Circadian biology: environmental regulation of a multi-oscillator network

The role of circadian genes in the pathogenesis of colorectal cancer

Colorectal cancer (CRC) is the third most frequent cancer in human beings and is also the major cause of death among the other gastrointestinal cancers. The exact mechanisms of CRC development in most patients remains unclear. So far, several genetically, environmental and epigenetically risk factors have been identified for CRC development. The circadian rhythm is a 24-h rhythm that drives several biologic processes. The circadian system is guided by a central pacemaker which is located in the suprachiasmatic nucleus (SCN) in the hypothalamus. Circadian rhythm is regulated by circadian clock genes, cytokines and hormones like melatonin. Disruptions in biological rhythms are known to be strongly associated with several diseases, including cancer. The role of the different circadian genes has been verified in various cancers, however, the pathways of different circadian genes in the pathogenesis of CRC are less investigated. Identification of the details of the pathways in CRC helps researchers to explore new therapies for the malignancy.

Identification of human circadian genes based on time course gene expression profiles by using a deep learning method

Circadian genes express periodically in an approximate 24-h period and the identification and study of these genes can provide deep understanding of the circadian control which plays significant roles in human health. Although many circadian gene identification algorithms have been developed, large numbers of false positives and low coverage are still major problems in this field. In this study we constructed a novel computational framework for circadian gene identification using deep neural networks (DNN) - a deep learning algorithm which can represent the raw form of data patterns without imposing assumptions on the expression distribution. Firstly, we transformed time-course gene expression data into categorical-state data to denote the changing trend of gene expression. Two distinct expression patterns emerged after clustering of the state data for circadian genes from our manually created learning dataset. DNN was then applied to discriminate the aperiodic genes and the two subtypes of periodic genes. In order to assess the performance of DNN, four commonly used machine learning methods including k-nearest neighbors, logistic regression, naïve Bayes, and support vector machines were used for comparison. The results show that the DNN model achieves the best balanced precision and recall. Next, we conducted large scale circadian gene detection using the trained DNN model for the remaining transcription profiles. Comparing with JTK_CYCLE and a study performed by Möller-Levet et al. (doi: https://doi.org/10.1073/pnas.1217154110), we identified 1132 novel periodic genes. Through the functional analysis of these novel circadian genes, we found that the GTPase superfamily exhibits distinct circadian expression patterns and may provide a molecular switch of circadian control of the functioning of the immune system in human blood. Our study provides novel insights into both the circadian gene identification field and the study of complex circadian-driven biological control. This article is part of a Special Issue entitled: Accelerating Precision Medicine through Genetic and Genomic Big Data Analysis edited by Yudong Cai & Tao Huang.

Mid-day siesta in natural populations of D. melanogaster from Africa exhibits an altitudinal cline and is regulated by splicing of a thermosensitive intron in the period clock gene

Background

Many diurnal animals exhibit a mid-day ‘siesta’, generally thought to be an adaptive response aimed at minimizing exposure to heat on warm days, suggesting that in regions with cooler climates mid-day siestas might be a less prominent feature of animal behavior. Drosophila melanogaster exhibits thermal plasticity in its mid-day siesta that is partly governed by the thermosensitive splicing of the 3’-terminal intron (termed dmpi8) from the key circadian clock gene period (per). For example, decreases in temperature lead to progressively more efficient splicing, which increasingly favors activity over sleep during the mid-day. In this study we sought to determine if the adaptation of D. melanogaster from its ancestral range in the lowlands of tropical Africa to the cooler temperatures found at high altitudes involved changes in mid-day sleep behavior and/or dmpi8 splicing efficiency.

Results

Using natural populations of Drosophila melanogaster from different altitudes in tropical Africa we show that flies from high elevations have a reduced mid-day siesta and less consolidated sleep. We identified a single nucleotide polymorphism (SNP) in the per 3’ untranslated region that has strong effects on dmpi8 splicing and mid-day sleep levels in both low and high altitude flies. Intriguingly, high altitude flies with a particular variant of this SNP exhibit increased dmpi8 splicing efficiency compared to their low altitude counterparts, consistent with reduced mid-day siesta. Thus, a boost in dmpi8 splicing efficiency appears to have played a prominent but not universal role in how African flies adapted to the cooler temperatures at high altitude.

Conclusions

Our findings point towards mid-day sleep behavior as a key evolutionary target in the thermal adaptation of animals, and provide a genetic framework for investigating daytime sleep in diurnal animals which appears to be driven by mechanisms distinct from those underlying nighttime sleep.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-0880-8) contains supplementary material, which is available to authorized users.

Sexual interactions influence the molecular oscillations in DN1 pacemaker neurons in Drosophila melanogaster

Circadian rhythms can synchronize to environmental time cues, such as light, temperature, humidity, and food availability. Previous studies have suggested that these rhythms can also be entrained by social interactions. Here, we used Drosophila melanogaster as a model to study the influence of socio-sexual interactions on the circadian clock in behavior and pacemaker neurons. If two flies of opposite sex were paired and kept in a small space, the daily activity patterns of the two flies were clearly different from the sum of the activity of single male and female flies. Compared with single flies, paired flies were more active in the night and morning, were more active during females’ active phase, and were less active during males’ active phase. These behavioral phenotypes are related to courtship behavior, but not to the circadian clock. Nevertheless, in male-female pairs of flies with clocks at different speeds (wild-type and per^S flies), clock protein cycling in the DN1 pacemaker neurons in the male brain were slightly influenced by their partners. These results suggest that sexual interactions between male-female couples can serve as a weak zeitgeber for the DN1 pacemaker neurons, but the effect is not sufficient to alter rhythms of behavioral activity.

