Analysis of Circadian Output Rhythms of Gene Expression in Neurospora and Mammalian Cells in Culture

The true biology of chronobiology lies in the spectrum of processes that are controlled by the circadian clock. Although this biology plays out at the level of the whole organism, it derives, finally, from clock-driven changes in physiology, and frequently in gene expression, that occur at the level of individual cells. For this reason, analysis of gene expression rhythms measured in cell culture or in organisms that elaborate only a few cell types provides insights not possible in multicellular organisms. In this context we have used mammalian fibroblasts in culture as well as the eukaryotic filamentous fungus Neurospora crassa to study circadian output, in particular the output rhythms in gene expression that underlie so much of circadian biology. Each cell type has its own advantages: Data from mammalian cells are obviously immediately pertinent to animal cell rhythms, but the system allows little genetics and only limited amounts of material can be collected. Alternatively, Neurospora allows genetic and molecular analyses and is useful for developing concepts and models of output that can be examined in other contexts. This methods article focuses on these two systems for analysis, providing an overview of how control is presently viewed followed by current methods for its analysis.