Genetic analysis of the circadian system in Drosophila melanogaster and mammals

Diversity of zebrafish peripheral oscillators revealed by luciferase reporting

In various multicellular organisms, circadian clocks are present not only in the central nervous system, but also in peripheral organs and tissues. In mammals peripheral oscillators are not directly responsive to light, but are entrained by the central oscillator in the suprachiasmatic nucleus. These individual oscillators are diverse in their free-running periods and phases. In contrast, cultured peripheral tissues and cell lines from zebrafish are not only rhythmic, but can also be directly entrained by light. Because of the convenience of studying rhythms in cultured cells, however, little has been known about properties of individual oscillators in intact zebrafish. Here, we show the remarkable diversity and consistency of oscillator properties in various peripheral organs and tissues from the period3-luciferase (per3-luc) transgenic zebrafish. Tissue-dependent differences were found in free-running period, phase, response to light, and temperature compensation. Furthermore, cycling amplitudes were reduced at lower temperatures in some, but not all, of the organs tested. Finally, we found that per3-luc rhythms can free run in both constant dark and constant light with remarkably similar amplitudes, phases, and periods, despite the fact that the mRNA of per2 and per1 has been shown not to oscillate in constant light.

Identification and expression pattern of Bmlark, a homolog of the Drosophila gene lark in Bombyx mori

Two Bombyx mori isoforms of the gene lark, which is shown to play an important role in Drosophila circadian rhythms, were identified and named Bmlark-PA and Bmlark-PB, respectively. Bmlark-PA consists of 5 exons and encodes a protein of 343 amino acid residues which contains 3 functional domains: two RRM (RNA recognization motif) domains and an RTZF (retroviral-type zinc finger) and shares 72% identity with the Drosophila gene lark at the amino acid level. Bmlark-PB lacks the sequence between 118 and 791 nt of Bmlark-PA and codes for a protein of 68 amino acid residues, which contains no distinct functional domains. Alignments of the cDNAs of Bmlark to the genomic draft sequence of B. mori showed that the gene Bmlark had a single copy in the genome, suggesting that an alternative splicing mechanism occurs in the gene Bmlark. RT-PCR analysis indicated that Bmlark-PA was expressed only in late pupae and adult but Bmlark-PB was broadly expressed in many tissues and throughout the developmental stages from embryo to adult.

Transcriptional and post-transcriptional regulation of the circadian clock of cyanobacteria and Neurospora

Circadian clocks are self-sustained oscillators modulating rhythmic transcription of large numbers of genes. Clock-controlled gene expression manifests in circadian rhythmicity of many physiological and behavioral functions. In eukaryotes, expression of core clock components is organized in a network of interconnected positive and negative feedback loops. This network is thought to constitute the pacemaker that generates circadian rhythmicity. The network of interconnected loops is embedded in a supra-net via a large number of interacting factors that affect expression and function of core clock components on transcriptional and post-transcriptional levels. In particular, phosphorylation and dephosphorylation of clock components are critical processes ensuring robust self-sustained circadian rhythmicity and entrainment of clocks to external cues. In cyanobacteria, three clock proteins have the capacity to generate a self-sustained circadian rhythm of autophosphorylation and dephosphorylation independent of transcription and translation. This phosphorylation rhythm regulates the function of these clock components, which then facilitate rhythmic gene transcription, including negative feedback on their own genes. In this article, we briefly present the mechanism of clock function in cyanobacteria. We then discuss in detail the contribution of transcriptional feedback and protein phosphorylation to various functional aspects of the circadian clock of Neurospora crassa.

Drosophila CRYPTOCHROME is a circadian transcriptional repressor

BACKGROUND

Although most circadian clock components are conserved between Drosophila and mammals, the roles assigned to the CRYPTOCHROME (CRY) proteins are very different: Drosophila CRY functions as a circadian photoreceptor, whereas mammalian CRY proteins (mCRY1 and 2) are transcriptional repressors essential for molecular clock oscillations.

RESULTS

Here we demonstrate that Drosophila CRY also functions as a transcriptional repressor. We found that RNA levels of genes directly activated by the transcription factors CLOCK (CLK) and CYCLE (CYC) are derepressed in cry(b) mutant eyes. Conversely, while overexpression of CRY and PERIOD (PER) in the eye repressed CLK/CYC activity, neither PER nor CRY repressed individually. Drosophila CRY also repressed CLK/CYC activity in cell culture. Repression by CRY appears confined to peripheral clocks, since neither cry(b) mutants nor overexpression of PER and CRY together in pacemaker neurons significantly affected molecular or behavioral rhythms. Increasing CLK/CYC activity by removing two repressors, PER and CRY, led to ectopic expression of the timeless clock gene, similar to overexpression of Clk itself.

CONCLUSIONS

Drosophila CRY functions as a transcriptional repressor required for the oscillation of peripheral circadian clocks and for the correct specification of clock cells.

Transcriptional regulation of the Neurospora circadian clock gene wc-1 affects the phase of circadian output

WHITE COLLAR-1 (WC-1) is the limiting component of the White Collar Complex (WCC) controlling expression of the Neurospora circadian clock protein Frequency (FRQ). Accumulation of WC-1 is supported by FRQ on a post-transcriptional level. Here, we show that transcription of wc-1 is organized in a complex way. Three promoters drive transcription of wc-1. Pdist is dependent on WCC. Pprox is independent of WCC in darkness, but inducible by light in a WCC-dependent manner. A third promoter, Pint, is located in the wc-1 open reading frame and promotes expression of an amino-terminally truncated WC-1 isoform of unknown function. Expression of wc-1 by Pdist or Pprox alone, or by a heterologous promoter, affects the entrained phase of circadian conidiation and the response of Neurospora to light. Our results indicate that transcriptional regulation of wc-1 is required to modulate the circadian phase of clock output.

Control of daily transcript oscillations in Drosophila by light and the circadian clock

The transcriptional circuits of circadian clocks control physiological and behavioral rhythms. Light may affect such overt rhythms in two ways: (1) by entraining the clock circuits and (2) via clock-independent molecular pathways. In this study we examine the relationship between autonomous transcript oscillations and light-driven transcript responses. Transcript profiles of wild-type and arrhythmic mutant Drosophila were recorded both in the presence of an environmental photocycle and in constant darkness. Systematic autonomous oscillations in the 12- to 48-h period range were detectable only in wild-type flies and occurred preferentially at the circadian period length. However, an extensive program of light-driven expression was confirmed in arrhythmic mutant flies. Many light-responsive transcripts are preferentially expressed in the compound eyes and the phospholipase C component of phototransduction, NORPA (no receptor potential), is required for their light-dependent regulation. Although there is evidence for the existence of multiple molecular clock circuits in cyanobacteria, protists, plants, and fungi, Drosophila appears to possess only one such system. The sustained photic expression responses identified here are partially coupled to the circadian clock and may reflect a mechanism for flies to modulate functions such as visual sensitivity and synaptic transmission in response to seasonal changes in photoperiod.

