CNOT1 regulates circadian behaviour through Per2 mRNA decay in a deadenylation-dependent manner

References

• Kondo T, Ishiura M. The circadian clock of cyanobacteria. BioEssays. 2000;22(1):10–15.
   PubMed Web of Science ®Google Scholar
• Takahashi JS, Hong HK, Ko CH, et al. The genetics of mammalian circadian order and disorder: implications for physiology and disease. Nat Rev Genet. 2008;9(10):764–775.
   PubMed Web of Science ®Google Scholar
• Dibner C, Schibler U, Albrecht U. The mammalian circadian timing system: organization and coordination of central and peripheral clocks. Annu. Rev. Physiol. 2010;72(1):517–549.
   PubMedGoogle Scholar
• Panda S, Hogenesch JB, Kay SA. Circadian rhythms from flies to human. Nature. 2002;417(6886):329–335.
   PubMed Web of Science ®Google Scholar
• Partch CL, Green CB, Takahashi JS. Molecular architecture of the mammalian circadian clock. Trends Cell Biol. 2014;24(2):90–99.
   PubMed Web of Science ®Google Scholar
• Reppert SM, Weaver DR. Coordination of circadian timing in mammals. Nature. 2002;418(6901):935–941.
   PubMed Web of Science ®Google Scholar
• Ko CH, Takahashi JS. Molecular components of the mammalian circadian clock. Hum. Mol. Genet. 2006;15(suppl_2):271–277.
   PubMedGoogle Scholar
• Lowrey PL, Shimomura, K, Antoch, MP, et al. Positional syntenic cloning and functional characterization of the mammalian circadian mutation tau. Science. 2000;288(80):483–491.
   PubMedGoogle Scholar
• Akashi M, Tsuchiya Y, Yoshino T, et al. Control of intracellular dynamics of mammalian period proteins by casein kinase I epsilon (CKIepsilon) and CKIdelta in cultured cells. Mol. Cell. Biol. 2002;22(6):1693–1703.
   PubMed Web of Science ®Google Scholar
• Gekakis N, Staknis D, Nguyen HB, et al. Role of the CLOCK protein in the mammalian circadian mechanism. Science. 1998;280(5369):1564–1569.
   PubMed Web of Science ®Google Scholar
• Kume K, Zylka MJ, Sriram S, et al. mCRY1 and mCRY2 are essential components of the negative limb of the circadian clock feedback loop. Cell. 1999;98(2):193–205.
   PubMed Web of Science ®Google Scholar
• Shearman LP, Sriram S, Weaver DR, et al. Interacting molecular loops in the mammalian circadian clock. Science. (2000);288:1013–1019.
   PubMed Web of Science ®Google Scholar
• Sato TK, Yamada RG, Ukai H, et al. Feedback repression is required for mammalian circadian clock function. Nat. Genet. 2006;38(3):312–319.
   PubMed Web of Science ®Google Scholar
• Duffield GE. DNA microarray analyses of circadian timing: the genomic basis of biological time. J Neuroendocrinol. 2003;15(10):991–1002.
   PubMed Web of Science ®Google Scholar
• Hughes ME, DiTacchio L, Hayes KR, et al. Harmonics of circadian gene transcription in mammals. PLoS Genet. 2009;5(e1000442):e1000442.
   PubMedGoogle Scholar
• Panda S, Antoch MP, Miller BH, et al. Coordinated transcription of key pathways in the mouse by the circadian clock. Cell. 2002;109(3):307–320.
   PubMed Web of Science ®Google Scholar
• Zhang R, Lahens NF, Ballance HI, et al. A circadian gene expression atlas in mammals: implications for biology and medicine. Proc Natl Acad Sci. 2014;111:16219–16224.
   PubMed Web of Science ®Google Scholar
• Koike N, Yoo SH, Huang HC, et al. Transcriptional architecture and chromatin landscape of the core circadian clock in mammals. Science. 2012;338(80–):349–354.
   PubMedGoogle Scholar
• Menet JS, Rodriguez J, Abruzzi KC, et al. Nascent-seq reveals novel features of mouse circadian transcriptional regulation. Elife. 2012;2012:1–16.
