Extent of circadian cycling observed in the transcriptome

Range Arabidopsis 6%: Drosophila between 1% and 5%: mouse 5% to 10% %
Organism Eukaryotes
Reference Doherty CJ, Kay SA (2010) Circadian control of global gene expression patterns. Annu Rev Genet 44(1):419–444. doi: 10.1146/annurev-genet-102209-163432. p.422 left column bottom paragraphPubMed ID20809800
Primary Source [23] Duffield GE. 2003. DNA microarray analyses of circadian timing: the genomic basis of biological time. J. Neuroendocrinol. 15(10):991–1002 [24] Duffield GE, Best JD, Meurers BH, Bittner A, Loros JJ, Dunlap JC. 2002. Circadian programs of transcriptional activation, signaling, and protein turnover revealed by microarray analysis of mammalian cells. Curr. Biol. 12(7):551–57 [35] Harmer SL, Hogenesch JB, Straume M, Chang H, Han B, et al. 2000. Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290(5499):2110–13 [97] Panda S, Antoch MP, Miller BH, Su AI, Schook AB, et al. 2002. Coordinated transcription of key pathways in the mouse by the circadian clock. 109(3):307–20PubMed ID12969245, 11937023, 11118138, 12015981
Comments p.422 left column bottom paragraph:"The extent of circadian cycling observed in the transcriptome was a surprise to many researchers. In Arabidopsis 6%, in Drosophila between 1% and 5%, and in mouse 5% to 10% of transcripts were identified as circadian (primary sources 24, 35, 97 reviewed in primary source 23). In addition, enhancer trapping in Arabidopsis found that one-third of the promoters examined showed circadian rhythmicity, confirming the impact of the clock on transcriptional regulation (ref 82). This large number of cycling transcripts may be one explanation for why forward genetic screens, which were very successful at identifying core-clock components, were relatively poor at identifying components of the output pathways given that compensation by other output signals could mask the loss of any individual component. A second commonality between the Arabidopsis, Drosophila, and mouse [specifically, the suprachiasmatic nucleus (SCN)] arrays was the observation of a bimodal distribution of the cycling transcripts. That is, most circadian expressed genes showed peak expression either immediately before dawn or dusk, reflecting the importance of anticipating daily light transitions."
Entered by Uri M
ID 111861