Abstract

The circadian timing of gene expression is determined by transcriptional regulation through upstream response elements present throughout the genome. Central to this regulation are the actions of a core group of transcriptional activators and repressors, which act through, and are themselves regulated by, a small set of canonical circadian response elements. Among these, the E-box (CACGTG) is crucial for daytime transcriptional activity. The mammalian Period (Per1-3) and Cryptochrome (Cry1-2) genes are E-box—regulated genes, but in peripheral tissues peak Cry1 mRNA expression is delayed by several hours relative to that of Per. It has been proposed that this delay originates from interactions between the proximal E-box and retinoic acid—related orphan receptor response elements (RORE) present in the Cry1 promoter. By using real-time luciferase reporter assays in NIH3T3 cells the authors show here that a proximal 47-bp E-box containing region of the Cry1 promoter is both necessary and sufficient to drive circadian Cry1 transcription with an appropriate phase delay (around 4 h) relative to Per2. The results therefore suggest that, at least in this in vitro model of the clock, RORE are not necessary for the appropriate circadian regulation of Cry1 expression and rather suggest that sequences surrounding the proximal E-boxes confer gene-specific circadian phasing.

Keywords

circadian cryptochrome period RORE E-box

References

Akashi M. , Ichise T. , Mamine T. , and Takumi T. (2006) Molecular mechanism of cell-autonomous circadian gene expression of Period2, a crucial regulator of the mammalian circadian clock. Mol Biol Cell 17:2555-2565.

Akashi M. and Takumi T. (2005) The orphan nuclear receptor RORalpha regulates circadian transcription of the mammalian core-clock Bmal1. Nat Struct Mol Biol 12:5441-5448.

Dardente H. and Cermakian N. (2007) Molecular circadian rhythms in central and peripheral clocks in mammals. Chronobiol Int 24:2195-2213.

Dardente H. , Menet JS , Poirel VJ , Streicher D. , Gauer F. , Vivien-Roels B. , Klosen P. , Pevet P. , and Masson-Pevet M. (2003) Melatonin induces Cry1 expression in the pars tuberalis of the rat. Brain Res Mol Brain Res 114:2101-2106.

Darlington TK , Wager-Smith K. , Ceriani MF , Staknis D. , Gekakis N. , Steeves TD , Weitz CJ , Takahashi JS , and Kay SA (1998) Closing the circadian loop: CLOCK-induced transcription of its own inhibitors per and tim. Science 280:1599-1603.

Etchegaray JP , Lee C. , Wade PA , and Reppert SM (2003) Rhythmic histone acetylation underlies transcription in the mammalian circadian clock. Nature 421:177-182.

Forger DB and Peskin CS (2003) A detailed predictive model of the mammalian circadian clock. Proc Natl Acad Sci U S A 100:14806-14811.

Forger DB and Peskin CS (2004) Model based conjectures on mammalian clock controversies . J Theor Biol 230:533-539.

Fustin JM , Dardente H. , Wagner GC , Carter DA , Johnston JD , Lincoln GA , and Hazlerigg DG (2008) Egr1 involvement in evening gene regulation by melatonin. Faseb J (Epub ahead of print: DOI: 10.1096/fj.08-121467).

10.

Gekakis N. , Staknis D. , Nguyen HB , Davis FC , Wilsbacher LD , King DP , Takahashi JS , and Weitz CJ (1998) Role of the CLOCK protein in the mammalian circadian mechanism. Science 280:1564-1569.

11.

Guillaumond F. , Dardente H. , Giguere V. , and Cermakian N. (2005) Differential control of Bmal1 circadian transcription by REV-ERB and ROR nuclear receptors. J Biol Rhythms 20:391-403.

12.

Hao H. , Allen DL , and Hardin PE (1997) A circadian enhancer mediates PER-dependent mRNA cycling in Drosophila melanogaster. Mol Cell Biol 17:687-693.

13.

Hastings MH , Maywood ES , and O'Neill JS (2008) Cellular circadian pacemaking and the role of cytosolic rhythms. Curr Biol 18:R805-R815.

14.

Johnston JD , Tournier BB , Andersson H. , Masson-Pevet M. , Lincoln GA , and Hazlerigg DG (2006) Multiple effects of melatonin on rhythmic clock gene expression in the mammalian pars tuberalis. Endocrinology 147:959-965.

15.

Kumaki Y. , Ukai-Tadenuma M. , Uno KI , Nishio J. , Masumoto KH , Nagano M. , Komori T. , Shigeyoshi Y. , Hogenesch JB , and Ueda HR (2008) Analysis and synthesis of high-amplitude Cis-elements in the mammalian circadian clock. Proc Natl Acad Sci U S A 105:14946-14951.

16.

Kume K. , Zylka MJ , Sriram S. , Shearman LP , Weaver DR , Jin X. , Maywood ES , Hastings MH , and Reppert SM (1999) mCRY1 and mCRY2 are essential components of the negative limb of the circadian clock feedback loop. Cell 98:193-205.

17.

Kyriacou CP and Rosato E. (2000) Squaring up the E-box. J Biol Rhythms 15:483-490.

18.

Liu AC , Tran HG , Zhang EE , Priest AA , Welsh DK , and Kay SA (2008) Redundant function of REV-ERBalpha and beta and non-essential role for Bmal1 cycling in transcriptional regulation of intracellular circadian rhythms. PLoS Genet 4:2e1000023.