   Google Scholar
• Crosby P, Partch CL. New insights into non-transcriptional regulation of mammalian core clock proteins. J. Cell Sci. 2020;133(18). DOI:10.1242/jcs.241174
   PubMed Web of Science ®Google Scholar
• Reddy AB, Karp NA, Maywood ES, et al. Circadian orchestration of the hepatic proteome. Curr. Biol. 2006;16(11):1107–1115.
   PubMed Web of Science ®Google Scholar
• Mauvoisin D, Wang J, Jouffe C, et al. Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver. Proc. Natl. Acad. Sci. U. S. A. 2014;111(1):167–172.
   PubMed Web of Science ®Google Scholar
• Vogel C, Marcotte EM. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat. Rev. Genet. 2012;13(4):227–232.
   PubMed Web of Science ®Google Scholar
• Lück S, Thurley K, Thaben PF, et al. Rhythmic degradation explains and unifies circadian transcriptome and proteome data. Cell Rep. 2014;9(2):741–751.
   PubMed Web of Science ®Google Scholar
• Wang J, Symul L, Yeung J, et al. Circadian clock-dependent and -independent posttranscriptional regulation underlies temporal mRNA accumulation in mouse liver. Proc Natl Acad Sci. 2018;115:E1916–E1925.
   PubMed Web of Science ®Google Scholar
• Goldstrohm AC, Wickens M. Multifunctional deadenylase complexes diversify mRNA control. Nat. Rev. Mol. Cell Biol. 2008;9(4):337–344.
   PubMed Web of Science ®Google Scholar
• Decker CJ, Parker R. A turnover pathway for both stable and unstable mRNAs in yeast: evidence for a requirement for deadenylation. Genes Dev. 1993;7(8):1632–1643.
   PubMed Web of Science ®Google Scholar
• Garneau NL, Wilusz J, Wilusz CJ. The highways and byways of mRNA decay. Nat. Rev. Mol. Cell Biol. 2007;8(2):113–126.
   PubMed Web of Science ®Google Scholar
• Collart MA. The Ccr4-Not complex is a key regulator of eukaryotic gene expression. Wiley Interdiscip Rev RNA. 2016;7(4):438–454.
   PubMed Web of Science ®Google Scholar
• Yamaguchi T, Suzuki T, Sato T, et al. The CCR4-NOT deadenylase complex controls Atg7-dependent cell death and heart function. Sci Signal. 2018;11(eaan3638). DOI:10.1126/scisignal.aan3638.
   Google Scholar
• Takahashi A, Kikuguchi C, Morita M, et al. Involvement of CNOT3 in mitotic progression through inhibition of MAD1 expression. Biochem. Biophys. Res. Commun. 2012;419(2):268–273.
   PubMed Web of Science ®Google Scholar
• Berthet C, Morera AM, Asensio MJ, et al. CCR4-associated factor CAF1 is an essential factor for spermatogenesis. Mol Cell Biol. 2004;24:5808–5820.
   PubMed Web of Science ®Google Scholar
• Shirai Y-T, Suzuki T, Morita M, et al. Multifunctional roles of the mammalian CCR4–NOT complex in physiological phenomena. Front Genet. 2014;5. 10.3389/fgene.2014.00286
   PubMed Web of Science ®Google Scholar
• Ito K, Takahashi A, Morita M, et al. The role of the CNOT1 subunit of the CCR4-NOT complex in mRNA deadenylation and cell viability. Protein Cell. 2011;2(9):755–763.
   PubMed Web of Science ®Google Scholar
• Temme C, Zhang L, Kremmer E, et al. Subunits of the drosophila CCR4-NOT complex and their roles in mRNA deadenylation. RNA. 2010;16(7):1356–1370.
   PubMed Web of Science ®Google Scholar
• Chen C, Ito K, Takahashi A, et al. Distinct expression patterns of the subunits of the CCR4-NOT deadenylase complex during neural development. Biochem. Biophys. Res. Commun. 2011;411(2):360–364.
   PubMed Web of Science ®Google Scholar
• Takahashi A, Suzuki T, Soeda S, et al. The CCR4-NOT complex maintains liver homeostasis through mRNA deadenylation. Life Sci. Alliance. 2020;3(5):e201900494.
