Cyclic Expression Patterns Research Articles

Diurnal variations of triglyceride accumulation in mouse and bovine adipocyte-derived cell lines.

Several studies have suggested a strong interaction between the circadian clock and lipid metabolism in mammals. The circadian clock is driven by endogenous cyclic gene expression patterns, commonly referred to as clock genes, and transcription-translation negative feedback loops. Clock genes regulate the transcription of some lipid metabolism-related genes; however, the relationship between the circadian clock and triglyceride (TG) accumulation at the cellular level remains unclear. Here, we evaluated rhythms of intracellular TG accumulation levels as well as the expression of clock genes and lipid metabolism-related genes for 54 h in mouse and bovine adipose-derived cell cultures. To the best of our knowledge, this study represents the first report demonstrating that TG accumulation exhibits diurnal variations, with the pattern differing among cell types. Furthermore, we found that expression of clock genes and corresponding lipid metabolism-related genes exhibited circadian rhythms. Our results suggest that the cellular clock regulates lipid metabolism-related genes to relate circadian rhythms of TG accumulation in each cell type. We anticipate that the amount of fat stored depends on the timing of the supply of glucose-the precursor of fat. The findings of this study will contribute to the advancement of chrono-nutrition.

Transcriptional Analysis of Tightly Synchronized Plasmodium falciparum Intraerythrocytic Stages by RT-qPCR.

In Plasmodium falciparum, the parasite responsible for the most severe forms of human malaria, many fundamental processes are controlled at the transcriptional level. Studies on diverse aspects of basic parasite biology as well as molecular epidemiology studies often rely on the ability to accurately measure transcript levels, but this is complicated by the cyclic expression patterns of the majority of malaria parasite genes. Here, we provide a complete workflow to measure transcript levels in P. falciparum intraerythrocytic blood stages, overcoming the confounding factors that are commonly encountered. The method described covers all the steps from synchronization of parasite cultures to reverse transcriptase quantitative PCR (RT-qPCR) analysis.

Global assessment of organ specific basal gene expression over a diurnal cycle with analyses of gene copies exhibiting cyclic expression patterns

BackgroundStudying functional divergences between paralogs that originated from genome duplication is a significant topic in investigating molecular evolution. Genes that exhibit basal level cyclic expression patterns including circadian and light responsive genes are important physiological regulators. Temporal shifts in basal gene expression patterns are important factors to be considered when studying genetic functions. However, adequate efforts have not been applied to studying basal gene expression variation on a global scale to establish transcriptional activity baselines for each organ. Furthermore, the investigation of cyclic expression pattern comparisons between genome duplication created paralogs, and potential functional divergence between them has been neglected. To address these questions, we utilized a teleost fish species, Xiphophorus maculatus, and profiled gene expression within 9 organs at 3-h intervals throughout a 24-h diurnal period.ResultsOur results showed 1.3–21.9% of genes in different organs exhibited cyclic expression patterns, with eye showing the highest fraction of cycling genes while gonads yielded the lowest. A majority of the duplicated gene pairs exhibited divergences in their basal level expression patterns wherein only one paralog exhibited an oscillating expression pattern, or both paralogs exhibit oscillating expression patterns, but each gene duplicate showed a different peak expression time, and/or in different organs.ConclusionsThese observations suggest cyclic genes experienced significant sub-, neo-, or non-functionalization following the teleost genome duplication event. In addition, we developed a customized, web-accessible, gene expression browser to facilitate data mining and data visualization for the scientific community.

Programming effects of maternal stress on the circadian system of adult offspring