19.

Lyons LC , Darlington TK , Hao H. , Houl J. , Kay SA , and Hardin PE (2000) Specific sequences outside the E-box are required for proper per expression and behavioral rescue. J Biol Rhythms 15:472-482.

20.

Miyamoto Y. and Sancar A. (1998) Vitamin B2-based blue-light photoreceptors in the retinohypothalamic tract as the photoactive pigments for setting the circadian clock in mammals. Proc Natl Acad Sci U S A 95:6097-6102.

21.

Munoz E. , Brewer M. , and Baler R. (2006) Modulation of BMAL/CLOCK/E-Box complex activity by a CT-rich cis-acting element. Mol Cell Endocrinol 252:74-81.

22.

Nakahata Y. , Yoshida M. , Takano A. , Soma H. , Yamamoto T. , Yasuda A. , Nakatsu T. , and Takumi T. (2008) A direct repeat of E-box-like elements is required for cell-autonomous circadian rhythm of clock genes. BMC Mol Biol 9:1.

23.

Obrietan K. , Impey S. , Smith D. , Athos J. , and Storm DR (1999) Circadian regulation of cAMP response element-mediated gene expression in the suprachiasmatic nuclei. J Biol Chem 274:17748-17756.

24.

Okamura H. , Miyake S. , Sumi Y. , Yamaguchi S. , Yasui A. , Muijtjens M. , Hoeijmakers JH , and van der Horst GT (1999) Photic induction of mPer1 and mPer2 in cry-deficient mice lacking a biological clock. Science 286:2531-2534.

25.

O'Neill JS and Hastings MH (2008) Increased coherence of circadian rhythms in mature fibroblast cultures. J Biol Rhythms 23:483-488.

26.

O'Neill JS , Maywood ES , Chesham JE , Takahashi JS , and Hastings MH (2008) cAMP-dependent signaling as a core component of the mammalian circadian pacemaker. Science 320:949-953.

27.

Paquet ER , Rey G. , and Naef F. (2008) Modeling an evolutionary conserved circadian cis-element . PLoS Comput Biol 2:e38.

28.

Poirel VJ , Boggio V. , Dardente H. , Pevet P. , Masson-Pevet M. , and Gauer F. (2003) Contrary to other non-photic cues, acute melatonin injection does not induce immediate changes of clock gene mRNA expression in the rat suprachiasmatic nuclei. Neuroscience 120:745-755.

29.

Preitner N. , Damiola F. , Lopez-Molina L. , Zakany J. , Duboule D. , Albrecht U. , and Schibler U. (2002) The orphan nuclear receptor REV-ERBalpha controls circadian transcription within the positive limb of the mammalian circadian oscillator. Cell 110:251-260.

30.

Sato TK , Yamada RG , Ukai H. , Baggs JE , Miraglia LJ , Kobayashi TJ , Welsh DK , Kay SA , Ueda HR , and Hogenesch JB (2006) Feedback repression is required for mammalian circadian clock function. Nat Genet 38:312-319.

31.

Sato TK , Panda S. , Miraglia LJ , Reyes TM , Rudic RD , McNamara P. , Naik KA , FitzGerald GA , Kay SA , and Hogenesch JB (2004) A functional genomics strategy reveals Rora as a component of the mammalian circadian clock. Neuron 43:527-537.

32.

Triqueneaux G. , Thenot S. , Kakizawa T. , Antoch MP , Safi R. , Takahashi JS , Delaunay F. , and Laudet V. (2004) The orphan receptor Rev-erbalpha gene is a target of the circadian clock pacemaker. J Mol Endocrinol 33: 585-608.

33.

Ueda HR , Hayashi S. , Chen W. , Sano M. , Machida M. , Shigeyoshi Y. , Iino M. , and Hashimoto S. (2005) System-level identification of transcriptional circuits underlying mammalian circadian clocks. Nat Genet 37:187-192.

34.

Ueda HR , Chen W. , Adachi A. , Wakamatsu H. , Hayashi S. , Takasugi T. , Nagano M. , Nakahama K. , Suzuki Y. , Sugano S. , et al. (2002) A transcription factor response element for gene expression during circadian night. Nature 418: 534-539.

35.

Ukai-Tadenuma M. , Kasukawa T. , and Ueda HR (2008) Proof-by-synthesis of the transcriptional logic of mammalian circadian clocks. Nat Cell Biol 10:54-63.

36.

Yamamoto T. , Nakahata Y. , Soma H. , Akashi M. , Mamine T. , and Takumi T. (2004) Transcriptional oscillation of canonical clock genes in mouse peripheral tissues. BMC Mol Biol 5:18.

37.

Yang X. , Downes M. , Yu RT , Bookout AL , He W. , Straume M. , Mangelsdorf DJ , and Evans RM (2006) Nuclear receptor expression links the circadian clock to metabolism. Cell 126:801-810.

38.

Yoo SH , Ko CH , Lowrey PL , Buhr ED , Song EJ , Chang S. , Yoo OJ , Yamazaki S. , Lee C. , and Takahashi JS (2005) A noncanonical E-box enhancer drives mouse Period2 circadian oscillations in vivo. Proc Natl Acad Sci U S A 102:2608-2613.