Journal of Biological Rhythms

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.

Investigations performed on adult insects revealed that putative components of the central pacemaker, the protein Period (PER) and the pigment-dispersing hormone (PDH), are immunocytochemically detectable in discrete sets of brain neurons throughout the class of Insecta, represented by a bristletail, mayfly, damselfly, 2 locust species, stonefly, 2 bug species, goldsmith beetle, caddisfly, honeybee, and 2 blowfly species. The PER-positive cells are localized in the frontal protocerebrum and in most species also in the optic lobes, which are their only location in damselfly and goldsmith beetle. Additional PER-positive cells occur in a few species either in the deuto- and tritocerebrum or in the suboesophageal ganglion. The PER staining was always confined to the cytoplasm. The PDH immunoreactivity consistently occurs in a cluster of perikarya located frontoventrally at the proximal edge of the medulla. The mayfly and both locust species possess additional PDH neurons in 2 posterior cell clusters at the proximal edge of the medulla, and mayfly, waterstrider, and 1 of the blowfly species in the central brain. PDH-positive fibers form a fanlike arrangement over the frontal side of the medulla. Two or just 1 bundle of PDH-positive fibers run from the optic lobe to the protocerebrum, with collaterals passing over to the contralateral optic lobe. Antisera to the prothoracicotropic (PTTH) and the eclosion (EH) hormones, which in some insects regulate the molting and ecdysis rhythms, respectively, typically react with a few neurons in the frontal protocerebrum. However, the PTTH-positive neurons of the mayfly and the damselfly and the EH-positive neurons of the caddisfly are located in the suboesophageal ganglion. No PTTH-like antigen was detected in locusts, and no EH-like antigens were detected in the damselfly, stonefly, locusts, and the honeybee. There are no signs of co-localization of the PER-, PDH-, PTTH-, and EH-like antigens in identical neurons.

Three homologs of the Drosophila Period gene have been identified in mammals. In mice, these three genes (mPer1, mPer2, and mPer3) have distinct roles in the circadian clockwork. While products of mPer1 and mPer2 play important roles in the maintenance of circadian rhythmicity, mPer3 gene products are dispensable for rhythmicity. Several studies also implicate mPER1 and mPER2 in transduction of photic information to the core circadian clockwork. The phase-shifting effects of light were examined in mPER1-deficient and mPER2-deficient mice using T cycle paradigms, in which mice received 1 h of light per day at an interval of T hours. To assess phase delays, repeated exposure to 1 h of light per day at T = 24 was used. To assess phase advances, exposure to 1-h light pulses at T = 22-h intervals was used. The degeneration of rhythmicity in the mutant mice prevented assessment of a response in most cases. Nevertheless, clear examples of phase delays and phase advances were observed in both mPer1 and mPer2 mutant mice. These results are not consistent with the hypothesis that mPER1 and mPER2 play necessary and nonoverlapping roles in mediating the effects of light on the circadian clock.

Rhythmicity of the rat suprachiasmatic nucleus (SCN), a site of the circadian pacemaker, is affected by daylength; that is, by the photoperiod. Whereas various markers of rhythmicity have been followed, so far there have been no studies on the effect of the photoperiod on the expression of the clock genes in the rat SCN. To fill the gap and to better understand the photoperiodic modulation of the SCN state, rats were maintained either under a long photoperiod with 16 h of light and 8 h of darkness per day (LD16:8) or under a short LD8:16 photoperiod, and daily profiles of Per1, Cry1, Bmal1 and Clock mRNA in darkness were assessed by in situ hybridization method. The photoperiod affected phase, waveform, and amplitude of the rhythmic gene expression as well as phase relationship between their profiles. Under the long period, the interval of elevated Per1 mRNA lasted for a longer and that of elevated Bmal1 mRNA for a shorter time than under the short photoperiod. Under both photoperiods, the morning and the daytime Per1 and Cry1 mRNA rise as well as the morning Bmal1 mRNA decline were closely linked to the morning light onset. Amplitude of Per1, Cry1, and Bmal1 mRNA rhythms was larger under the short than under the long photoperiod. Also, under the short photoperiod, the daily Clock mRNA profile exhibited a significant rhythm. Altogether, the data indicate that the whole complex molecular clockwork in the rat SCN is photoperiod dependent and hence may differ according to the season of the year.

