Circadian control of global gene expression patterns.
An internal time-keeping mechanism has been observed in almost every organism studied from archaea to humans. This circadian clock provides a competitive advantage in fitness and survival ( 18, 30, 95, 129, 137 ). Researchers have uncovered the molecular composition of this internal clock by combining enzymology, molecular biology, genetics, and modeling approaches. However, understanding the mechanistic link between the clock and output responses has been elusive. In three model organisms, Arabidopsis thaliana, Drosophila melanogaster, and Mus musculus, whole-genome expression arrays have enabled researchers to investigate how maintaining a time-keeping mechanism connects to an adaptive advantage. Here, we review the impacts transcriptomics have had on our understanding of the clock and how this molecular clock connects with system-level circadian responses. We explore the discoveries made possible by high-throughput RNA assays, the network approaches used to investigate these large transcript datasets, and potential future directions.
Doherty
Colleen J
CJ
Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, USA. cdoherty@ucsd.edu
Kay
Steve A
SA
D000818:Animals; D017360:Arabidopsis / Q000235:genetics / Q000502:physiology; D057906:Circadian Clocks; D002940:Circadian Rhythm; D004331:Drosophila melanogaster / Q000235:genetics / Q000502:physiology; D005786:Gene Expression Regulation; D006801:Humans; D051379:Mice
Cell. 2009 Oct 2;139(1):199-210
19765810
Curr Biol. 2000 Aug 24;10(16):951-6
10985381
Mol Cells. 2009 Aug 31;28(2):75-80
19714310
Bioinformatics. 2005 Apr 1;21(7):1164-71
15513999
J Biol Chem. 2007 Aug 24;282(34):25053-66
17597072
Science. 2008 Dec 19;322(5909):1832-5
19095940
FEBS J. 2007 Jan;274(2):335-45
17229141
Bioessays. 2006 May;28(5):534-45
16615085
Proc Natl Acad Sci U S A. 2005 Feb 1;102(5):1572-7
15659551
Cold Spring Harb Symp Quant Biol. 2007;72:319-30
18419289
Plant Cell. 2010 Mar;22(3):594-605
20233950
Hum Mol Genet. 2006 Oct 15;15 Spec No 2:R271-7
16987893
Science. 2007 Dec 14;318(5857):1730-1
18006706
BMC Bioinformatics. 2005 May 13;6:117
15892890
PLoS Comput Biol. 2007 Jun;3(6):e120
17571920
J Neurosci. 2002 Nov 1;22(21):9305-19
12417656
Curr Biol. 2006 Jun 6;16(11):1107-15
16753565
Cold Spring Harb Symp Quant Biol. 2007;72:145-56
18419272
Curr Opin Plant Biol. 2009 Oct;12(5):574-9
19709921
J Appl Physiol (1985). 2009 Dec;107(6):1972-80
19696364
Science. 2000 Dec 15;290(5499):2110-3
11118138
Nature. 2003 Feb 27;421(6926):948-52
12607002
Science. 2002 Apr 26;296(5568):752-5
11923494
PLoS Genet. 2008 Feb;4(2):e14
18248097
Curr Biol. 2002 Apr 2;12(7):551-7
11937023
J Neuroendocrinol. 2003 Oct;15(10):991-1002
12969245
Trends Microbiol. 2007 Sep;15(9):381-8
17804240
EURASIP J Bioinform Syst Biol. 2009;:683463
19390635
Proc Natl Acad Sci U S A. 1998 Jul 21;95(15):8660-4
9671734
Genome Biol. 2009;10(11):R130
19919682
BMC Bioinformatics. 2007 Jul 02;8:233
17605777
J Biol Rhythms. 2004 Oct;19(5):361-73
15534317
PLoS Comput Biol. 2008 Feb;4(2):e38
18282089
Nature. 2002 May 2;417(6884):78-83
11967526
Proc Natl Acad Sci U S A. 2005 Jul 19;102(29):10387-92
16006522
BMC Bioinformatics. 2008 Aug 12;9 Suppl 9:S18
18793463
Proc Natl Acad Sci U S A. 2009 Dec 15;106(50):21453-8
19940241
PLoS Genet. 2008 Jul 11;4(7):e1000123
18617998
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D354-7
16381885
Curr Opin Microbiol. 2008 Dec;11(6):541-6
18983934
Trends Biochem Sci. 2009 Oct;34(10):483-90
19740663
Nat Cell Biol. 2006 Nov;8(11):1183-9
17060904
Insect Mol Biol. 2008 Sep;17(5):447-63
18828836
Bioinformatics. 2004 Feb 12;20(3):332-9
14960459
FEBS Lett. 2009 Dec 17;583(24):3900-4
19769971
PLoS Biol. 2008 Sep 16;6(9):e225
18798691
Mol Microbiol. 2008 Apr;68(2):255-62
18312266
Annu Rev Plant Biol. 2009;60:357-77
19575587
Cell Cycle. 2007 Dec 15;6(24):3034-5
18075311
Annu Rev Plant Biol. 2006;57:181-201
16669760
Genome Biol. 2008;9(8):R130
18710561
Cold Spring Harb Symp Quant Biol. 2007;72:353-63
18419293
Science. 2009 Mar 13;323(5920):1481-5
