Transcriptomics

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Transcription profiling of mouse liver from adrenalectomized (ADX) and sham-operated mice to identofy circadian expressed genes regulated by endogenous glucocorticoids


ABSTRACT: Genome-wide expression analysis of two circadian oscillatory mechanisms in the mouse liver; To identify the genes of which the circadian expression is regulated by endogenous glucocorticoids, we performed DNA microarray analysis using hepatic RNA from adrenalectomized (ADX) and sham-operated mice. Mice were housed in a 12:12 h light-dark cycle (LD12:12; lights on at zeitgeber time (ZT) 0) for at least two weeks before the day of the experiment. Liver samples were dissected, quickly frozen, and stored in liquid nitrogen. Total RNA was purified from pools of 3 animal tissues collected at each time-point using ISOGEN (Nippon Gene Co., Ltd., Japan). Hybridization to Affymetrix GeneChip (MG-U74Av2) arrays proceeded as described (Oishi K et al., J Biol Chem, 278, 41519-41527, 2003). The average difference (AD) value for each gene was provided by GeneChip software. To identify putative glucocorticoid-regulated circadian genes, we compared AD values between two time points (ZT2 and ZT14) in sham operated and in ADX mice. We applied three criteria to the selection of putative glucocorticoid-regulated circadian genes: (i) the AD value is marked as “present” by the GeneChip software in at least one of two time points, (ii) the AD value exhibits a 2-fold or greater change in sham-operated mice and (iii) the fold change is below 2-fold in ADX mice. We identified 169 genes that fluctuated between day and night in the livers of sham-operated mice. Among these, 100 lost circadian rhythmicity in ADX mice. On the other hand, the circadian expression of clock or clock-related genes such as mPer2 and DBP remained almost totally intact in the liver of ADX mice. The present study showed that the circadian expression of one type of liver genes in the mouse is governed by core components of the circadian clock such as CLOCK and BMAL1, and the other depends on endogenous glucocorticoids.

INSTRUMENT(S): 418 [Affymetrix]

ORGANISM(S): Mus musculus  

SUBMITTER: Norio Ishida  

PROVIDER: E-GEOD-2162 | ArrayExpress | 2008-06-12

SECONDARY ACCESSION(S): GSE2162GDS1870PRJNA91429

REPOSITORIES: GEO, ArrayExpress

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Publications

Genome-wide expression analysis reveals 100 adrenal gland-dependent circadian genes in the mouse liver.

Oishi Katsutaka K   Amagai Noriko N   Shirai Hidenori H   Kadota Koji K   Ohkura Naoki N   Ishida Norio N  

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes 20050101 3


Recent progress in genome-wide expression analysis has identified hundreds of circadian genes not only in the suprachiasmatic nucleus (the mammalian master clock) but also in peripheral tissues, such as heart, liver and kidney of mammals. Glucocorticoid is thought to be a circadian time cue for mammalian peripheral clocks. To identify the genes of which the circadian expression is regulated by endogenous glucocorticoids, we performed DNA microarray analysis using hepatic RNA from adrenalectomize  ...[more]

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