Maternal stress has long-lasting influences on the brain functions of offspring, and several brain regions have been proposed to mediate such programming. Although perinatal programming of crosstalk between the circadian and stress systems has been proposed, the functional consequences of prenatal stress on the circadian system and the underlying mechanisms remain largely unknown. Therefore, we investigated whether exposing pregnant mice to chronic restraint stress had prolonged effects on the suprachiasmatic nucleus (SCN), which bears the central pacemaker for mammalian circadian rhythms, of offspring. SCN explants from maternally stressed mice exhibited altered cyclic expression patterns of a luciferase reporter under control of the mouse Per1 promoter (mPer1::LUC), which manifested as a decreased amplitude and impaired stability of the rhythm. Bioluminescence imaging at the single-cell level subsequently revealed that impaired synchrony among individual cells was responsible for the impaired rhythmicity. These intrinsic defects appeared to persist during adulthood. Adult male offspring from stressed mothers showed advanced-phase behavioral rhythms with impaired stability as well as altered clock gene expression in the SCN. In addition to affecting the central rhythm, maternal stress also had prolonged influences on the circadian characteristics of the adrenal gland and liver, as determined by circulating corticosterone levels and hepatic glycogen content, and on canonical clock gene mRNA expression in those tissues. Taken together, our findings suggest that the SCN is a key target of the programming effects of maternal stress. The widespread effects of circadian disruptions caused by a misprogrammed clock may have further impacts on metabolic and mental health in later life.

The Clocks within Our Cells.

The article focuses on the role of circadian rhythms has on medication timing to treat diseases (chronomedicine). It states that up to 82 percent of mammalian genes undergo cyclic expression patterns of highs and lows meaning that there is a time aspect to biology. It talks about old medical compendiums which found some medical disorders had daily variations in manifestations, including asthma, blood pressure, and chest pains. It mentions research into gene expression cyclic patterns

Validation of house-keeping genes for normalization of gene expression data during diurnal/circadian studies in rice by RT-qPCR

The circadian clock in plants is the intrinsic rhythmic expression of thousands of genes in a 24 h period, which is set by the day-night cycles in the environment. The study of the circadian clock often requires expression profiling of genes over a large number of samples for which RT-qPCR is invariably used. Reliability of the results depends largely on the house-keeping genes, which serve as control and thus should be chosen carefully to prevent erroneous results. In this study, ten house-keeping genes were chosen from rice for stability analysis with 48 tissue samples harvested from plants subjected to diurnal/circadian cycles. Although, all the genes were found to be stable, however, six of them showed cyclic expression patterns and caused major changes in the expression profiles of the target genes when used to normalize their expression data, thereby making them poor candidates for diurnal/circadian studies. In conclusion, reference genes need to be selected for diurnal/circadian studies with extra caution as more than 80% of transcriptome in plants undergoes cycling, which remains undetected by the gene stability assessment software and can severely affect the RT-qPCR based gene expression profiling. The geometric mean of two or more most stable reference genes is hence recommended for diurnal/circadian studies in plants.

RNA sequencing reveals distinct gene expression patterns during the development of parasitic larval stages of the salmon louse (Lepeophtheirus salmonis).

The salmon louse (Lepeophtheirus salmonis), an ectoparasitic copepod on salmonids, has become a major threat for the aquaculture industry. In search for new drugs and vaccines, transcriptome analysis is increasingly used to find differently regulated genes and pathways in response to treatment. However, the underlying gene expression changes going along with developmental processes could confound such analyses. The life cycle of L.salmonis consists of eight stages divided by moults. The developmental rate of salmon lice on the host is not uniform. Individual- and sex-related differences are found leading to individuals of unlike developmental status at same sampling time point after infection. In this study, we analyse L.salmonis from a time series by RNA sequencing applying a method of separating individuals of different instar age independent of sampling time point. Lice of four stages divided into up to four age groups within the stage were analysed in triplicate (total of 66 samples). Gene expression analysis shows that the method for sorting individuals was successful. Many genes show cyclic expression patterns over the moulting cycles. Overall gene expression differs more between lice of different age within the same stage than between lice of different stage but same instar age.

Genetics of Circadian Rhythms.

Nearly all organisms exhibit time-dependent behavior and physiology across a 24-hourday known as circadian rhythms. These outputs are manifestations of endogenous cyclic gene expression patterns driven by the activity of a core transcription/translation feedback loop. Cyclic gene expression determines highly tissue-specific functional activity regulating such processes as metabolic state, endocrine activity, and neural excitability. Entrainment of these cellular clocks is achieved through exogenous daily inputs, such as light and food. Dysregulation of the transcription/translation feedback loop has been shown to result in a wide range of disorders and diseases driving increased interest in circadian therapies.