   PubMed Web of Science ®Google Scholar
• Tsien JZ, Chen DF, Gerber D, et al. Subregion- and cell type–restricted gene knockout in mouse brain. Cell. 1996;87(7):1317–1326.
   PubMed Web of Science ®Google Scholar
• Ross J. mRNA stability in mammalian cells. Microbiol Rev. 1995;59(3):423–450.
   PubMedGoogle Scholar
• Ashworth W, Stoney PN, Yamamoto T. States of decay: the systems biology of mRNA stability. 2019;Curr. Opin. Syst. Biol. 15:48–57.
   Google Scholar
• Adachi S, Homoto M, Tanaka R, et al. ZFP36L1 and ZFP36L2 control LDLR mRNA stability via the ERK-RSK pathway. Nucleic Acids Res. 2014;42(15):10037–10049.
   PubMed Web of Science ®Google Scholar
• Takahashi A, Adachi S, Morita M, et al. Post-transcriptional stabilization of Ucp1 mRNA protects mice from diet-induced obesity. Cell Rep. 2015;13(12):2756–2767.
   PubMed Web of Science ®Google Scholar
• Storch K-F, Lipan O, Leykin I, et al. Extensive and divergent circadian gene expression in liver and heart. Nature. 2002;417(6884):78–83.
   PubMed Web of Science ®Google Scholar
• Lück S, Thurley K, Thaben PF, et al. Rhythmic degradation explains and unifies circadian transcriptome and proteome data. Cell Rep. 2014;9(2):741–751.
   PubMed Web of Science ®Google Scholar
• Mauvoisin D, Dayon L, Gachon F, et al. Proteomics and circadian rhythms: it ’ s all about signaling ! Proteomics. 2014;15:1–15.
   Web of Science ®Google Scholar
• Menet JS, Rodriguez J, Abruzzi KC, et al. Nascent-seq reveals novel features of mouse circadian transcriptional regulation. eLife Pp. 2012;2012:1–25.
   Google Scholar
• Torres M, Becquet D, Franc J-L, et al. Circadian processes in the RNA life cycle. Wiley Interdiscip Rev RNA. 2018;9(e1467). DOI:10.1002/wrna.1467
   PubMedGoogle Scholar
• Miller JE, Reese JC. Ccr4-Not complex: the control freak of eukaryotic cells. Crit. Rev. Biochem. Mol. Biol. 2012;47(4):315–333.
   PubMed Web of Science ®Google Scholar
• Huang G, He Q, Guo J, et al. The Ccr4-Not protein complex regulates the phase of the neurospora circadian clock by controlling WHITE COLLAR protein stability and activity. J. Biol. Chem. 2013;288(43):31002–31009.
   PubMed Web of Science ®Google Scholar
• Zhang EE, Liu AC, Hirota T, et al. A genome-wide RNAi screen for modifiers of the circadian clock in human cells. Cell. 2009;139(1):199–210.
   PubMed Web of Science ®Google Scholar
• Fabian MR, Sonenberg N. The mechanics of miRNA-mediated gene silencing: a look under the hood of miRISC. Nat. Struct. Mol. Biol. 2012;19(6):586–593.
   PubMed Web of Science ®Google Scholar
• Chapat C, Jafarnejad SM, Matta-Camacho E, et al. Cap-binding protein 4EHP effects translation silencing by microRNAs. Proc. Natl. Acad. Sci. U. S. A. 2017;114(21):5425–5430.
   PubMed Web of Science ®Google Scholar
• Chen R, D’Alessandro M, Lee C. MiRNAs are required for generating a time delay critical for the circadian oscillator. Curr. Biol. 2013;23(20):1959–1968.
   PubMed Web of Science ®Google Scholar
• Du NH, Arpat AB, De Matos M, et al. MicroRNAs shape circadian hepatic gene expression on a transcriptome-wide scale. Elife. 2014;2014:1–29.
   Google Scholar
• Cheng HYM, Papp JW, Varlamova O, et al. microRNA modulation of circadian-clock period and entrainment. Neuron. 2007;54(5):813–829.
