Zhang, E. E. & Kay, S. A. Clocks not winding down: unravelling circadian networks. Nat. Rev. Mol. Cell Biol. 11, 764–776 (2010).
Rosbash, M. The implications of multiple circadian clock origins. PLoS Biol. 7, e1000062 (2009).
Hardin, P. E., Hall, J. C. & Rosbash, M. Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels. Nature 343, 536–540 (1990).
Takahashi, J. S. Transcriptional architecture of the mammalian circadian clock. Nat. Rev. Genet. 18, 164–179 (2017).
Johnson, C. H., Stewart, P. L. & Egli, M. The cyanobacterial circadian system: from biophysics to bioevolution. Annu. Rev. Biophys. 40, 143–167 (2011).
Lane, N. & Martin, W. The energetics of genome complexity. Nature 467, 929–934 (2010).
Cheng, Y., Chi, Y., Sun, L. & Wang, G.-Z. Dominant constraints on the evolution of rhythmic gene expression. Comput. Struct. Biotechnol. J. 21, 4301–4311 (2023).
Wagner, A. Energy constraints on the evolution of gene expression. Mol. Biol. Evol. 22, 1365–1374 (2005).
Elowitz, M. B. & Leibler, S. A synthetic oscillatory network of transcriptional regulators. Nature 403, 335–338 (2000).
Fung, E. et al. A synthetic gene–metabolic oscillator. Nature 435, 118–122 (2005).
Tigges, M., Marquez-Lago, T. T., Stelling, J. & Fussenegger, M. A tunable synthetic mammalian oscillator. Nature 457, 309–312 (2009).
Nakajima, M. et al. Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro. Science 308, 414–415 (2005).
Terauchi, K. et al. ATPase activity of KaiC determines the basic timing for circadian clock of cyanobacteria. Proc. Natl Acad. Sci. USA 104, 16377–16381 (2007).
Abe, J. et al. Atomic-scale origins of slowness in the cyanobacterial circadian clock. Science 349, 312–316 (2015).
Pitsawong, W. et al. From primordial clocks to circadian oscillators. Nature 616, 183–189 (2023).
Ju, D. et al. Chemical perturbations reveal that RUVBL2 regulates the circadian phase in mammals. Sci. Transl. Med. 12, eaba0769 (2020).
Takahashi, J. S., Shimomura, K. & Kumar, V. Searching for genes underlying behavior: lessons from circadian rhythms. Science 322, 909–912 (2008).
Michel, B. C. et al. A non-canonical SWI/SNF complex is a synthetic lethal target in cancers driven by BAF complex perturbation. Nat. Cell Biol. 20, 1410–1420 (2018).
Zhang, E. E. et al. A genome-wide RNAi screen for modifiers of the circadian clock in human cells. Cell 139, 199–210 (2009).
Xu, Y. et al. Modeling of a human circadian mutation yields insights into clock regulation by PER2. Cell 128, 59–70 (2007).
Hirota, T. et al. A chemical biology approach reveals period shortening of the mammalian circadian clock by specific inhibition of GSK-3β. Proc. Natl Acad. Sci. USA 105, 20746–20751 (2008).
Konopka, R. J. & Benzer, S. Clock Mutants of Drosophila melanogaster. Proc. Natl Acad. Sci. USA 68, 2112–2116 (1971).
Price, J. L. et al. double-time is a novel Drosophila clock gene that regulates PERIOD protein accumulation. Cell 94, 83–95 (1998).
Sehgal, A., Price, J. L., Man, B. & Young, M. W. Loss of circadian behavioral rhythms and per RNA oscillations in the Drosophila mutant timeless. Science 263, 1603–1606 (1994).
Vitaterna, M. H. et al. Mutagenesis and mapping of a mouse gene, Clock, essential for circadian behavior. Science 264, 719–725 (1994).
Dauden, M. I., López-Perrote, A. & Llorca, O. RUVBL1–RUVBL2 AAA-ATPase: a versatile scaffold for multiple complexes and functions. Curr. Opin. Struct. Biol. 67, 78–85 (2021).
Li, Y. et al. Epigenetic inheritance of circadian period in clonal cells. eLife 9, e54186 (2020).
Cermakian, N. & Sassone-Corsi, P. Multilevel regulation of the circadian clock. Nat. Rev. Mol. Cell Biol. 1, 59–67 (2000).
Yao, Z. & Shafer, O. T. The Drosophila circadian clock is a variably coupled network of multiple peptidergic units. Science 343, 1516–1520 (2014).
Liu, N. et al. A highland-adaptation mutation of the Epas1 protein increases its stability and disrupts the circadian clock in the plateau pika. Cell Rep. 39, 110816 (2022).