Eumetazoan Cryptochrome Phylogeny and Evolution

Cryptochromes (Crys) are light sensing receptors that are present in all eukaryotes. They mainly absorb light in the UV/blue spectrum. The extant Crys consist of two subfamilies, which are descendants of photolyases but are now involved in the regulation of circadian rhythms. So far, knowledge about the evolution, phylogeny, and expression of cry genes is still scarce. The inclusion of cry sequences from a wide range of bilaterian species allowed us to analyze their phylogeny in detail, identifying six major Cry subgroups. Selective gene inactivations and stabilizations in multiple chordate as well as arthropod lineages suggest several sub- and/or neofunctionalization events. An expression study performed in zebrafish, the model organism harboring the largest amount of crys, showed indeed only partially overlapping expression of paralogous mRNA, supporting gene sub- and/or neofunctionalization. Moreover, the daily cry expression in the adult zebrafish retina indicated varying oscillation patterns in different cell types. Our extensive phylogenetic analysis provides for the first time an overview of cry evolutionary history. Although several, especially parasitic or blind species, have lost all cry genes, crustaceans have retained up to three crys, teleosts possess up to seven, and tetrapods up to four crys. The broad and cyclic expression pattern of all cry transcripts in zebrafish retinal layers implies an involvement in retinal circadian processes and supports the hypothesis of several autonomous circadian clocks present in the vertebrate retina.

Prevalence, Evolution, andcis-Regulation of Diel Transcription inChlamydomonas reinhardtii

Endogenous (circadian) and exogenous (e.g., diel) biological rhythms are a prominent feature of many living systems. In green algal species, knowledge of the extent of diel rhythmicity of genome-wide gene expression, its evolution, and its cis-regulatory mechanism is limited. In this study, we identified cyclically expressed genes under diel conditions in Chlamydomonas reinhardtii and found that ~50% of the 17,114 annotated genes exhibited cyclic expression. These cyclic expression patterns indicate a clear succession of biological processes during the course of a day. Among 237 functional categories enriched in cyclically expressed genes, >90% were phase-specific, including photosynthesis, cell division, and motility-related processes. By contrasting cyclic expression between C. reinhardtii and Arabidopsis thaliana putative orthologs, we found significant but weak conservation in cyclic gene expression patterns. On the other hand, within C. reinhardtii cyclic expression was preferentially maintained between duplicates, and the evolution of phase between paralogs is limited to relatively minor time shifts. Finally, to better understand the cis regulatory basis of diel expression, putative cis-regulatory elements were identified that could predict the expression phase of a subset of the cyclic transcriptome. Our findings demonstrate both the prevalence of cycling genes as well as the complex regulatory circuitry required to control cyclic expression in a green algal model, highlighting the need to consider diel expression in studying algal molecular networks and in future biotechnological applications.

DETECTION AND DECOMPOSITION: TREATMENT-INDUCED CYCLIC GENE EXPRESSION DISRUPTION IN HIGH-THROUGHPUT TIME-SERIES DATASETS

Higher organisms possess many genes which cycle under normal conditions, to allow the organism to adapt to expected environmental conditions throughout the course of a day. However, treatment-induced disruption of regular cyclic gene expression patterns presents a significant challenge in novel gene discovery experiments because these disruptions can induce strong differential regulation events for genes that are not involved in an adaptive response to the treatment. To address this cycle disruption problem, we reviewed the state-of-art periodic pattern detection algorithms and a pattern decomposition algorithm (PRIISM), which is a knowledge-based Fourier analysis algorithm designed to distinguish the cyclic patterns from the rest gene expression patterns, and discussed potential future improvements.