A colorful model of the circadian clock

The migration of the colorful monarch butterfly provides biologists with a unique model system with which to study the cellular and molecular mechanisms underlying a sophisticated circadian clock. The monarch circadian clock is involved in the induction of the migratory state and navigation over long distances, using the sun as a compass.

GABA modulates Drosophila circadian clock neurons via GABAB receptors and decreases in calcium

Circadian clocks play vital roles in the control of daily rhythms in physiology and behavior of animals. In Drosophila, analysis of the molecular and behavioral rhythm has shown that the master clock neurons are entrained by sensory inputs and are synchronized with other clock neurons. However, little is known about the neuronal circuits of the Drosophila circadian system and the neurotransmitters that act on the clock neurons. Here, we provide evidence for a new neuronal input pathway to the master clock neurons, s-LN(v)s, in Drosophila that utilizes GABA as a slow inhibitory neurotransmitter. We monitored intracellular calcium levels in dissociated larval s-LN(v)s with the calcium-sensitive dye Fura-2. GABA decreased intracellular calcium in the s-LN(v)s and blocked spontaneous oscillations in calcium levels. The duration of this response was dose-dependent between 1 nM and 100 microM. The response to GABA was blocked by a metabotropic GABA(B) receptor (GABA(B)-R) antagonist, CGP54626, but not by an ionotropic receptor antagonist, picrotoxin. The GABA(B)-R agonist, 3-APMPA, produced a response similar to GABA. An antiserum against one of the Drosophila GABA(B)-Rs (GABA(B)-R2) labeled the dendritic regions of the s-LN(v)s in both adults and larvae, as well as the dissociated s-LN(v)s. We found that some GABAergic processes terminate at the dendrites of the LN(v)s, as revealed by GABA immunostaining and a GABA-specific GAL4 line (GAD1-gal4). Our results suggest that the s-LN(v)s receive slow inhibitory GABAergic inputs that decrease intracellular calcium of these clock neurons and block their calcium cycling. This response is mediated by postsynaptic GABA(B) receptors.

The double-time protein kinase regulates the subcellular localization of the Drosophila clock protein period

The Period (PER), Timeless (TIM), and Double-Time (DBT) proteins are essential components of one feedback loop in the Drosophila circadian molecular clock. PER and TIM physically interact. Coexpression of PER and TIM promotes their nuclear accumulation and influences the activity of DBT: although DBT phosphorylates and destabilizes PER, this is suppressed by TIM. Experiments using Drosophila cells in culture have indicated that PER can translocate to the nucleus without TIM and will repress transcription in a DBT-potentiated manner. In this study, we examined the control of PER subcellular localization in Drosophila clock cells in vivo. We found that PER can translocate to the nucleus in tim(01) null mutants but only if DBT kinase activity is inhibited. We also found that nuclear PER is a potent transcriptional repressor in dbt mutants in vivo without TIM. Thus, in vivo, DBT regulates PER subcellular localization, in addition to its previously documented role as a mediator of PER stability. However, DBT does not seem essential for transcriptional repression by PER. It was reported previously that overexpression of a second kinase, Shaggy (SGG)/Glycogen Synthase Kinase 3, accelerates PER nuclear accumulation. Here, we show that these effects of SGG on PER nuclear accumulation require TIM. We propose a revised clock model that incorporates this tight kinase regulation of PER and TIM nuclear entry.

Mapping of serotonin, dopamine, and histamine in relation to different clock neurons in the brain of Drosophila

Several sets of clock neurons cooperate to generate circadian activity rhythms in Drosophila melanogaster. To extend the knowledge on neurotransmitters in the clock circuitry, we analyzed the distribution of some biogenic amines in relation to identified clock neurons. This was accomplished by employing clock neuron-specific GAL4 lines driving green fluorescent protein (GFP) expression, combined with immunocytochemistry with antisera against serotonin, histamine, and tyrosine hydroxylase (for dopamine). In the larval and adult brain, serotonin-immunoreactive (-IR) neuron processes are in close proximity of both the dendrites and the dorsal terminals of the major clock neurons, the s-LN(v)s. Additionally, the terminals of the l-LN(v) clock neurons and serotonergic processes converge in the distal medulla. No histamine (HA)-IR processes contact the s-LN(v)s in the larval brain, but possibly impinge on the dorsal clock neurons, DN2. In the adult brain, HA-IR axons of the extraocular eyelet photoreceptors terminate on the dendritic branches of the LN(v)s. A few tyrosine hydroxylase (TH)-IR processes were seen close to the dorsal terminals of the s-LN(v)s, but not their dendrites, in the larval and adult brain. TH-IR processes also converge with the distal medulla branches of the l-LN(v)s in adults. None of the monoamines was detectable in the different clock neurons. By using an imaging system to monitor intracellular Ca(2+) levels in dissociated GFP-labeled larval s-LN(v)s, loaded with Fura-2, we demonstrated that application of serotonin induced dose-dependent decreases in Ca(2+). Thus, serotonergic neurons form functional inputs on the s-LN(v)s in the larval brain and possibly also in adults.

PER-TIM interactions in living Drosophila cells: an interval timer for the circadian clock

In contrast to current models, fluorescence resonance energy transfer measurements using a single-cell imaging assay with fluorescent forms of PER and TIM showed that these proteins bind rapidly and persist in the cytoplasm while gradually accumulating in discrete foci. After approximately 6 hours, complexes abruptly dissociated, as PER and TIM independently moved to the nucleus in a narrow time frame. The per(L) mutation delayed nuclear accumulation in vivo and in our cultured cell system, but without affecting rates of PER/TIM assembly or dissociation. This finding points to a previously unrecognized form of temporal regulation that underlies the periodicity of the circadian clock.

