Circadian profiling of the transcriptome in immortalized rat SCN cells

Physiological Genomics

Volumn 21, Issue , 2005, Pages 370-381

  Menger, Gus J ^b   Lu, Kim ^b   Thomas, Terry ^b   Cassone, Vincent M ^b   Earnest, David J ^a,b  

^a TEXAS A AND M HEALTH SCIENCE CENTER   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

Author keywords

Clock; Oscillator; Pacemaker; Rhythm; SCN2.2; Suprachiasmatic nucleus

Indexed keywords

TRANSCRIPTOME;

ANIMAL CELL; ARTICLE; CELL COMMUNICATION; CELL IMMORTALIZATION; CELL RESPIRATION; CIRCADIAN RHYTHM; CONTROLLED STUDY; DNA MICROARRAY; EXPRESSED SEQUENCE TAG; FATTY ACID METABOLISM; GENE EXPRESSION; GENE EXPRESSION REGULATION; NONHUMAN; PRIORITY JOURNAL; RAT; STEROIDOGENESIS; SUPRACHIASMATIC NUCLEUS; TRANSCRIPTOMICS;

ANIMALS; CELLS, CULTURED; CIRCADIAN RHYTHM; DARKNESS; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; LIGHT; MALE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHOTOPERIOD; RATS; RATS, LONG-EVANS; SUPRACHIASMATIC NUCLEUS; TRANSCRIPTION, GENETIC;

MAMMALIA;

EID: 21244477916     PISSN: 15312267     EISSN: None     Source Type: Journal    
DOI: 10.1152/physiolgenomics.00224.2004     Document Type: Article

References (77)

