Recent large-scale efforts in genome sequencing, expression profiling, and functional screening have produced an embarrassment of riches for life sciences researchers, and biological data can now be accessed in quantities that are orders of magnitude greater than were available even a few years ago. The growing need for interpretation of data sets, as well as the accelerating demand for their integration to a higher-level understanding of life, has set the stage for the advent of systems biology [1,2], in which biological processes and phenomena are approached as complex and dynamic systems. Systems biology is a natural extension of molecular biology and can be defined as “biology after identification of key gene(s).” We see systems biological research as a multistage process, beginning with the comprehensive identification and quantitative analysis of individual system components and their networked interactions, and leading to the ability to control existing systems toward the desired state and design new ones based on an understanding of structure and underlying dynamical principles (Fig. 1).
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References
Kitano H (2002) Systems biology: a brief overview. Science 295:1662–1664
Kitano H (2002) Computational systems biology. Nature (Lond) 420:206–210
Reppert SM, Weaver DR (2002) Coordination of circadian timing in mammals. Nature (Lond) 418:935–941
Dunlap JC, Loros JJ, DeCoursey PJ (eds) (2004) Chronobiology: Biological Timekeeping. Sinauer Associates, Sunderland, MA
Panda S, Hogenesch JB, Kay SA (2002) Circadian rhythms from flies to human. Nature (Lond) 417:329–335
King DP, Zhao Y, Sangoram AM et al (1997) Positional cloning of the mouse circadian clock gene. Cell 89:641–653
Bunger MK, Wilsbacher LD, Moran SM et al (2000) Mop3 is an essential component of the master circadian pacemaker in mammals. Cell 103:1009–1017
Bae K, Jin X, Maywood ES et al (2001) Differential functions of mPer1, mPer2, and mPer3 in the SCN circadian clock. Neuron 30:525–536
Zheng B, Albrecht U, Kaasik K et al (2001) Nonredundant roles of the mPer1 and mPer2 genes in the mammalian circadian clock. Cell 105:683–694
van der Horst GT, Muijtjens M, Kobayashi K et al (1999) Mammalian Cry1 and Cry2 are essential for maintenance of circadian rhythms. Nature (Lond) 398:627–630
Vitaterna MH, Selby CP, Todo T et al (1999) Differential regulation of mammalian period genes and circadian rhythmicity by cryptochromes 1 and 2. Proc Natl Acad Sci USA 96:12114–12119
Lowrey PL, Shimomura K, Antoch MP et al (2000) Positional syntenic cloning and functional characterization of the mammalian circadian mutation tau. Science 288:483–492
Sato TK, Panda S, Miraglia LJ et al (2004) A functional genomics strategy reveals Rora as a component of the mammalian circadian clock. Neuron 43:527–537
Preitner N, Damiola F, Lopez-Molina L et al (2002) The orphan nuclear receptor REV-ERB-alpha controls circadian transcription within the positive limb of the mammalian circadian oscillator. Cell 110:251–260
Wuarin J, Schibler U (1990) Expression of the liver-enriched transcriptional activator protein DBP follows a stringent circadian rhythm. Cell 63:1257–1266
Mitsui S, Yamaguchi S, Matsuo T et al (2001) Antagonistic role of E4BP4 and PAR proteins in the circadian oscillatory mechanism. Genes Dev 15:995–1006
Honma S, Kawamoto T, Takagi Y et al (2002) Dec1 and Dec2 are regulators of the mammalian molecular clock. Nature (Lond) 419:841–844
Zylka MJ, Shearman LP, Weaver DR et al (1998) Three period homologs in mammals: differential light responses in the suprachiasmatic circadian clock and oscillating transcripts outside of brain. Neuron 20:1103–1110
Reick M, Garcia JA, Dudley C et al (2001) NPAS2: an analog of clock operative in the mammalian forebrain. Science 293:506–509
Ueda HR, Chen W, Adachi A et al (2002) A transcription factor response element for gene expression during circadian night. Nature (Lond) 418:534–539
Ueda HR, Hayashi S, Chen W et al (2005) System-level identification of transcriptional circuits underlying mammalian circadian clocks. Nat Genet 37:187–192
Yamazaki S, Numano R, Abe M et al (2000) Resetting central and peripheral circadian oscillators in transgenic rats. Science 288:682–685
Balsalobre A, Damiola F, Schibler U (1998) A serum shock induces circadian gene expression in mammalian tissue culture cells. Cell 93:929–937
Yagita K, Tamanini F, van Der Horst GT et al (2001) Molecular mechanisms of the biological clock in cultured fibroblasts. Science 292:278–281
Akashi M, Nishida E (2000) Involvement of the MAP kinase cascade in resetting of the mammalian circadian clock. Genes Dev 14:645–649
Gekakis N, Staknis D, Nguyen HB et al (1998) Role of the CLOCK protein in the mammalian circadian mechanism. Science 280:1564–1569.
Kume K, Zylka MJ, Sriram S et al (1999) mCRY1 and mCRY2 are essential components of the negative limb of the circadian clock feedback loop. Cell 98:193–205.
Shearman LP, Sriram S, Weaver DR et al (2000) Interacting molecular loops in the mammalian circadian clock. Science 288:1013–1019
Lipshutz RJ, Fodor SP, Gingeras TR et al (1999) High density synthetic oligonucleotide arrays. Nat Genet 21:20–24
Suzuki Y, Taira H, Tsunoda T et al (2001) Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites. EMBO Rep 2:388–393
Hogenesch JB, Gu YZ, Jain S et al (1998) The basic-helix-loop-helix-PAS orphan MOP3 forms transcriptionally active complexes with circadian and hypoxia factors. Proc Natl Acad Sci USA 95:5474–5479
Yoo SH, Ko CH, Lowrey PL et al (2005) A noncanonical E-box enhancer drives mouse Period 2 circadian oscillations in vivo. Proc Natl Acad Sci USA 102:2608–2613
Falvey E, Marcacci L, Schibler U (1996) DNA-binding specificity of PAR and C/EBP leucine zipper proteins: a single amino acid substitution in the C/EBP DNA-binding domain confers PAR-like specificity to C/EBP. Biol Chem 377:797–809
Harding HP, Lazar MA (1993) The orphan receptor Rev-ErbA alpha activates transcription via a novel response element. Mol Cell Biol 13:3113–3121
Ukai-Tadenuma M, Kasukawa T, Ueda HR (2008) Proof-by-synthesis of the transcriptional logic of mammalian circadian clocks. Nat Cell Biol 10:1154–1163
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Ueda, H.R. (2009). Systems Biology of Mammalian Circadian Clocks. In: Nakanishi, S., Kageyama, R., Watanabe, D. (eds) Systems Biology. Springer, Tokyo. https://doi.org/10.1007/978-4-431-87704-2_6
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DOI: https://doi.org/10.1007/978-4-431-87704-2_6
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