The circadian system of Drosophila melanogaster and its light input pathways

The fruit fly Drosophila melanogaster has been a grateful object for circadian rhythm researchers over several decades. Behavioral, genetic, and molecular studies in the little fly have aided in understanding the bases of circadian time keeping and rhythmic behaviors not only in Drosophila, but also in other organisms, including mammals. This review summarizes our present knowledge about the fruit fly's circadian system at the molecular and neurobiological level, with special emphasis on its entrainment by environmental light-dark cycles. The results obtained for Drosophila are discussed with respect to parallel findings in mammals.

Neural circuits underlying circadian behavior in Drosophila melanogaster

Circadian clocks include control systems for organizing daily behavior. Such a system consists of a time-keeping mechanism (the clock or pacemaker), input pathways for entraining the clock, and output pathways for producing overt rhythms in behavior and physiology. In Drosophila melanogaster, as in mammals, neural circuits play vital roles in all three functional subdivisions of the circadian system. Regarding the pacemaker, multiple clock neurons, each with cell-autonomous pacemaker capability, are coupled to each other in a network. The outputs of different sets of clock neurons in this network combine to produce the normal bimodal pattern of locomotor activity observed in Drosophila. Regarding input, multiple sensory modalities (including light, temperature, and pheromones) use their own circuitry to entrain the clock. Regarding output, distinct circuits are likely involved for controlling the timing of eclosion and for generating the locomotor activity rhythms. This review summarizes work on all of these circadian circuits, and discusses the broader utility of studying the fly's circadian system.

Phosphorylation-dependent maturation of Neurospora circadian clock protein from a nuclear repressor toward a cytoplasmic activator

Frequency (FRQ) is a central component of interconnected negative and positive limbs of feedback loops of the circadian clock of Neurospora. In the negative limb, FRQ inhibits its transcriptional activator White Collar Complex (WCC) and in the positive limb, FRQ supports accumulation of WCC. We show that these conflicting functions are confined to distinct subcellular compartments and coordinated in temporal fashion. Inactivation of the transcriptional activator WCC requires nuclear FRQ and occurs early after the onset of FRQ expression. Support of WCC accumulation requires cytosolic FRQ and occurs on a post-translational level, when high amounts of FRQ have accumulated. The transcriptional function of FRQ in the negative loop and its post-translational function in the positive loop are independent and associated with distinct regions of FRQ. Phosphorylation of FRQ at the PEST-2 region triggers its maturation from a nuclear repressor toward a cytoplasmic activator.

Synaptic connections between pigment-dispersing factor-immunoreactive neurons and neurons in the pars lateralis of the blow fly Protophormia terraenovae

In females of the blow fly Protophormia terraenovae, neurons with cell bodies in the pars lateralis (PL) projecting to the retrocerebral complex (designated as PL neurons) are necessary for the induction of reproductive diapause under short-day and low-temperature conditions. In the present study, neural connections between PL neurons and pigment-dispersing factor (PDF)-immunoreactive neurons were examined via immunolight microscopy and immunoelectron microscopy combined with backfills through the cardiac-recurrent nerve. Immunolight microscopy showed that fibers of PL neurons overlapped with PDF-immunoreactive fibers in the dorsolateral region of the superior protocerebral neuropil. Immunoelectron microscopy showed that PDF-immunoreactive fibers formed output synapses with fibers of PL neurons and unlabeled neurons in a region dorsoanteriorly located with respect to the calyx of the mushroom body. The distribution of synaptic connections between PDF-immunoreactive fibers and the fibers of PL neurons was sparse. According to the projection patterns, PDF-immunoreactive fibers with synaptic connections with PL neurons appeared to originate from PDF-immunoreactive neurons with cell bodies at the base of the medulla of the optic lobe (medulla PDF neurons), which are putative circadian clock neurons in P. terraenovae. PDF immunoreactivity was restrictively detected in dense-core vesicles but not in clear synaptic vesicles. The present results suggest that medulla PDF neurons convey time or photoperiodic information to PL neurons for diapause induction through direct synaptic connections.

Diurnal and circadian rhythms in melatonin synthesis in the turkey pineal gland and retina

The pineal gland and retina of the turkey rhythmically produce melatonin. In birds kept under a daily light-dark (LD) illumination cycle melatonin concentrations in the pineal gland and retina were low during the light phase and high during the dark phase. A similar melatonin rhythm with high night-time values was also observed in the plasma. The pineal and retinal melatonin rhythms mirror oscillations in the activity of serotonin N-acetyltransferase (AANAT; the penultimate enzyme in the melatonin biosynthetic pathway). In contrast, in both the pineal gland and retina the activity of the enzyme hydroxyindole-O-methyltransferase (HIOMT) did not exhibit significant changes throughout the 24-h period. Acute exposure of turkeys to light at night dramatically decreased melatonin levels in the pineal gland, retina and plasma. The rhythms in AANAT activity and melatonin concentrations in the turkey pineal gland and retina were circadian in nature as they persisted under conditions of constant darkness (DD). Under DD, however, the amplitudes of AANAT and melatonin rhythms were significantly lower (by 50-80%) than those found under the LD cycle. The findings indicate that melatonin rhythmicity in the turkey pineal gland and retina is regulated both by light and the endogenous circadian clock. The rapid dampening of the rhythms under DD suggests that of these two regulatory factors, environmental light may be the primary stimulus in the maintenance of the high amplitude melatonin rhythms in the turkey.

The candidate gene, Clock, localizes to a strong spawning time quantitative trait locus region in rainbow trout

We applied a candidate gene mapping approach to an existing quantitative trait loci (QTL) data set for spawning date in rainbow trout (Oncorynchus mykiss) to ascertain whether these genes could potentially account for any observed QTL effects. Several genes were chosen for their known or suspected roles in reproduction, circadian, or circannual timing, including salmon-type gonadotropin-releasing hormone 3A and 3B (GnRH3A and GnRH3B), Clock, Period1, and arylalkylamine N-acetlytransferase-1 and -2 (AANAT-1 and AANAT-2). Genes were sequenced, and polymorphisms were identified in parents of two rainbow trout mapping families, one of which was used previously to detect spawn timing QTL. Interval mapping was used to identify associations between genetic markers and spawning date effects. Using a genetic map that was updated with 574 genetic markers (775 total), we found evidence for 11 significant or suggestive QTL regions. Most QTL were only localized within one of the parents; however, a strong QTL region was identified in both female and male parents on linkage group RT-8 that explained 20% and 50% of trait variance, respectively. The Clock gene mapped to this region. Period1 mapped to a region in the female parent associated with a marginal effect (P = .056) on spawn timing. Other candidate genes were not associated with significant QTL effects.