1. Akashi M and Nishida E. Involvement of the MAP kinase cascade in resetting of the mammalian circadian clock. Genes Dev 14: 645-649, 2000.
2. Akhtar RA, Reddy AB, Maywood ES, Clayton JD, King VM, Smith AG, Gant TW, Hastings MH, and Kyriacou CP. Circadian cycling of the mouse liver transcriptome, as revealed by cDNA microarray, is driven by the suprachiasmatic nucleus. Curr Biol 12: 540-550, 2002.
3. Allen G, Rappe J, Earnest DJ, and Cassone VM. Oscillating on borrowed time: diffusible signals from immortalized suprachiasmatic nucleus cells regulate circadian rhythmicity in cultured fibroblasts. J Neurosci 21: 7937-7943, 2001.
4. Allen GC, Farnell Y, Bell-Pedersen D, Cassone VM, and Earnest DJ. Effects of altered clock gene expression on the pacemaker properties of SCN2.2 cells and oscillatory properties of NIH/3T3 cells. Neuroscience 127: 989-999, 2004.
5. Altschul SF, Gish W, Miller W, Myers EW, and Lipman DJ. Basic local alignment search tool. J Mol Biol 215: 403-410, 1990.
6. Bailey MJ, Beremand PD, Hammer R, Bell-Pedersen D, Thomas TL, and Cassone VM. Transcriptional profiling of the chick pineal gland, a photoreceptive circadian oscillator and pacemaker. Mol Endocrinol 17: 2084-2095, 2003.
7. Balsalobre A, Damiola F, and Schibler U. A serum shock induces circadian gene expression in mammalian tissue culture cells. Cell 93: 929-937, 1998.
8. Balsalobre A, Brown SA, Marcacci L, Tronche F, Kellendonk C, Reichardt HM, Schutz G, and Schibler U. Resetting of circadian time in peripheral tissues by glucocorticoid signaling. Science 289: 2344-2347, 2000.
9. Bercovich B, Stancovski I, Mayer A, Blumenfeld N, Laszlo A, Schwartz AL, and Ciechanover A. Ubiquitin-dependent degradation of certain protein substrates in vitro requires the molecular chaperone Hsc70. J Biol Chem 272: 9002-9010, 1997.
10. Carbajo-Perez E, Carbajo S, Orfao A, Vicente-Villardon JL, and Vazquez R. Circadian variation in the distribution of cells throughout the different phases of the cell cycle in the anterior pituitary gland of adult male rats as analysed by flow cytometry. J Endocrinol 129: 329-333, 1991.
11. Castel M, Belenky M, Cohen S, Ottersen OP, and Storm-Mathisen J. Glutamate-like immunoreactivity in retinal terminals of the mouse suprachiasmatic nucleus. Eur J Neurosci 5: 368-381, 1993.
12. Ceriani MF, Gre JB, Yanovsky M, Panda S, Straume M, and Kay SA. Genome-wide expression analysis in Drosophila reveals genes controlling circadian behavior. J Neurosci 22: 9305-9319, 2002.
13. Correa A, Lewis ZA, Greene AV, March IJ, Gomer RH, and Bell-Pedersen D. Multiple oscillators regulate circadian gene expression in Neurospora. Proc Natl Acad Sci USA 100: 13597-13602, 2003.
14. Dahlquist KD, Salomonis N, Vranizan K, Lawlor SC, and Conklin BR. GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat Genet 31: 19-20, 2002.
15. Ding JM, Chen D, Weber ET, Faiman LE, Rea MA, and Gillette MU. Resetting the biological clock: mediation of nocturnal circadian shifts by glutamate and NO. Science 266: 1713-1717, 1994.
16. Doniger SW, Salomonis N, Dahlquist KD, Vranizan K, Lawlor SC, and Conklin BR. MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol 4: R7, 2003.
17. Duffield GE. DNA microarray analyses of circadian timing: the genomic basis of biological time. J Neuroendocrinol 15: 991-1002, 2003.
18. Duffield GE, Best JD, Meurers BH, Bittner A, Loros JJ, and Dunlap JC. Circadian programs of transcriptional activation, signaling and protein turnover revealed by microarray analysis of mammalian cells. Curr Biol 12: 551-557, 2002.
19. Earnest DJ and Sladek CD. Circadian vasopressin release from perifused rat suprachiasmatic explants in vitro: effects of acute stimulation. Brain Res 422: 398-402, 1987.
20. Earnest DJ, Liang FQ, DiGiorgio S, Gallagher M, Harvey B, Earnest B, and Seigel G. Establishment and characterization of adenoviral E1A immortalized cell lines derived from the rat suprachiasmatic nucleus. J Neurobiol 39: 1-13, 1999.
21. Earnest DJ, Liang FQ, Ratcliff M, and Cassone VM. Immortal time: circadian clock properties of rat suprachiasmatic cell lines. Science 283: 693-695, 1999.
22. Gannon RL and Rea MA. Glutamate receptor immunoreactivity in the rat suprachiasmatic nucleus. Brain Res 622: 337-342, 1993.
23. Gillette MU and Reppert SM. The hypothalamic suprachiasmatic nuclei: circadian patterns of vasopressin secretion and neuronal activity in vitro. Brain Res Bull 19: 135-139, 1987.