19286557
Nat Genet. 2000 May;25(1):25-9
10802651
BMC Genomics. 2008 Feb 19;9:83
18284684
Annu Rev Physiol. 1993;55:16-54
8466172
Trends Plant Sci. 2010 May;15(5):259-65
20382065
PLoS Biol. 2007 Aug;5(8):e222
17683202
J Biol Rhythms. 2004 Oct;19(5):348-60
15534316
OMICS. 2009 Aug;13(4):313-24
19645592
J Biol Rhythms. 2003 Apr;18(2):96-105
12693865
Nat Neurosci. 2010 Jan;13(1):60-8
19966839
Proc Natl Acad Sci U S A. 2003 May 27;100(11):6878-83
12736379
Plant Cell Physiol. 2008 Mar;49(3):481-7
18202002
Nat Cell Biol. 2008 Oct;10(10):1154-63
18806789
Science. 2003 Nov 7;302(5647):1049-53
14605371
Cell. 2008 Sep 5;134(5):728-42
18775307
Curr Opin Genet Dev. 2008 Aug;18(4):354-61
18617392
J Biol Chem. 2001 Dec 14;276(50):46751-8
11598123
Bioinformatics. 2004 Jan 1;20(1):5-20
14693803
Plant Physiol. 2005 Jun;138(2):585-90
15955922
Bioinformatics. 2006 Feb 1;22(3):310-6
16303799
Genetics. 2008 Mar;178(3):1147-55
18385110
Curr Biol. 2004 Aug 24;14(16):1481-6
15324665
Nature. 2007 Jul 19;448(7151):358-61
17589502
Plant Physiol. 2007 Nov;145(3):925-32
17873091
Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):15172-7
18779586
PLoS Comput Biol. 2007 Nov;3(11):e208
17983263
Ecol Lett. 2009 Sep;12(9):970-81
19566794
Genome Biol. 2009 Feb 11;10(2):R17
19210792
Bioinformatics. 2009 Dec 1;25(23):3114-20
19773336
Plant Physiol. 2003 Jun;132(2):629-39
12805593
Nat Genet. 2005 Feb;37(2):187-92
15665827
Science. 2007 Dec 14;318(5857):1789-92
18084825
Curr Biol. 2007 Sep 4;17(17):R760-2
17803925
Biometrics. 2009 Mar;65(1):40-51
18537947
Plant Cell. 2005 Jul;17(7):1926-40
15923346
BMC Evol Biol. 2010 Feb 12;10:41
20152032
PLoS One. 2010 Feb 19;5(2):e9285
20174573
Curr Biol. 2008 Jan 22;18(2):R84-93
18211849
Nucleic Acids Res. 2009 Jan;37(1):1-13
19033363
J Biol Rhythms. 2008 Dec;23(6):463-71
19060255
Plant Physiol. 2002 Oct;130(2):627-38
12376630
Physiol Genomics. 2007 May 11;29(3):280-9
17284666
Science. 1984 Jul 13;225:232-4
11540800
Trends Plant Sci. 2005 Aug;10(8):397-406
16027030
Curr Opin Plant Biol. 2009 Oct;12(5):643-9
19717332
Plant Mol Biol. 2009 Mar;69(4):419-27
18855103
Science. 2005 Jul 22;309(5734):630-3
16040710
Mol Biol Cell. 1998 Dec;9(12):3273-97
9843569
Plant Cell. 2006 Apr;18(4):792-803
16595397
Nat Rev Genet. 2001 Sep;2(9):702-15
11533719
Plant J. 1999 Jan;17(1):63-71
10069068
Plant J. 2009 Nov;60(4):703-15
19682285
Genome Biol. 2009;10(5):107
19519932
Cell. 2002 May 3;109(3):307-20
12015981
Annu Rev Neurosci. 2000;23:713-42
10845079
BMC Bioinformatics. 2009 Jan 11;10:15
19134222
PLoS Comput Biol. 2008 Oct;4(10):e1000193
18846204
Plant Physiol. 2003 Dec;133(4):1605-16
14681527
Bioessays. 2002 Jun;24(6):494-8
12111731
Nucleic Acids Res. 2008 Jan;36(Database issue):D480-4
18077471
PLoS Genet. 2009 Apr;5(4):e1000442
19343201
Plant Cell Physiol. 2003 Mar;44(3):360-5
12668783
Methods Enzymol. 2004;383:149-66
15063650
BMC Mol Biol. 2008 Jan 04;9:1
18177499
Mol Syst Biol. 2009;5:320
19888215
Nucleic Acids Res. 2000 Jan 1;28(1):27-30
10592173
Proc Natl Acad Sci U S A. 1989 Aug;86(16):6201-5
2762323
Curr Opin Plant Biol. 2010 Feb;13(1):83-9
19836294
Plant Cell Environ. 2007 Mar;30(3):333-349
17263778
Ann N Y Acad Sci. 2008;1129:350-7
18591494
Nucleic Acids Res. 2004 Jan 22;32(2):447-55
14739237
Plant Physiol. 2002 Jun;129(2):576-84
12068102
Curr Opin Biotechnol. 2005 Feb;16(1):73-8
15722018
J Biol Chem. 2002 Apr 19;277(16):14048-52
11854264
BMC Bioinformatics. 2007 Nov 01;8 Suppl 7:S15
18047714
Curr Biol. 2008 Sep 9;18(17):R826-R835
18786388
J Cell Sci. 2006 Dec 1;119(Pt 23):4793-5
17130292
BMC Bioinformatics. 2006 Sep 06;7 Suppl 2:S10
17118131
Curr Opin Plant Biol. 2008 Oct;11(5):514-20
18678522
PLoS Genet. 2007 Apr 6;3(4):e54
17411344
Cell Tissue Res. 2002 Jul;309(1):27-34
12111534
Adv Genet. 2007;58:25-66
17452245
Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):14946-51
18815372
Novartis Found Symp. 2003;253:171-80; discussion 52-5, 102-9, 180-3 passim
14712921
J Biol Rhythms. 2004 Oct;19(5):414-24
15534321
Cell. 1998 May 29;93(5):805-14
9630224
Genome Biol. 2007;8(7):R146
17650318