Mapping of binding regions for the circadian regulators BMAL1 and CLOCK within the mouse Rev-erbalpha gene

Two major interconnected feedback loops govern circadian rhythmicity in mammals. The transcriptional activators BMAL1/MOP3 and CLOCK drive one loop by binding to E-box motifs in the regulatory regions of circadian target genes. Time-of-day-dependent inhibition of the activity of BMAL1 and CLOCK by PERIOD (PER) and CRYPTOCHROME (CRY) proteins provokes consequent rhythmic gene expression. In this fashion, the Per and Cry genes can feedback onto their own synthesis. The orphan nuclear receptor Rev-erbalpha manifests the second feedback loop. Genetically linked to the molecular oscillator, it was identified as a repressor of the Bmal1 and Clock genes. In an attempt to understand the circadian regulation of the mouse Rev-erbalpha gene, we developed a screening technique for BMAL1 and CLOCK binding regions consisting of chromatin-immunoprecipitation. Here we show that the mouse Rev-erbalpha gene contains at least two binding regions for the transcriptional activators close to its previously identified promoter region and in its first intron. However, our data also indicate that not all potential E-box motifs in vitro are occupied in vivo.

Disruption of Cryptochrome partially restores circadian rhythmicity to the arrhythmic period mutant of Drosophila

The Drosophila melanogaster circadian clock is generated by interlocked feedback loops, and null mutations in core genes such as period and timeless generate behavioral arrhythmicity in constant darkness. In light-dark cycles, the elevation in locomotor activity that usually anticipates the light on or off signals is severely compromised in these mutants. Light transduction pathways mediated by the rhodopsins and the dedicated circadian blue light photoreceptor cryptochrome are also critical in providing the circadian clock with entraining light signals from the environment. The cry(b) mutation reduces the light sensitivity of the fly's clock, yet locomotor activity rhythms in constant darkness or light-dark cycles are relatively normal, because the rhodopsins compensate for the lack of cryptochrome function. Remarkably, when we combined a period-null mutation with cry(b), circadian rhythmicity in locomotor behavior in light-dark cycles, as measured by a number of different criteria, was restored. This effect was significantly reduced in timeless-null mutant backgrounds. Circadian rhythmicity in constant darkness was not restored, and TIM protein did not exhibit oscillations in level or localize to the nuclei of brain neurons known to be essential for circadian locomotor activity. Therefore, we have uncovered residual rhythmicity in the absence of period gene function that may be mediated by a previously undescribed period-independent role for timeless in the Drosophila circadian pacemaker. Although we do not yet have a molecular correlate for these apparently iconoclastic observations, we provide a systems explanation for these results based on differential sensitivities of subsets of circadian pacemaker neurons to light.

The Ion Channel Narrow Abdomen Is Critical for Neural Output of the Drosophila Circadian Pacemaker

Circadian clocks consist of transcriptional feedback loops housed in interdependent pacemaker neurons. Yet little is known about the neuronal output components essential for rhythmic behavior. Drosophila mutants of a putative ion channel, narrow abdomen (na), exhibit poor circadian rhythms and suppressed daylight activity. We find that NA is expressed in pacemaker neurons and induced expression within circadian neurons is sufficient to rescue these mutant phenotypes. Selective na rescue in distinct pacemaker neurons influences rhythmicity and timing of behavior. Oscillations of the clock protein PERIOD are intact in na mutants, indicating an output role. Pore residues are required for robust rescue consistent with NA action as an ion channel. In na mutants, expression of potassium currents and the key neuropeptide PDF are elevated, the latter consistent with reduced release. These data implicate NA and the pacemaker neural network in controlling phase and rhythmicity.

Organization of endogenous clocks in insects

Insect and mammalian circadian clocks show striking similarities. They utilize homologous clock genes, generating self-sustained circadian oscillations in distinct master clocks of the brain, which then control rhythmic behaviour. The molecular mechanisms of rhythm generation were first uncovered in the fruit fly Drosophila melanogaster, whereas cockroaches were among the first animals where the brain master clock was localized. Despite many similarities, there exist obvious differences in the organization and functioning of insect master clocks. These similarities and differences are reviewed on a molecular and anatomical level.

Comments on selected fundamental aspects of microarray analysis

Microarrays are becoming a ubiquitous tool of research in life sciences. However, the working principles of microarray-based methodologies are often misunderstood or apparently ignored by the researchers who actually perform and interpret experiments. This in turn seems to lead to a common over-expectation regarding the explanatory and/or knowledge-generating power of microarray analyses. In this note we intend to explain basic principles of five (5) major groups of analytical techniques used in studies of microarray data and their interpretation: the principal component analysis (PCA), the independent component analysis (ICA), the t-test, the analysis of variance (ANOVA), and self organizing maps (SOM). We discuss answers to selected practical questions related to the analysis of microarray data. We also take a closer look at the experimental setup and the rules, which have to be observed in order to exploit microarrays efficiently. Finally, we discuss in detail the scope and limitations of microarray-based methods. We emphasize the fact that no amount of statistical analysis can compensate for (or replace) a well thought through experimental setup. We conclude that microarrays are indeed useful tools in life sciences but by no means should they be expected to generate complete answers to complex biological questions. We argue that even well posed questions, formulated within a microarray-specific terminology, cannot be completely answered with the use of microarray analyses alone.

Molecular mechanism of temperature sensing by the circadian clock of Neurospora crassa

Expression levels and ratios of the long (l) and short (s) isoforms of the Neurospora circadian clock protein FREQUENCY (FRQ) are crucial for temperature compensation of circadian rhythms. We show that the ratio of l-FRQ versus s-FRQ is regulated by thermosensitive splicing of intron 6 of frq, a process removing the translation initiation site of l-FRQ. Thermosensitivity is due to inefficient recognition of nonconsensus splice sites at elevated temperature. The temperature-dependent accumulation of FRQ relative to bulk protein is controlled at the level of translation. The 5'-UTR of frq RNA contains six upstream open reading frames (uORFs) that are in nonconsensus context for translation initiation. Thermosensitive trapping of scanning ribosomes at the uORFs leads to reduced translation of the main ORF and allows adjustment of FRQ levels according to ambient temperature.