24. Gladstone Institutes. Gene archives and GenMAPPs. In: GenMAPP: Gene Map Annotator and Pathway Profiler. http://www.GenMAPP.org (10 Sept. 2003).
25. Golden SS and Canales SR. Cyanobacterial circadian clocks-timing is everything. Nat Rev Microbiol 1: 191-199, 2003.
26. Grima B, Lamouroux A, Chelot E, Papin C, Limbourg-Bouchon B, and Rouyer F. The F-box protein slimb controls the levels of clock proteins period and timeless. Nature 420: 178-182, 2002.
27. Harley CW, Farrell RC, and Rusak B. Daily variation in the distribution of glycogen phosphorylase in the suprachiasmatic nucleus of syrian hamsters. J Comp Neurol 435: 249-258, 2001.
28. Heid CA, Stevens J, Livak KJ, and Williams PM. Real time quantitative PCR. Genome Res 6: 986-994, 1996.
29. Hille B. Potassium channels and chloride channels. In: Ionic Channels of Excitable Membranes, edited by Sinauer HB. Sunderland, MA: Sinauer, 1992, p. 130-135.
30. Hollnagel A, Oehlmann V, Heymer J, Rüther U, and Nordheim A. Id genes are direct targets of bone morphogenetic protein induction in embryonic stem cells. J Biol Chem 274: 19838-19845, 1999.
31. Holmes RP and Assimos DG. Glyoxylate synthesis, and its modulation and influence on oxalate synthesis. J Urol 160: 1617-1624, 1998.
32. Hurst WJ, Mitchell JW, and Gillette MU. Synchronization and phase-resetting by glutamate of an immortalized SCN cell line. Biochem Biophys Res Commun 298: 133-143, 2002.
33. Kleiber J, Kalousek F, Swaroop M, and Rosenberg LE. The general mitochondrial matrix processing protease from rat liver: structural characterization of the catalytic subunit. Proc Natl Acad Sci USA 87: 7978-7982, 1990.
34. Klein DC, Moore RY, and Reppert SM (Editors). Suprachiasmatic Nucleus: The Mind's Clock. New York: Oxford Univ. Press, 1991.
35. Ko HW, Jiang J, and Edery I. Role of Slimb in the degradation of Drosophila protein phosphorylated by doubletime. Nature 240: 673-678, 2002.
36. -/-). J Biol Rhythms 14: 20-27, 1999.
37. -/-). J Biol Rhythms 16: 142-148, 2001.
38. Lavialle M and Serviére J. Circadian fluctuations in GFAP distribution in the Syrian hamster suprachiasmatic nucleus. Neuroreport 4: 1243-1246, 1993.
39. Lee CK, Klopp RG, Weidruch R, and Prolla TA. Gene expression profile of aging and its retardation by caloric restriction. Science 285: 1390-1393, 1999.
40. 7) implicated in the regulation of mammalian circadian rhythms. Neuron 11: 449-458, 1993.
41. Matsuo T, Yamaguchi S, Mitsui S, Emi A, Shimoda F, and Okamura H. Control mechanism of the circadian clock for timing of cell division in vivo. Science 302: 255-259, 2003.
42. McCallum CD, Do H, Johnson AE, and Frydman J. The interaction of the chaperonin tailless complex polypeptide 1 (TCP1) ring complex (TRiC) with ribosome-bound nascent chains examined using photo-crosslinking. J Cell Biol 149: 591-602, 2000.
43. McDonald MJ and Rosbash M. Microarray analysis and organization of circadian gene expression in Drosophila. Cell 107: 567-578, 2001.
44. McGowan KM, Long SD, and Pekala PH. Glucose transporter gene expression: regulation of transcription and mRNA stability. Pharmacol Ther 66: 465-505, 1995.
45. Meijer JH and Schwartz WJ. In search of the pathways for light-induced pacemaker resetting in the suprachiasmatic nucleus. J Biol Rhythms 18: 235-249, 2003.
46. Meijer JH, van der Zee EA, and Dietz M. Glutamate phase shifts circadian activity rhythms in hamsters. Neurosci Lett 86: 177-183, 1988.
47. Mirande M and Waller JP. Molecular cloning and primary structure of cDNA encoding the catalytic domain OT rat liver aspartyl-tRNA synthetase. J Biol Chem 264: 842-847, 1989.
48. Mizzen LA, Chang C, Garrels JI, and Welch WJ. Identification, characterization, and purification of two mammalian stress proteins present in mitochondria, grp 75, a member of the hsp 70 family and hsp 58, a homolog of the bacterial groEL protein. J Biol Chem 264: 20664-20675, 1989.
49. Moore RY. Organization and function of a central nervous system circadian oscillator: the suprachiasmatic hypothalamic nucleus: Fed Proc 42: 2783-2789, 1983.
50. Mori T, Binder B, and Johnson CH. Circadian gating of cell division in cyanobacteria growing with average doubling times of less than 24 hours. Proc Natl Acad Sci USA 93: 10183-10188, 1996.
51. National Center for Biotechnology Information. Tools for data mining. In: National Center for Biotechnology Information Homepage. http://www.ncbi.nlm. nih.gov/ (10 Sept. 2003).
