Implications of circadian gene expression in kidney, liver and the effects of fasting on pharmacogenomic studies

DNA arrays: applications and implications for circadian biology

DNA arrays can be powerful tools to investigate transcriptional regulation of biological systems in a highly parallel and genome-wide manner. Their use has furthered the investigation of basic cell and developmental biology and is now being applied toward the understanding and diagnosis of human disease. DNA arrays are of particular use in the study of circadian biology because the clock is, at its heart, a transcriptional/translational feedback loop. Here, we review the underlying technology behind DNA arrays, discuss general applications, and focus on the use of the arrays in the study of circadian biology in plants, flies, and mice.

Time after time: inputs to and outputs from the mammalian circadian oscillators

Oscillating levels of clock gene transcripts in the suprachiasmatic nucleus (SCN) are essential components of the mammalian circadian pacemaker. Their synchronization with daily light cycles involves neural connections from light-sensitive photoreceptor-containing retinal ganglion cells. This clock orchestrates rhythmic expression for approximately 10% of the SCN gene transcripts, of which only 10% are also rhythmically expressed in other tissues. Many of the transcripts expressed rhythmically only in the SCN are involved in neurosecretion, and their secreted products could mediate SCN control over physiological rhythms by coordinating rhythmicity in other nuclei within the brain. The coordination of clock gene transcript oscillations in peripheral tissues could be controlled directly by specific signals or indirectly by rhythmic behavior such as feeding.

Circadian regulation of nocturnin transcription by phosphorylated CREB in Xenopus retinal photoreceptor cells

Although CLOCK/BMAL1 heterodimers have been implicated in transcriptional regulation of several rhythmic genes in vitro through E-box sequence elements, little is known about how the circadian clock regulates rhythmic genes with diverse phases in vivo. The gene nocturnin is rhythmically transcribed in Xenopus retinal photoreceptor cells, which contain endogenous circadian clocks. Transcription of nocturnin peaks in these cells in the middle of the night, while CLOCK/BMAL1 activity peaks during the early morning. We have identified a novel protein-binding motif within the nocturnin promoter, which we designated the nocturnin element (NE). Although the NE sequence closely resembles an E-box, our data show that it functions as a cyclic AMP response element (CRE) by binding CREB. Furthermore, phosphorylated CREB (P-CREB) levels are rhythmic in Xenopus photoreceptors, with a phase similar to that of nocturnin transcription. Our results suggest that P-CREB controls the rhythmic regulation of nocturnin transcription and perhaps that of other night phase genes. The NE may be an evolutionary intermediate between the E-box and CRE sequences, both of which seem to be involved in the circadian control of transcription, but have evolved to drive transcription with different phases in these clock-containing cells.

Coordination of circadian timing in mammals

Time in the biological sense is measured by cycles that range from milliseconds to years. Circadian rhythms, which measure time on a scale of 24 h, are generated by one of the most ubiquitous and well-studied timing systems. At the core of this timing mechanism is an intricate molecular mechanism that ticks away in many different tissues throughout the body. However, these independent rhythms are tamed by a master clock in the brain, which coordinates tissue-specific rhythms according to light input it receives from the outside world.

Coordinated transcription of key pathways in the mouse by the circadian clock

In mammals, circadian control of physiology and behavior is driven by a master pacemaker located in the suprachiasmatic nuclei (SCN) of the hypothalamus. We have used gene expression profiling to identify cycling transcripts in the SCN and in the liver. Our analysis revealed approximately 650 cycling transcripts and showed that the majority of these were specific to either the SCN or the liver. Genetic and genomic analysis suggests that a relatively small number of output genes are directly regulated by core oscillator components. Major processes regulated by the SCN and liver were found to be under circadian regulation. Importantly, rate-limiting steps in these various pathways were key sites of circadian control, highlighting the fundamental role that circadian clocks play in cellular and organismal physiology.

Renal medullary genes in salt-sensitive hypertension: a chromosomal substitution and cDNA microarray study

Substitution of chromosome 13 from Brown Norway BN/SsNHsd/Mcw (BN/Mcw) rats into the Dahl salt-sensitive SS/JrHsd/Mcw (SS/Mcw) rats resulted in substantial reduction of blood pressure salt sensitivity in this consomic rat strain designated SSBN13. In the present study, we attempted to identify genes associated with salt-sensitive hypertension by utilizing a custom, known-gene cDNA microarray to compare the mRNA expression profiles in the renal medulla (a tissue playing a pivotal role in long-term blood pressure regulation) of SS/Mcw and SSBN13 rats on either low-salt (0.4% NaCl) or high-salt (4% NaCl, 2 wk) diets. To increase the reliability of microarray data, we designed a four-way comparison experiment incorporating several levels of replication and developed a conservative yet robust data analysis method. Using this approach, from the 1,751 genes examined (representing more than 80% of all currently known rat genes), we identified 80 as being differentially expressed in at least 1 of the 4 comparisons. Substantial agreements were found between the microarray results and the results predicted on the basis of the four-way comparison as well as the results of Northern blots of 20 randomly selected genes. Analysis of the four-way comparison further indicated that approximately 75% of the 80 differentially expressed genes were likely related to salt-sensitive hypertension. Many of these genes had not previously been recognized to be important in hypertension, whereas several genes/pathways known to be involved in hypertension were confirmed. These results should provide an informative source for designing future functional studies in salt-sensitive hypertension.