Circadian rhythms in mouse blood coagulation

The circadian clock, influencing many biological processes, has been demonstrated to modulate levels of specific coagulation factors, but its impact on the coagulation efficiency is unknown. In a mouse model, the authors evaluated the temporal variations in the initial rate of activated factor X (FXa) and thrombin generation. Upon coagulation activation through the FVIIa-TF pathway (extrinsic activation), both parameters showed rhythmic variations with a significant peak at ZT 12, the light-to-dark transition. In mice subjected to a 6-h delayed light-dark cycle, the peak was shifted as expected. These cyclic oscillations were also observed in constant darkness, thus demonstrating, for the first time, the existence of strong circadian rhythms of the initial rate of either FXa or thrombin generation activity levels. These circadian variations overlapped with those that have been recently described in factor VII (FVII) activity. The peak of FXa generation activity was simulated by the addition of purified human FVII, thus indicating that circadian variations in FVII activity are important determinants of the circadian rhythm of the procoagulant cascade efficiency. These findings help to elucidate the complex control on the coagulation process and might contribute in explaining the temporal variations in the frequency of cardiovascular events observed in humans.

Caenorhabditis elegans opens up new insights into circadian clock mechanisms

The roundworm, Caenorhabditis elegans, is known to carry homologues of clock genes such as per (=period) and tim (=timeless), which constitute the core of the circadian clock in Drosophila and mammals: lin-42 and tim-1. Analyses using WormBase (C. elegans gene database) have identified with relatively high identity analogous of the clock genes recognized in Drosophila and mammals, with the notable exception of cry (=cryptochrome), which is lacking in C. elegans. All of these C. elegans cognates of the clock genes appear to belong to members of the PAS-superfamily and to participate in development or responsiveness to the environment but apparently are not involved in the C. elegans circadian clock. Nevertheless, C. elegans exhibits convincing circadian rhythms in locomotor behavior in the adult stage and in resistance to hyperosmotic stress in starved larvae (L1) after hatching, indicating that it has a circadian clock with a core design entirely different from that of Drosophila and mammals. Here two possibilities are considered. First, the core of the C. elegans circadian clock includes transcriptional/translational feedback loops between genes and their protein products that are entirely different from those of Drosophila and mammals. Second, a more basic principle such as homeostasis governs the circadian cellular physiology, and was established primarily to minimize the accumulation of DNA damage in response to an environment cycling at 24 h intervals.

Transcriptional Feedback of Neurospora Circadian Clock Gene by Phosphorylation-Dependent Inactivation of Its Transcription Factor

The circadian clock protein Frequency (FRQ) feedback-regulates its own expression by inhibiting its transcriptional activator, White Collar Complex (WCC). We present evidence that FRQ regulates the bulk of WCC through modulation of its phosphorylation status rather than via direct complex formation. In the absence of FRQ, WCC is hypophosphorylated and transcriptionally active, while WCC is hyperphosphorylated and transcriptionally inactive when FRQ is expressed. The phosphorylation status of WCC changes rhythmically over a circadian cycle. Dephosphorylation and activation of WCC depend on protein phosphatase 2A (PP2A), and WCC is a substrate of PP2A in vitro. Hypophosphorylated WCC binds to the clock box of the frq promoter even in the presence of FRQ, while binding of hyperphosphorylated WCC is compromised even when FRQ is depleted. We propose that negative feedback in the circadian clock of Neurospora is mediated by FRQ, which rhythmically promotes phosphorylation of WCC, functionally equivalent to a cyclin recruiting cyclin-dependent kinase to its targets.

Evolution of temporal order in living organisms

Circadian clocks are believed to have evolved in parallel with the geological history of the earth, and have since been fine-tuned under selection pressures imposed by cyclic factors in the environment. These clocks regulate a wide variety of behavioral and metabolic processes in many life forms. They enhance the fitness of organisms by improving their ability to efficiently anticipate periodic events in their external environments, especially periodic changes in light, temperature and humidity. Circadian clocks provide fitness advantage even to organisms living under constant conditions, such as those prevailing in the depth of oceans or in subterranean caves, perhaps by coordinating several metabolic processes in the internal milieu. Although the issue of adaptive significance of circadian rhythms has always remained central to circadian biology research, it has never been subjected to systematic and rigorous empirical validation. A few studies carried out on free-living animals under field conditions and simulated periodic and aperiodic conditions of the laboratory suggest that circadian rhythms are of adaptive value to their owners. However, most of these studies suffer from a number of drawbacks such as lack of population-level replication, lack of true controls and lack of adequate control on the genetic composition of the populations, which in many ways limits the potential insights gained from the studies. The present review is an effort to critically discuss studies that directly or indirectly touch upon the issue of adaptive significance of circadian rhythms and highlight some shortcomings that should be avoided while designing future experiments.

Reduced sleep in Drosophila Shaker mutants

Most of us sleep 7-8 h per night, and if we are deprived of sleep our performance suffers greatly; however, a few do well with just 3-4 h of sleep-a trait that seems to run in families. Determining which genes underlie this phenotype could shed light on the mechanisms and functions of sleep. To do so, we performed mutagenesis in Drosophila melanogaster, because flies also sleep for many hours and, when sleep deprived, show sleep rebound and performance impairments. By screening 9,000 mutant lines, we found minisleep (mns), a line that sleeps for one-third of the wild-type amount. We show that mns flies perform normally in a number of tasks, have preserved sleep homeostasis, but are not impaired by sleep deprivation. We then show that mns flies carry a point mutation in a conserved domain of the Shaker gene. Moreover, after crossing out genetic modifiers accumulated over many generations, other Shaker alleles also become short sleepers and fail to complement the mns phenotype. Finally, we show that short-sleeping Shaker flies have a reduced lifespan. Shaker, which encodes a voltage-dependent potassium channel controlling membrane repolarization and transmitter release, may thus regulate sleep need or efficiency.

Circadian pacemaker neurons transmit and modulate visual information to control a rapid behavioral response

Circadian pacemaker neurons contain a molecular clock that oscillates with a period of approximately 24 hr, controlling circadian rhythms of behavior. Pacemaker neurons respond to visual system inputs for clock resetting, but, unlike other neurons, have not been reported to transmit rapid signals to their targets. Here we show that pacemaker neurons are required to mediate a rapid behavior. The Drosophila larval visual system, Bolwig's organ (BO), projects to larval pacemaker neurons to entrain their clock. BO also mediates larval photophobic behavior. We found that ablation or electrical silencing of larval pacemaker neurons abolished light avoidance. Thus, circadian pacemaker neurons receive input from BO not only to reset the clock but also to transmit rapid photophobic signals. Furthermore, as clock gene mutations also affect photophobicity, the pacemaker neurons modulate the sensitivity of larvae to light, generating a circadian rhythm in visual sensitivity.