Local serotonin mediates cyclic strain-induced phenotype transformation, matrix degradation, and glycosaminoglycan synthesis in cultured sheep mitral valves

This study addressed the following questions: 1) Does cyclic tensile strain induce protein expression patterns consistent with myxomatous degeneration in mitral valves? 2) Does cyclic strain induce local serotonin synthesis in mitral valves? 3) Are cyclic strain-induced myxomatous protein expression patterns in mitral valves dependent on local serotonin? Cultured sheep mitral valve leaflets were subjected to 0, 10, 20, and 30% cyclic strain for 24 and 72 h. Protein levels of activated myofibroblast phenotype markers, α-smooth muscle actin (α-SMA) and nonmuscle embryonic myosin (SMemb); matrix catabolic enzymes, matrix metalloprotease (MMP) 1 and 13, and cathepsin K; and sulfated glycosaminoglycan (GAG) content in mitral valves increased with increased cyclic strain. Serotonin was present in the serum-free media of cultured mitral valves and concentrations increased with cyclic strain. Expression of the serotonin synthetic enzyme tryptophan hydroxylase 1 (TPH1) increased in strained mitral valves. Pharmacologic inhibition of the serotonin 2B/2C receptor or TPH1 diminished expression of phenotype markers (α-SMA and SMemb) and matrix catabolic enzyme (MMP1, MMP13, and cathepsin K) expression in 10- and 30%-strained mitral valves. These results provide first evidence that mitral valves synthesize serotonin locally. The results further demonstrate that tensile loading modulates local serotonin synthesis, expression of effector proteins associated with mitral valve degeneration, and GAG synthesis. Inhibition of serotonin diminishes strain-mediated protein expression patterns. These findings implicate serotonin and tensile loading in mitral degeneration, functionally link the pathogeneses of serotoninergic (carcinoid, drug-induced) and degenerative mitral valve disease, and have therapeutic implications.

Quantitative Time-course Profiling of Parasite and Host Cell Proteins in the Human Malaria Parasite Plasmodium falciparum

Studies of the Plasmodium falciparum transcriptome have shown that the tightly controlled progression of the parasite through the intra-erythrocytic developmental cycle (IDC) is accompanied by a continuous gene expression cascade in which most expressed genes exhibit a single transcriptional peak. Because the biochemical and cellular functions of most genes are mediated by the encoded proteins, understanding the relationship between mRNA and protein levels is crucial for inferring biological activity from transcriptional gene expression data. Although studies on other organisms show that <50% of protein abundance variation may be attributable to corresponding mRNA levels, the situation in Plasmodium is further complicated by the dynamic nature of the cyclic gene expression cascade. In this study, we simultaneously determined mRNA and protein abundance profiles for P. falciparum parasites during the IDC at 2-hour resolution based on oligonucleotide microarrays and two-dimensional differential gel electrophoresis protein gels. We find that most proteins are represented by more than one isoform, presumably because of post-translational modifications. Like transcripts, most proteins exhibit cyclic abundance profiles with one peak during the IDC, whereas the presence of functionally related proteins is highly correlated. In contrast, the abundance of most parasite proteins peaks significantly later (median 11 h) than the corresponding transcripts and often decreases slowly in the second half of the IDC. Computational modeling indicates that the considerable and varied incongruence between transcript and protein abundance may largely be caused by the dynamics of translation and protein degradation. Furthermore, we present cyclic abundance profiles also for parasite-associated human proteins and confirm the presence of five human proteins with a potential role in antioxidant defense within the parasites. Together, our data provide fundamental insights into transcript-protein relationships in P. falciparum that are important for the correct interpretation of transcriptional data and that may facilitate the improvement and development of malaria diagnostics and drug therapy.

A Synthesis Method of Gene Networks Having Cyclic Expression Pattern Sequences by Network Learning

Recently, the synthesis of gene networks having desired functions has become of interest to many researchers and several studies have been done. Synthesis methods of gene networks possessing desired expression pattern sequences are proposed. Periodic phenomena, e.g. circadian rhythm, are the important functions of cells. In this paper, we consider a synthesis problem of gene networks possessing the desired persistent cyclic expression pattern sequences. We have proposed the synthesis method of gene networks possessing the desired expression pattern sequences. Desired cyclic expression pattern sequences can be realized by using the synthesis method. But the behavior may not be persistent. We derive a sufficient condition such that the desired cyclic expression pattern sequences are persistent and propose a synthesis method realizing the persistent desired behavior by network learning.