52. Newman GC, Hospod FE, Patlak CS, and Moore RY. Analysis of in vitro glucose utilization in a circadian pacemaker model. J Neurosci 12: 2015-2021, 1992.
53. Niethammer M, Kim E, and Sheng M. Interaction between the C terminus of NMDA receptor subunits and multiple members of the PSD-95 family of membrane-associated guanylate kinases. J Neurosci 16: 2157-2163, 1996.
54. Panda S, Antoch MP, Miller BH, Su AI, Schook AB, Straume M, Schultz G, Kay SA, Takahashi JS, and Hogenesch JB. Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 109: 307-320, 2002.
55. Pellerin L and Magistretti PJ. Neuroenergetics: calling upon astrocytes to satisfy hungry neurons. Neuroscientist 10: 53-62, 2004.
56. Pittendrigh CS. Temporal organization: reflections of a Darwinian clock-watcher. Annu Rev Physiol 55: 16-54, 1993.
57. Prosser RA, Dean RR, Edgar DM, Heller HC, and Miller JD. Serotonin and the mammalian circadian system. I. In vitro phase shifts by serotonergic agonists and antagonists. J Biol Rhythms 8: 1-16, 1993.
58. Pruitt KD and Maglott DR. RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res 29: 137-140, 2001.
59. Ralph MR, Foster RG, Davis FC, and Menaker M. Transplanted suprachiasmatic nucleus determines circadian period. Science 247: 975-978, 1990.
60. Rea MA, Glass JD, and Colwell CS. Serotonin modulates photic responses in the hamster suprachiasmatic nuclei. J Neurosci 14: 3635-3642, 1994.
61. Reppert SM and Weaver DR. Molecular analysis of mammalian circadian rhythms. Annu Rev Physiol 63: 647-676, 2001.
62. Reppert SM and Weaver DR. Coordination of circadian timing in mammals. Nature 418: 935-941, 2002.
63. Resendez E Jr, Wooden SK, and Lee AS. Identification of highly conserved regulatory domains and protein-binding sites in the promoters of the rat and human genes encoding the stress-inducible 78-kilodalton glucose-regulated protein. Mol Cell Biol 8: 4579-4584, 1988.
64. Rutter J, Reick M, and McKnight SL. Metabolism and the control of circadian rhythms. Annu Rev Biochem 71: 307-331, 2002.
65. Schaffer R, Landgraf J, Accerbi M, Simon V, Larson M, and Wisman E. Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis. Plant Cell 13: 113-123, 2001.
66. Schwartz WJ. SCN metabolic activity in vitro. In: Suprachiasmatic Nucleus: The Mind's Clock, edited by Klein DC, Moore RY, and Reppert SM. New York: Oxford Univ. Press, 1991, p. 144-156.
67. Shen H, Watanabe M, Tomasiewicz H, and Glass JD. Genetic deletions of NCAM and PSA impair circadian function in the mouse. Physiol Behav 73: 185-193, 2001.
68. Shirakawa S and Moore RY. Glutamate shifts the phase of the circadian neuronal firing rhythm in the rat suprachiasmatic nucleus in vitro. Neurosci Lett 178: 47-50, 1994.
69. Storch KF, Lipan O, Leykin I, Viswanathan N, Davis FC, Wong WH, and Weitz CJ. Extensive and divergent circadian gene expression in liver and heart. Nature 417: 78-83, 2002.
70. Ueda HR, Chen W, Adachi A, Wakamatsu H, Hayashi S, Takasugi T, Nagano M, Nakahama K, Suzuki Y, Sugano S, Iino M, Shigeyoshi Y, and Hashimoto S. A transcription factor response element for gene expression during circadian night. Nature 418: 534-539, 2002.
71. Ueda HR, Matsumoto A, Kawamura M, Iino M, Tanimura T, and Hashimoto S. Genome-wide transcriptional orchestration of circadian rhythms in Drosophila. J Biol Chem 277: 14048-14052, 2002.
72. van den Pol AN, Hermans-Borgmeyer I, Hofer M, Ghosh P, and Heinemann S. Ionotropic glutamate-receptor gene expression in hypothalamus: localization of AMPA, kainate, and NMDA receptor RNA with in situ hybridization. J Comp Neurol 343: 428-444, 1994.
73. Vannucci SJ and Simpson IA. Developmental switch in brain nutrient transporter expression in the rat. Am J Physiol Endocrinol Metab 285: E1127-E1134, 2003.
74. Wang D, Kranz-Eble P, and De Vivo DC. Mutational analysis of GLUT1 (SLC2A1) in Glut-1 deficiency syndrome. Hum Mutat 16: 224-231, 2000.
75. Wang J, Yang X, Zhou P, and Han H. Cloning of mouse genomic ribosomal protein L6 and analysis of its promoter. Biochim Biophys Acta 1576: 219-224, 2002.
76. Watanabe A, Hamada T, Shibata S, and Watanabe S. Effects of nitric oxide synthase inhibitors on N-methyl-D-aspartate-induced phase delay of circadian rhythm of neuronal activity in the rat suprachiasmatic nucleus in vitro. Brain Res 646: 161-164, 1994.
77. Young MW. Life's 24-hour clock: molecular control of circadian rhythms in animal cells. Trends Biochem Sci 25: 601-606, 2000.