Light-dependent development of circadian gene expression in transgenic zebrafish

The roles of environmental stimuli in initiation and synchronization of circadian oscillation during development appear to vary among different rhythmic processes. In zebrafish, a variety of rhythms emerge in larvae only after exposure to light-dark (LD) cycles, whereas zebrafish period3 (per3) mRNA has been reported to be rhythmic from day 1 of development in constant conditions. We generated transgenic zebrafish in which expression of the firefly luciferase (luc) gene is driven by the zebrafish per3 promoter. Live larvae from these lines are rhythmically bioluminescent, providing the first vertebrate system for high-throughput measurement of circadian gene expression in vivo. Circadian rhythmicity in constant conditions was observed only after 5-6 d of development, and only if the fish were exposed to LD signals after day 4. Regardless of light exposure, a novel developmental profile was observed, with low expression during the first few days and a rapid increase when active swimming begins. Ambient temperature affected the developmental profile and overall levels of per3 and luc mRNA, as well as the critical days in which LD cycles were needed for robust bioluminescence rhythms. In summary, per3-luc zebrafish has revealed complex interactions among developmental events, light, and temperature in the expression of a clock gene.

FLR-4, a novel serine/threonine protein kinase, regulates defecation rhythm in Caenorhabditis elegans

The defecation behavior of the nematode Caenorhabditis elegans is controlled by a 45-s ultradian rhythm. An essential component of the clock that regulates the rhythm is the inositol trisphosphate receptor in the intestine, but other components remain to be discovered. Here, we show that the flr-4 gene, whose mutants exhibit very short defecation cycle periods, encodes a novel serine/threonine protein kinase with a carboxyl terminal hydrophobic region. The expression of functional flr-4::GFP was detected in the intestine, part of pharyngeal muscles and a pair of neurons, but expression of flr-4 in the intestine was sufficient for the wild-type phenotype. Furthermore, laser killing of the flr-4-expressing neurons did not change the defecation phenotypes of wild-type and flr-4 mutant animals. Temperature-shift experiments with a temperature-sensitive flr-4 mutant suggested that FLR-4 acts in a cell-functional rather than developmental aspect in the regulation of defecation rhythms. The function of FLR-4 was impaired by missense mutations in the kinase domain and near the hydrophobic region, where the latter allele seemed to be a weak antimorph. Thus, a novel protein kinase with a unique structural feature acts in the intestine to increase the length of defecation cycle periods.

Systems approaches to biological rhythms in Drosophila

The chronobiological system of Drosophila is considered from the perspective of rhythm-regulated genes. These factors are enumerated and discussed not so much in terms of how the gene products are thought to act on behalf of circadian-clock mechanisms, but with special emphasis on where these molecules are manufactured within the organism. Therefore, with respect to several such cell and tissue types in the fly head, what is the "systems meaning" of a given structure's function insofar as regulation of rest-activity cycles is concerned? (Systematic oscillation of daily behavior is the principal overt phenotype analyzed in studies of Drosophila chronobiology). In turn, how do the several separate sets of clock-gene-expressing cells interact--or in some cases act in parallel--such that intricacies of the fly's sleep-wake cycles are mediated? Studying Drosophila chrono-genetics as a system-based endeavor also encompasses the fact that rhythm-related genes generate their products in many tissues beyond neural ones and during all stages of the life cycle. What, then, is the meaning of these widespread gene-expression patterns? This question is addressed with regard to circadian rhythms outside the behavioral arena, by considering other kinds of temporally based behaviors, and by contemplating how broadly systemic expression of rhythm-related genes connects with even more pleiotropic features of Drosophila biology. Thus, chronobiologically connected factors functioning within this insect comprise an increasingly salient example of gene versatility--multi-faceted usages of, and complex interactions among, entities that set up an organism's overall wherewithal to form and function. A corollary is that studying Drosophila development and adult-fly actions, even when limited to analysis of rhythm-systems phenomena, involves many of the animal's tissues and phenotypic capacities. It follows that such chronobiological experiments are technically demanding, including the necessity for investigators to possess wide-ranging expertise. Therefore, this chapter includes several different kinds of Methods set-asides. These techniques primers necessarily lack comprehensiveness, but they include certain discursive passages about why a given method can or should be applied and concerning real-world applicability of the pertinent rhythm-related technologies.

Membranes, Ions, and Clocks: Testing the Njus–Sulzman–Hastings Model of the Circadian Oscillator

Current circadian clock models based on interlocking autoregulatory transcriptional?translational negative feedback loops have arisen out of an explosion of molecular genetic data obtained over the last decade (for review, see Stanewsky, 2003; Young and Kay, 2001). An earlier model of circadian oscillation was based on feedback interactions between membrane ion transport systems and ion concentration gradients (Njus et al., 1974, 1976). This membrane model was posited as a more plausible alternative at the time to the even earlier "chronon" model, which was based on autoregulatory genetic feedback loops (Ehret and Trucco, 1967). The membrane model has been tested in a number of experimental systems by pharmacologically manipulating either ionic gradients across the plasma membrane or ion transport systems, but with inconsistent results. In the meantime, the scope and explanatory power of the genetic models overshadowed inquiries into the role of membrane ion fluxes in clock function. However, several recently developed techniques described in this article have provided a new glimpse into the essential role that membrane ion fluxes play in the mechanism of the core circadian oscillator and indicate that a complete understanding of the clock must include both genetic and membrane-based feedback loops.

Lmo mutants reveal a novel role for circadian pacemaker neurons in cocaine-induced behaviors

Drosophila has been developed recently as a model system to investigate the molecular and neural mechanisms underlying responses to drugs of abuse. Genetic screens for mutants with altered drug-induced behaviors thus provide an unbiased approach to define novel molecules involved in the process. We identified mutations in the Drosophila LIM-only (LMO) gene, encoding a regulator of LIM-homeodomain proteins, in a genetic screen for mutants with altered cocaine sensitivity. Reduced Lmo function increases behavioral responses to cocaine, while Lmo overexpression causes the opposite effect, reduced cocaine responsiveness. Expression of Lmo in the principal Drosophila circadian pacemaker cells, the PDF-expressing ventral lateral neurons (LN(v)s), is sufficient to confer normal cocaine sensitivity. Consistent with a role for Lmo in LN(v)function,Lmomutants also show defects in circadian rhythms of behavior. However, the role for LN(v)s in modulating cocaine responses is separable from their role as pacemaker neurons: ablation or functional silencing of the LN(v)s reduces cocaine sensitivity, while loss of the principal circadian neurotransmitter PDF has no effect. Together, these results reveal a novel role for Lmo in modulating acute cocaine sensitivity and circadian locomotor rhythmicity, and add to growing evidence that these behaviors are regulated by shared molecular mechanisms. The finding that the degree of cocaine responsiveness is controlled by the Drosophila pacemaker neurons provides a neuroanatomical basis for this overlap. We propose that Lmo controls the responsiveness of LN(v)s to cocaine, which in turn regulate the flies' behavioral sensitivity to the drug.