Effect of continuous light on diurnal rhythms in Cyanothece sp. ATCC 51142

BackgroundLife on earth is strongly affected by alternating day and night cycles. Accordingly, many organisms have evolved an internal timekeeping system with a period of approximately 24 hours. Cyanobacteria are the only known prokaryotes with robust rhythms under control of a central clock. Numerous studies have been conducted to elucidate components of the circadian clock and to identify circadian-controlled genes. However, the complex interactions between endogenous circadian rhythms and external cues are currently not well understood, and a direct and mathematical based comparison between light-mediated and circadian-controlled gene expression is still outstanding. Therefore, we combined and analyzed data from two independent microarray experiments, previously performed under alternating light-dark and continuous light conditions in Cyanothece sp. ATCC 51142, and sought to classify light responsive and circadian controlled genes.ResultsFourier Score-based methods together with random permutations and False Discovery Rates were used to identify genes with oscillatory expression patterns, and an angular distance based criterion was applied to recognize transient behaviors in gene expression under constant light conditions. Compared to previously reported mathematical approaches, the combination of these methods also facilitated the detection of modified amplitudes and phase-shifts of gene expression. Our analysis showed that the majority of diurnally regulated genes, essentially those genes that are maximally expressed during the middle of the light and dark period, are in fact light responsive. In contrast, most of the circadian controlled genes are up-regulated during the beginning of the dark or subjective dark, and are greatly enriched for genes associated with energy metabolism. Many of the circadian controlled and light responsive genes are found in gene clusters within the Cyanothece sp. ATCC 51142 genome. Interestingly, in addition to cyclic expression patterns with a period of 24 hours, we also found several genes that oscillate with an ultradian period of 12 hours, a novel finding among cyanobacteria.ConclusionWe demonstrate that a combination of different analytical methods significantly improved the identification of cyclic and transient gene expression in Cyanothece sp. ATCC 51142. Our analyses provide an adaptable and novel analytical tool to study gene expression in a variety of organisms with diurnal, circadian and ultradian behavior.

Interactions between the circadian clock and cold-response in Arabidopsis

Low temperature negatively affects plant growth and metabolism. Plant responses to cold involve massive transcriptional changes, and much effort has been made to identify these changes and their contribution to freezing tolerance. However, the influence of differences in environmental and developmental factors between experiments had not been investigated. We found that diurnal- and circadian-regulated genes are responsible for the majority of variation between experiments. Moreover, we demonstrated that the cyclic expression pattern of circadian clock components is affected by cold and that the cold induction of many transcription factors is dependent on the time of day. This means that genes identified so far as cold responsive are dependent on the time of day the experiment was performed and that paired diurnal controls are not sufficient to correct for this effect. Ongoing work to dissect the biological relevance of cold-diurnal regulatory interactions demonstrated that some circadian mutants have altered freezing tolerance but that time-of-day appears not to affect freezing tolerance.Addendum to: Bieniawska Z, Espinoza C, Schlereth A, Sulpice R, Hincha DK, Hannah MA. Disruption of the Arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcriptome. Plant Physiol 2008; 147:263-79.

The organic cation transporters (OCT1, OCT2, EMT) and the plasma membrane monoamine transporter (PMAT) show differential distribution and cyclic expression pattern in human endometrium and early pregnancy decidua

The non-neuronal monoamine transporters (OCT1, OCT2, EMT, and PMAT) play a key role in the clearance of monoamines from extracellular compartments. In a previous report we described endometrial distribution and cyclic variation of the vesicular monoamine transporter (VMAT2) mRNA and the neuronal norepinephrine transporter (NET) mRNA. In the present study we used in situ hybridization, real-time PCR and immunohistochemistry to reveal tissue distribution and cyclic variation of mRNA for the non-neuronal monoamine transporters in the human endometrium and early pregnancy decidua. We found that non-neuronal monoamine transporters are predominantly expressed in the stroma. The plasma membrane monoamine transporter (PMAT) mRNA expression peaked in the proliferative phase, whereas the extra-neuronal monoamine transporter (EMT) mRNA expression peaked in the secretory phase. The organic cation transporter 2 (OCT2) mRNA expression was exclusively detected in few scattered stromal cells and OCT1 mRNA was not detected at all. Our present results demonstrate that PMAT, EMT, and OCT2 transporters are expressed in the endometrial stroma and can potentially regulate reuptake of monoamines in general and histamine in particular. Taken together with our previous finding of VMAT2 mRNA in epithelial cells, we suggest a paracrine interaction between stromal and epithelial cells, which may modulate certain steps of the reproductive process.

