Hepatic gene expression changes throughout the day in the Fischer rat: implications for toxicogenomic experiments

There is increasing use of transcriptional profiling in hepatotoxicity studies in the rat. Understanding hepatic gene expression changes over time is critical, since tissue collection may occur throughout the day. Furthermore, when comparing results from different data sets, times of dosing and tissue collection may vary. Circadian effects on the mouse hepatic transcriptome have been well documented. However, limited reports exist for the rat. In one study approximately 7% of the hepatic genes showed a diurnal expression pattern in a comparison of rat liver samples collected during the day versus livers collected at night. The results of a second study comparing rat liver samples collected at multiple time points over a circadian day suggest only minimal variation of the hepatic transcriptome. We studied temporal hepatic gene expression in 48 untreated F344/N rats using both approaches employed in these previous studies. Statistical analysis of microarray (SAM) identified differential expression in day/night comparisons, but was less sensitive for liver samples collected at multiple times of day. However, a Fourier analysis identified numerous periodically expressed genes in these samples including period genes, clock genes, clock-controlled genes, and genes involved in metabolic pathways. Furthermore, rhythms in gene expression were identified for several circadian genes not previously reported in the rat liver. Transcript levels for twenty genes involved in circadian and metabolic pathways were confirmed using quantitative RT-PCR. The results of this study demonstrate a prominent circadian rhythm in gene expression in the rat that is a critical factor in planning toxicogenomic experiments.