The circadian Clock mutant mouse: impaired masking response to light

Synchronization of an internal clock (entrainment) and a direct response to light (masking) are complementary ways of restricting activity of an animal to day or night. The protein CLOCK has an important role in the oscillatory mechanism of mammalian pacemakers. Our data show that it is also involved in masking responses. Mice with the Clock/Clock mutation reduced their wheel running less than wildtypes when given 1-h light pulses of light (2-1,600 lx) in the night. With dimmer lights (<2 lx), there were no significant differences between mutant and wildtype mice. Impaired masking responses to light in Clock/Clock mice were confirmed in tests with ultradian light-dark cycles (3.5:3.5 h and 1:1 h). Tests with pulses of light longer than 1 h revealed that, although the mutants responded more slowly to light, they sustained the suppression of activity over the course of the 3-h tests better than wildtypes.

Regulation of copulation duration by period and timeless in Drosophila melanogaster

The circadian clock involves several clock genes encoding interacting transcriptional regulators. Mutations in clock genes in Drosophila melanogaster, period (per), timeless (tim), Clock (Clk), and cycle (cyc), produce multiple phenotypes associated with physiology, behavior, development, and morphology. It is not clear whether these genes always work as clock components or may also act in some unknown pleiotropic fashion. We report here that per and tim are involved in a novel, male-specific phenotype that affects behavioral timing on the order of minutes. Males lacking per or tim copulate significantly longer than males with normal per or tim function, while females do not show this effect. No correlation between fertility and extended copulation duration was found. Several lines of evidence suggest that the time in copula (TIC) is not regulated by the known clock mechanism. First, the period of free-running clock oscillations does not appear to affect this phenotype. Second, constant light, which abolishes the clock function, does not alter TIC. Finally, mutations in the positively acting clock transcription factors, Clk and cyc, do not affect TIC. Our study extends the repertoire of behavioral functions involving per and tim genes and uncovers another time scale over which these genes may act.

A clock gene, period, plays a key role in long-term memory formation in Drosophila

The cAMP-responsive transcription factor, CREB, is required for formation of long-term memory (LTM) in Drosophila melanogaster and regulates transcription of a circadian clock gene, period (per). Involvement of CREB both in LTM and circadian rhythm raises the possibility that per also plays a role in LTM. Assaying the experience-dependent courtship inhibition in male flies as a measure for LTM, we show here that per mutants are defective in LTM formation. This defect was rescued by induction of a wild-type per transgene in a per-null mutant, and overexpression of per enhanced LTM formation in the wild-type background. Furthermore, we found that synaptic transmission through per-expressing cells is most likely to be required during retrieval of LTM. In contrast, mutations in other clock genes (timeless, dClock, and cycle) did not affect LTM formation. Thus, independent of the core oscillator of circadian clock, per plays a key role in LTM formation.

The novel Drosophila tim(blind) mutation affects behavioral rhythms but not periodic eclosion

Circadian clock function depends on the tightly regulated exclusion or presence of clock proteins within the nucleus. A newly induced long-period timeless mutant, tim(blind), encodes a constitutively hypophosphorylated TIM protein. The mutant protein is not properly degraded by light, and tim(blind) flies show abnormal behavioral responses to light pulses. This is probably caused by impaired nuclear accumulation of TIM(BLIND) protein, which we observed in brain pacemaker neurons and photoreceptor cells of the compound eye. tim(blind) encodes two closely spaced amino acid changes compared to the wild-type TIM protein; one of them is within a putative nuclear export signal of TIM. Under constant conditions, tim(blind) flies exhibit 26-hr free-running locomotor rhythms, which are not correlated with a period lengthening of eclosion rhythms and period-luciferase reporter-gene oscillations. Therefore it seems possible that TIM--in addition to its well-established role as core clock factor--functions as a clock output factor, involved in determining the period length of adult locomotor rhythms.

Neurobiology of the fruit fly's circadian clock

Studying the fruit fly Drosophila melanogaster has revealed mechanisms underlying circadian clock function. Rhythmic behavior could be assessed to the function of several clock genes that generate circadian oscillations in certain brain neurons, which finally modulate behavior in a circadian manner. This review outlines how individual circadian pacemaker neurons in the fruit fly's brain control rhythm in locomotor activity and eclosion.

period expression in the honey bee brain is developmentally regulated and not affected by light, flight experience, or colony type

Changes in circadian rhythms of behavior are related to age-based division of labor in honey bee colonies. The expression of the clock gene period (per) in the bee brain is associated with age-related changes in circadian rhythms of behavior, but previous efforts to firmly associate per brain expression with division of labor or age have produced variable results. We explored whether this variability was due to differences in light and flight experience, which vary with division of labor, or differences in colony environment, which are known to affect honey bee behavioral development. Our results support the hypothesis that per mRNA expression in the bee brain is developmentally regulated. One-day-old bees had the lowest levels of expression and rarely showed evidence of diurnal fluctuation, while foragers and forager-age bees (> 21 days of age) always had high levels of brain per and strong and consistent diurnal patterns. Results from laboratory and field experiments do not support the hypothesis that light, flight experience, and colony type influence per expression. Our results suggest that the rate of developmental elevation in per expression is influenced by factors other than the ones studied in our experiments, and that young bees are more sensitive to these factors than foragers.

The mammalian circadian timing system: from gene expression to physiology

Many physiological processes in organisms from bacteria to man are rhythmic, and some of these are controlled by self-sustained oscillators that persist in the absence of external time cues. Circadian clocks are perhaps the best characterized biological oscillators and they exist in virtually all light-sensitive organisms. In mammals, they influence nearly all aspects of physiology and behavior, including sleep-wake cycles, cardiovascular activity, endocrinology, body temperature, renal activity, physiology of the gastro-intestinal tract, and hepatic metabolism. The master pacemaker is located in the suprachiasmatic nuclei, two small groups of neurons in the ventral part of the hypothalamus. However, most peripheral body cells contain self-sustained circadian oscillators with a molecular makeup similar to that of SCN (suprachiasmatic nucleus) neurons. This organization implies that the SCN must synchronize countless subsidiary oscillators in peripheral tissues, in order to coordinate cyclic physiology. In this review, we will discuss some recent studies on the structure and putative functions of the mammalian circadian timing system, but we will also point out some apparent inconsistencies in the currently publicized model for rhythm generation.