Combined analysis reveals a core set of cycling genes

The simultaneous analysis of expression data from multiple species reveals a core set of conserved cycling genes that is much larger than previously thought.

Cytokine responses during chronic denervation

BackgroundThe aim of the present study was to examine inflammatory responses during Wallerian degeneration in rat peripheral nerve when the regrowth of axons was prevented by suturing.MethodsTransected rat sciatic nerve was sutured and ligated to prevent reinnervation. The samples were collected from the left sciatic nerve distally and proximally from the point of transection. The endoneurium was separated from the surrounding epi- and perineurium to examine the expression of cytokines in both of these compartments. Macrophage invasion into endoneurium was investigated and Schwann cell proliferation was followed as well as the expression of cytokines IL-1β, IL-10, IFN-γ and TNF-α mRNA. The samples were collected from 1 day up to 5 weeks after the primary operation.ResultsAt days 1 to 3 after injury in the epi-/perineurium of the proximal and distal stump, a marked expression of the pro-inflammatory cytokines TNF-α and IL-1β and of the anti-inflammatory cytokine IL-10 was observed. Concurrently, numerous macrophages started to gather into the epineurium of both proximal and distal stumps. At day 7 the number of macrophages decreased in the perineurium and increased markedly in the endoneurium of both stumps. At this time point marked expression of TNF-α and IFN-γ mRNA was observed in the endo- and epi-/perineurium of the proximal stump. At day 14 a marked increase in the expression of IL-1β could be noted in the proximal stump epi-/perineurium and in the distal stump endoneurium. At that time point many macrophages were observed in the longitudinally sectioned epineurium of the proximal 2 area as well as in the cross-section slides from the distal stump. At day 35 TNF-α, IL-1β and IL-10 mRNA appeared abundantly in the proximal epi-/perineurium together with macrophages.ConclusionThe present studies show that even during chronic denervation there is a cyclic expression pattern for the studied cytokines. Contrary to the previous findings on reinnervating nerves the studied cytokines show increased expression up to 35 days. The high expressions of pro-inflammatory and anti-inflammatory cytokines in the proximal epi-/perineurial area at day 35 may be involved in the formation of fibrosis due to irreversible nerve injury and thus may have relevance to the formation of traumatic neuroma.

Modelling the evolution of genetic regulatory networks

An evolutionary model of genetic regulatory networks is developed, based on a model of network encoding and dynamics called the Artificial Genome (AG). This model derives a number of specific genes and their interactions from a string of (initially random) bases in an idealized manner analogous to that employed by natural DNA. The gene expression dynamics are determined by updating the gene network as if it were a simple Boolean network. The generic behaviour of the AG model is investigated in detail. In particular, we explore the characteristic network topologies generated by the model, their dynamical behaviours, and the typical variance of network connectivities and network structures. These properties are demonstrated to agree with a probabilistic analysis of the model, and the typical network structures generated by the model are shown to lie between those of random networks and scale-free networks in terms of their degree distribution. Evolutionary processes are simulated using a genetic algorithm, with selection acting on a range of properties from gene number and degree of connectivity through periodic behaviour to specific patterns of gene expression. The evolvability of increasingly complex patterns of gene expression is examined in detail. When a degree of redundancy is introduced, the average number of generations required to evolve given targets is reduced, but limits on evolution of complex gene expression patterns remain. In addition, cyclic gene expression patterns with periods that are multiples of shorter expression patterns are shown to be inherently easier to evolve than others. Constraints imposed by the template-matching nature of the AG model generate similar biases towards such expression patterns in networks in initial populations, in addition to the somewhat scale-free nature of these networks. The significance of these results on current understanding of biological evolution is discussed.