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Plant Physiology 132:629-639 (2003)
© 2003 American Society of Plant Biologists

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RESEARCH PAPERS ON SYSTEMS BIOLOGY/GENOMICS/BIOINFORMATICS

Enhancer Trapping Reveals Widespread Circadian Clock Transcriptional Control in Arabidopsis1,[w]

Todd P. Michael and C. Robertson McClung*

Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755

The circadian clock synchronizes the internal biology of an organism with the environment and has been shown to be widespread among organisms. Microarray experiments have shown that the circadian clock regulates mRNA abundance of about 10% of the transcriptome in plants, invertebrates, and mammals. In contrast, the circadian clock regulates the transcription of the virtually all cyanobacterial genes. To determine the extent to which the circadian clock controls transcription in Arabidopsis, we used in vivo enhancer trapping. We found that 36% of our enhancer trap lines display circadian-regulated transcription, which is much higher than estimates of circadian regulation based on analysis of steady-state mRNA abundance. Individual lines identified by enhancer trapping exhibit peak transcription rates at circadian phases spanning the complete circadian cycle. Flanking genomic sequence was identified for 23 enhancer trap lines to identify clock-controlled genes (CCG-ETs). Promoter analysis of CCG-ETs failed to predict new circadian clock response elements (CCREs), although previously defined CCREs, the CCA1-binding site, and the evening element were identified. However, many CCGs lack either the CCA1-binding site or the evening element; therefore, the presence of these CCREs is insufficient to confer circadian regulation, and it is clear that additional elements play critical roles.

Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.021006.

1 This work was supported by the National Science Foundation (grant nos. IBN 9817603 and MCB 0091008) and by the U.S. Department of Agriculture (National Research Initiative Competitive Grants Program grant no. 9602632 to C.R.M.).

[w] The online version of this article contains Web-only data. The supplemental material is available at http://www.plantphysiol.org.

* Corresponding author; e-mail mcclung{at}dartmouth.edu; fax 603–646–1347.

Received January 26, 2003; returned for revision February 21, 2003; accepted March 1, 2003.




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