Adaptive significance of circadian clocks

Circadian clocks are ubiquitous and are found in organisms ranging from bacteria to mammals. This ubiquity of occurrence implies adaptive significance, but to date there has been no rigorous empirical evidence to support this. It is believed that an organism possessing circadian clocks gains fitness advantage in two ways: (i) by synchronizing its behavioral and physiological processes to cyclic environmental factors (extrinsic adaptive value); (ii) by coordinating its internal metabolic processes (intrinsic adaptive value). There is preliminary circumstantial evidence to support both. Several studies using organisms living in constant environments have shown that these organisms possess functional circadian clocks, suggesting that circadian clocks may have some intrinsic adaptive value. Studies to assess the adaptive value of circadian clocks in periodic environments suggest that organisms may have a fitness advantage in those periodic environments, which closely match their own intrinsic periodicity. Furthermore, evidence from organisms living in the wild, selection studies, and studies on latitudinal clines suggest that circadian clocks may have an extrinsic adaptive value as well. In this paper, I have presented several hypotheses for the emergence of circadian clocks and have reviewed some major empirical studies suggesting adaptive significance of circadian clocks.

Entrainment of eclosion rhythm in Drosophila melanogaster populations reared for more than 700 generations in constant light environment

In this paper, we report the results of our extensive study on eclosion rhythm of four independent populations of Drosophila melanogaster that were reared in constant light (LL) environment of the laboratory for more than 700 generations. The eclosion rhythm of these flies was assayed under LL, constant darkness (DD) and three periodic light-dark (LD) cycles (T20, T24, and T28). The percentage of vials from each population that exhibited circadian rhythm of eclosion in DD and in LL (intensity of approximately 100 lux) was about 90% and 18%, respectively. The mean free-running period (tau) of eclosion rhythm in DD was 22.85 +/- 0.87 h (mean +/- SD). Eclosion rhythm of these flies entrained to all the three periodic LD cycles, and the phase relationship (psi) of the peak of eclosion with respect to "lights-on" of the LD cycle was significantly different in the three periodic light regimes (T20, T24, and T28). The results thus clearly demonstrate that these flies have preserved the ability to exhibit circadian rhythm of eclosion and the ability to entrain to a wide range of periodic LD cycles even after being in an aperiodic environment for several hundred generations. This suggests that circadian clocks may have intrinsic adaptive value accrued perhaps from coordinating internal metabolic cycles in constant conditions, and that the entrainment mechanisms of circadian clocks are possibly an integral part of the clockwork.

Noncircadian regulation and function of clock genes period and timeless in oogenesis of Drosophila melanogaster

Circadian clock genes are ubiquitously expressed in the nervous system and peripheral tissues of complex animals. While clock genes in the brain are essential for behavioral rhythms, the physiological roles of these genes in the periphery are not well understood. Constitutive expression of the clock gene period was reported in the ovaries of Drosophila melanogaster; however, its molecular interactions and functional significance remained unknown. This study demonstrates that period (per) and timeless (tim) are involved in a novel noncircadian function in the ovary. PER and TIM are constantly expressed in the follicle cells enveloping young oocytes. Genetic evidence suggests that PER and TIM interact in these cells, yet they do not translocate to the nucleus. The levels of TIM and PER in the ovary are affected neither by light nor by the lack of clock-positive elements Clock (Clk) and cycle (cyc). Taken together, these data suggest that per and tim are regulated differently in follicle cells than in clock cells. Experimental evidence suggests that a novel fitness-related phenotype may be linked to noncircadian expression of clock genes in the ovaries. Mated females lacking either per or tim show nearly a 50% decline in progeny, and virgin females show a similar decline in the production of mature oocytes. Disruption of circadian mechanism by either the depletion of TIM via constant light treatment or continuous expression of PER via GAL4/UAS expression system has no adverse effect on the production of mature oocytes.

The circadian clock in the brain: a structural and functional comparison between mammals and insects

The circadian master clocks in the brains of mammals and insects are compared in respect to location, organization and function. They show astonishing similarities. Both clocks are anatomically and functionally connected to the optic system and possess multiple output pathways allowing synchronization with the environmental light-dark cycles as well as the control of diverse endocrine, autonomic and behavioral functions. Both circadian master clocks are composed of multiple neurons, which are organized in populations with different morphology, physiology and neurotransmitter content and appear to subserve different functions. In the hamster and in the cockroach, the master clock consists of a core region that gets input from the eyes, and a shell region from which the majority of output projections originate. Communication between core and shell, between all other populations of clock neurons as well as between the master clocks of both brain hemispheres is a prerequisite of normal rhythmic function. Phenomena like rhythm splitting and internal desynchronization can be observed under constant light conditions and are caused by the "uncoupling" of the master clocks of both brain hemispheres.

The operons, a criterion to compare the reliability of transcriptome analysis tools: ICA is more reliable than ANOVA, PLS and PCA

The number of statistical tools used to analyze transcriptome data is continuously increasing and no one, definitive method has so far emerged. There is a need for comparison and a number of different approaches has been taken to evaluate the effectiveness of the different statistical tools available for microarray analyses. In this paper, we describe a simple and efficient protocol to compare the reliability of different statistical tools available for microarray analyses. It exploits the fact that genes within an operon exhibit the same expression patterns. In order to compare the tools, the genes are ranked according to the most relevant criterion for each tool; for each tool we look at the number of different operons represented within the first twenty genes detected. We then look at the size of the interval within which we find the most significant genes belonging to each operon in question. This allows us to define and estimate the sensitivity and accuracy of each statistical tool. We have compared four statistical tools using Bacillus subtilis expression data: the analysis of variance (ANOVA), the principal component analysis (PCA), the independent component analysis (ICA) and the partial least square regression (PLS). Our results show ICA to be the most sensitive and accurate of the tools tested. In this article, we have used the protocol to compare statistical tools applied to the analysis of differential gene expression. However, it can also be applied without modification to compare the statistical tools developed for other types of transcriptome analyses, like the study of gene co-expression.