Quantitative analyses of circadian gene expression in mammalian cell cultures

Izumo, M., Sato, T. R., Straume, M., Johnson, C. H. (October 2006) Quantitative analyses of circadian gene expression in mammalian cell cultures. PLoS Computational Biology, 2 (10). pp. 1248-1261. ISSN 1553734X

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URL: http://www.ncbi.nlm.nih.gov/pubmed/17040123
DOI: 10.1371/journal.pcbi.0020136

Abstract

The central circadian pacemaker is located in the hypothalamus of mammals, but essentially the same oscillating system operates in peripheral tissues and even in immortalized cell lines. Using luciferase reporters that allow automated monitoring of circadian gene expression in mammalian fibroblasts, we report the collection and analysis of precise rhythmic data from these cells. We use these methods to analyze signaling pathways of peripheral tissues by studying the responses of Rat-1 fibroblasts to ten different compounds. To quantify these rhythms, which show significant variation and large non-stationarities (damping and baseline drifting), we developed a new fast Fourier transform-nonlinear least squares analysis procedure that specifically optimizes the quantification of amplitude for circadian rhythm data. This enhanced analysis method successfully distinguishes among the ten signaling compounds for their rhythm-inducing properties. We pursued detailed analyses of the responses to two of these compounds that induced the highest amplitude rhythms in fibroblasts, forskolin (an activator of adenylyl cyclase), and dexamethasone (an agonist of glucocorticoid receptors). Our quantitative analyses clearly indicate that the synchronization mechanisms by the cAMP and glucocorticoid pathways are different, implying that actions of different genes stimulated by these pathways lead to distinctive programs of circadian synchronization. © 2006 Izumo et al.

Item Type: Paper
Subjects: organs, tissues, organelles, cell types and functions > tissues types and functions > suprachiasmatic nucleus > hypothalamus
organs, tissues, organelles, cell types and functions > tissues types and functions > hypothalamus

bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > enzymes > luciferase
CSHL Authors:
Communities: CSHL labs > Svoboda lab
Depositing User: Editor Margaret Fantz
Date: October 2006
Date Deposited: 24 Feb 2012 16:27
Last Modified: 01 Mar 2013 15:04
PMCID: PMC1599765
Related URLs:
URI: http://repository.cshl.edu/id/eprint/24885

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