Serotonin (5-HT) is thought to play a role in regulating nonphotic phase shifts and modulating photic phase shifts of the mammalian circadian system, but results with different species (rats vs. hamsters) and techniques (in vivo vs. in vitro; systemic vs. intracerebral drug delivery) have been discordant. Here we examined the effects of the 5-HT_1A/7 agonist 8-OH-DPAT and the 5-HT_1/2 agonist quipazine on the circadian system in mice, with some parallel experiments conducted with hamsters for comparative purposes. In mice, neither drug, delivered systemically at a range of circadian phases and doses, induced phase shifts significantly different from vehicle injections. In hamsters, quipazine intraperitoneally (i.p.) did not induce phase shifts, whereas 8-OH-DPAT induced phase shifts after i.p. but not intra-SCN injections. In mice, quipazine modestly increased c-Fos expression in the SCN (site of the circadian pacemaker) during the subjective day, whereas 8-OH-DPAT did not affect SCN c-Fos. In hamsters, both drugs suppressed SCN c-Fos in the subjective day. In both species, both drugs strongly induced c-Fos in the paraventricular nucleus (within-subject positive control). 8-OH-DPAT did not significantly attenuate light-induced phase shifts in mice but did in hamsters (between-species positive control). These results indicate that in the intact mouse in vivo, acute activation of 5-HT_1A/2/7 receptors in the circadian system is not sufficient to reset the SCN pacemaker or to oppose phase-shifting effects of light. There appear to be significant species differences in the susceptibility of the circadian system to modulation by systemically delivered serotonergics.

Aging alters numerous aspects of circadian biology, including the amplitude of rhythms generated by the suprachiasmatic nuclei (SCN) of the hypothalamus, the site of the central circadian pacemaker in mammals, and the response of the pacemaker to environmental stimuli such as light. Although previous studies have described molecular correlates of these behavioral changes, to date only 1 study in rats has attempted to determine if there are age-related changes in the expression of genes that comprise the circadian clock itself. We used in situ hybridization to examine the effects of age on the circadian pattern of expression of a subset of the genes that comprise the molecular machinery of the circadian clock in golden hamsters. Here we report that age alters the 24-h expression profile of Clock and its binding partner Bmal1 in the hamster SCN. There is no effect of age on the 24-h profile of either Per1 or Per2 when hamsters are housed in constant darkness. We also found that light pulses, which induce smaller phase shifts in old animals than in young, lead to decreased induction of Per1, but not of Per2, in the SCN of old hamsters.

It is not clear whether shifting of sleep per se, without a concomitant change in the light-dark cycle, can induce a phase shift of the human circadian pacemaker. Two 9-day protocols (crossover, counterbalanced order) were completed by 4 men and 6 women (20-34 years) after adherence to a 2330 to 0800 h sleep episode at home for 2 weeks. Following a modified baseline constant routine (CR) protocol on day 2, they remained under continuous near-darkness (< 0.2 lux, including sleep) for 6 days. Four isocaloric meals were equally distributed during scheduled wakefulness, and their timing was held constant. Subjects remained supine in bed from 2100 to 0800 h on all days; sleep was fixed from 2330 to 0800 h in the control condition and was gradually advanced 20 min per day during the sleep advance condition until a 2-h difference had been attained. On day 9, a 25 to 27 h CR protocol (~0.1 lux) was carried out. Phase markers were the evening decline time of the core body temperature (CBT) rhythm and salivary melatonin onset (3 pg/ml threshhold). In the fixed sleep condition, the phase drift over 7 days ranged from +1.62 to –2.56 h (for both CBT and melatonin rhythms, which drifted in parallel). The drifts were consistently advanced in the sleep advance schedule by +0.66 ± 0.23 (SEM) h for CBT (p = 0.02) and by 0.27 ± 0.14 h for melatonin rhythms (p = 0.09). However, this advance was small to medium according to effect size. Sleep per se may feed back onto the circadian pacemaker, but it appears to be a weak zeitgeber in humans.