Arnold, C. N. et al. A forward genetic screen reveals roles for Nfkbid, Zeb1, and Ruvbl2 in humoral immunity. Proc. Natl Acad. Sci. USA 109, 12286–12293 (2012).
Wang, G. et al. Somatic genetics analysis of sleep in adult mice. J. Neurosci. 42, 5617–5640 (2022).
Swan, J. A. et al. Coupling of distant ATPase domains in the circadian clock protein KaiC. Nat. Struct. Mol. Biol. 29, 759–766 (2022).
Assimon, V. A. et al. CB-6644 is a selective inhibitor of the RUVBL1/2 complex with anticancer activity. ACS Chem. Biol. 14, 236–244 (2019).
Erzberger, J. P. & Berger, J. M. Evolutionary relationships and structural mechanisms of AAA+ proteins. Annu. Rev. Biophys. Biomol. Struct. 35, 93–114 (2006).
Chavan, A. G. et al. Reconstitution of an intact clock reveals mechanisms of circadian timekeeping. Science 374, eabd4453 (2021).
Baggs, J. E. et al. Network features of the mammalian circadian clock. PLoS Biol. 7, e1000052 (2009).
Chen, W., Werdann, M. & Zhang, Y. The auxin-inducible degradation system enables conditional PERIOD protein depletion in the nervous system of Drosophila melanogaster. FEBS J. 285, 4378–4393 (2018).
Hirota, T. et al. Identification of small molecule activators of cryptochrome. Science 337, 1094–1097 (2012).
Emery, P., So, W. V., Kaneko, M., Hall, J. C. & Rosbash, M. CRY, a Drosophila clock and light-regulated cryptochrome, is a major contributor to circadian rhythm resetting and photosensitivity. Cell 95, 669–679 (1998).
Park, J. H. et al. Differential regulation of circadian pacemaker output by separate clock genes in Drosophila. Proc. Natl Acad. Sci. USA 97, 3608–3613 (2000).
Aronson, B. D., Johnson, K. A., Loros, J. J. & Dunlap, J. C. Negative feedback defining a circadian clock: autoregulation of the clock gene frequency. Science 263, 1578–1584 (1994).
Dunlap, J. C. Molecular bases for circadian clocks. Cell 96, 271–290 (1999).
Sehgal, A. et al. Rhythmic expression of timeless: a basis for promoting circadian cycles in period gene autoregulation. Science 270, 808–810 (1995).
Ito-Miwa, K., Terauchi, K. & Kondo, T. in Circadian Rhythms in Bacteria and Microbiomes (eds Johnson, C. H. & Rust, M. J.) 79–91 (Springer, 2021).
Zhou, Y. et al. High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells. Nature 509, 487–491 (2014).
Colot, H. V. et al. A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors. Proc. Natl Acad. Sci. USA 103, 10352–10357 (2006).
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
Savelyev, S. A., Larsson, K. C., Johansson, A. S. & Lundkvist, G. B. Slice preparation, organotypic tissue culturing and luciferase recording of clock gene activity in the suprachiasmatic nucleus. J. Vis. Exp. 10.3791/2439 (2011).
Zhou, M. et al. Non-optimal codon usage affects expression, structure and function of clock protein FRQ. Nature 495, 111–115 (2013).
Larrondo, L. F., Olivares-Yañez, C., Baker, C. L., Loros, J. J. & Dunlap, J. C. Circadian rhythms. Decoupling circadian clock protein turnover from circadian period determination. Science 347, 1257277 (2015).
Yuan, L. et al. BBX19 fine-tunes the circadian rhythm by interacting with PSEUDO-RESPONSE REGULATOR proteins to facilitate their repressive effect on morning-phased clock genes. Plant Cell 33, 2602–2617 (2021).
Chiu, J. C., Low, K. H., Pike, D. H., Yildirim, E. & Edery, I. Assaying locomotor activity to study circadian rhythms and sleep parameters in Drosophila. J. Vis. Exp. 10.3791/2157 (2010).
Schmid, B., Helfrich-Förster, C. & Yoshii, T. A new ImageJ plug-in “ActogramJ” for chronobiological analyses. J. Biol. Rhythms 26, 464–467 (2011).
Tiscornia, G., Singer, O. & Verma, I. M. Production and purification of lentiviral vectors. Nat. Protoc. 1, 241–245 (2006).
Fu, J. et al. Codon usage affects the structure and function of the Drosophila circadian clock protein PERIOD. Genes Dev 30, 1761–1775 (2016).
Tyanova, S., Temu, T. & Cox, J. The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nat. Protoc. 11, 2301–2319 (2016).
Ritchie, M. E. et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015).
Fang, M., Chavan, A. G., LiWang, A. & Golden, S. S. Synchronization of the circadian clock to the environment tracked in real time. Proc. Natl Acad. Sci. USA 120, e2221453120 (2023).