   PubMed Web of Science ®Google Scholar
• Green CB, Douris N, Kojima S, et al. Loss of Nocturnin, a circadian deadenylase, confers resistance to hepatic steatosis and diet-induced obesity. Proc. Natl. Acad. Sci. U. S. A. 2007;104(23):9888–9893.
   PubMed Web of Science ®Google Scholar
• Wang Y, Osterbur DL, Megaw PL, et al. Rhythmic expression of nocturnin mRNA in multiple tissues of the mouse. BMC Dev. Biol. 2001;1(9):9.
   PubMedGoogle Scholar
• Isojima Y, Nakajimac M, Ukaic H, et al. CKIepsilon/delta-dependent phosphorylation is a temperature-insensitive, period-determining process in the mammalian circadian clock. Proc. Natl. Acad. Sci. U. S. A. 2009;106(37):15744–15749.
   PubMed Web of Science ®Google Scholar
• Chen R, Schirmer A, Lee Y, et al. Rhythmic PER abundance defines a critical nodal point for negative feedback within the circadian clock mechanism. Mol Cell. 2009;36(3):417–430.
   PubMed Web of Science ®Google Scholar
• Woo KC, Kim TD, Lee KH, et al. Mouse period 2 mRNA circadian oscillation is modulated by PTB-mediated rhythmic mRNA degradation. Nucleic Acids Res. 2009;37(1):26–37.
   PubMed Web of Science ®Google Scholar
• Yoo S-H, Kojima S, Shimomura K, et al. Period2 3′-UTR and microRNA-24 regulate circadian rhythms by repressing PERIOD2 protein accumulation. Proc. Natl. Acad. Sci. U. S. A. 2017;114(42):E8855–E8864.
   PubMed Web of Science ®Google Scholar
• Chou C-F, Zhu X, Lin YY, et al. KSRP is critical in governing hepatic lipid metabolism through controlling Per2 expression. J. Lipid Res. 2015;56(2):227–240.
   PubMed Web of Science ®Google Scholar
• Zheng B, Larkin DW, Albrecht U, et al. The mPer2 gene encodes a functional component of the mammalian circadian clock. Nature. 1999;400(6740):169–173.
   PubMed Web of Science ®Google Scholar
• Stoney PN, Yanagiya A, Nishijima S, et al. CNOT7 outcompetes its paralog CNOT8 for integration into the CCR4-NOT complex. J. Mol. Biol. 2022;434(167523):167523.
   PubMedGoogle Scholar
• Kim DY, Woo KC, Lee KH, et al. T. hnRNP Q and PTB modulate the circadian oscillation of mouse Rev-erb α via IRES-mediated translation. Nucleic Acids Res. 2010;38(20):7068–7078.
   PubMed Web of Science ®Google Scholar
• Otsuka H, Fukao A, Tomohiro T, et al. ARE-binding protein ZFP36L1 interacts with CNOT1 to directly repress translation via a deadenylation-independent mechanism. Biochimie. 2020;174:49–56.
   PubMed Web of Science ®Google Scholar
• Casanova E, Fehsenfeld S, Mantamadiotis T, et al. A CamKIIα iCre BAC allows brain-specific gene inactivation. Genesis. 2001;31(1):37–42.
   PubMed Web of Science ®Google Scholar
• Refinetti R. Non-stationary time series and the robustness of circadian rhythms. J. Theor. Biol. 2004;227(4):571–581.
   PubMed Web of Science ®Google Scholar
• Yamaguchi Y, Suzuki T, Mizoro Y, et al. Mice genetically deficient in vasopressin V1a and V1b receptors are resistant to jet lag. Science. 2013;342(80–):85–90.
   PubMedGoogle Scholar
• Shigeyoshi Y, Taguchi K, Yamamoto S, et al. Light-induced resetting of a mammalian circadian clock is associated with rapid induction of the mPer1 transcript. Cell. 1997;91(7):1043–1053.
   PubMed Web of Science ®Google Scholar
• Takahashi A, Morita M, Yokoyama K, et al. Tob2 inhibits peroxisome proliferator-activated receptor 2 expression by sequestering smads and C/EBP during adipocyte differentiation. Mol. Cell. Biol. 2012;32(24):5067–5077.
   PubMed Web of Science ®Google Scholar