A PDF/NPF neuropeptide signaling circuitry of male Drosophila melanogaster controls rival-induced prolonged mating

A primary function of males for many species involves mating with females for reproduction. Drosophila melanogaster males respond to the presence of other males by prolonging mating duration to increase the chance of passing on their genes. To understand the basis of such complex behaviors, we examine the genetic network and neural circuits that regulate rival-induced Longer-Mating-Duration (LMD). Here, we identify a small subset of clock neurons in the male brain that regulate LMD via neuropeptide signaling. LMD requires the function of pigment-dispersing factor (PDF) in four s-LNv neurons and its receptor PDFR in two LNd neurons per hemisphere, as well as the function of neuropeptide F (NPF) in two neurons within the sexually dimorphic LNd region and its receptor NPFR1 in four s-LNv neurons per hemisphere. Moreover, rival exposure modifies the neuronal activities of a subset of clock neurons involved in neuropeptide signaling for LMD.

Differences in timing of mating swarms in sympatric populations of Anopheles coluzzii and Anopheles gambiae s.s. (formerly An. gambiae M and S molecular forms) in Burkina Faso, West Africa

Background

The M and S molecular forms of Anopheles gambiae s.s. Giles appear to have speciated in West Africa and the M form is now formally named An. coluzzii Coetzee & Wilkerson sp.n. and the S form retains the nominotypical name (abbreviated here to An. gambiae). Reproductive isolation is thought to be the main barrier to hybridisation; even though both species are found in the same mating swarms, hybrid fertilisations in copulae have not been found in the study area. The aim of the study, therefore, was to determine whether differences in circadian and/or environmental control over the timing of swarming in the two species contribute to reproductive isolation.

Methods

The timing of male swarming in these species was recorded four nights per month over four years at five swarming sites in each of two villages. The timing of the start and end of swarming, and the concurrent environmental parameters, temperature, humidity and light intensity, were recorded for n = 20 swarms/month/species. The timing of 'spontaneous’ activity at dusk of individual An. coluzzii and An. gambiae males was video-recorded in an actograph outdoors for 21 nights.

Results

Of the environmental parameters considered, swarming was most strongly correlated with sunset (r² > 0.946). Anopheles gambiae started and stopped swarming earlier than An. coluzzii (3:35 ± 0:68 min:sec and 4:51 ± 1:21, respectively), and the mean duration of swarming was 23:37 ± 0:33 for An. gambiae and 21:39 ± 0:33 for An. coluzzii. Accordingly, in principle, whenever both species swarm over the same marker, a mean of 15.3 ± 3.1% of An. gambiae swarming would occur before An. coluzzii males arrived, and 19.5 ± 4.55% of An. coluzzii swarming would occurred after An. gambiae males had stopped swarming. These results are consistent with the finding that An. gambiae males became active in the actograph 09:35 ± 00:22 min:sec earlier than An. coluzzii males.

Conclusions

The timing of swarming and spontaneous activity at dusk are primarily under circadian control, with the phase linked closely to sunset throughout the year. The mating activity of these two species is temporally segregated for 15-20% of the swarming period, which may contribute to the observed reproductive isolation of these species in local sympatric populations.

Contribution of visual and circadian neural circuits to memory for prolonged mating induced by rivals

Rival exposure causes Drosophila melanogaster males to prolong mating. Longer-Mating-Duration (LMD) may enhance reproductive success, but its underlying mechanism is currently unknown. Here we report that LMD is context-dependent and can be induced solely via visual stimuli. We further show that LMD involves neural circuits important for visual memory, including central neurons in the ellipsoid body but not the mushroom bodies or the fan-shaped bodies, and may rely on the rival exposure memory lasting several hours. LMD is affected by a subset of learning and memory mutants. LMD depends on the circadian clock genes timeless and period but not Clock or cycle, and persists in many arrhythmic conditions. Moreover, LMD critically depends on a subset of pigment dispersing factor (PDF) neurons rather than the entire circadian neural circuit. Our study thus delineates parts of the molecular and cellular basis for LMD – a plastic social behavior elicited by visual cues.

Molecular genetic analysis of circadian timekeeping in Drosophila

A genetic screen for mutants that alter circadian rhythms in Drosophila identified the first clock gene-the period (per) gene. The per gene is a central player within a transcriptional feedback loop that represents the core mechanism for keeping circadian time in Drosophila and other animals. The per feedback loop, or core loop, is interlocked with the Clock (Clk) feedback loop, but whether the Clk feedback loop contributes to circadian timekeeping is not known. A series of distinct molecular events are thought to control transcriptional feedback in the core loop. The time it takes to complete these events should take much less than 24h, thus delays must be imposed at different steps within the core loop. As new clock genes are identified, the molecular mechanisms responsible for these delays have been revealed in ever-increasing detail and provide an in-depth accounting of how transcriptional feedback loops keep circadian time. The phase of these feedback loops shifts to maintain synchrony with environmental cycles, the most reliable of which is light. Although a great deal is known about cell-autonomous mechanisms of light-induced phase shifting by CRYPTOCHROME (CRY), much less is known about non-cell autonomous mechanisms. CRY mediates phase shifts through an uncharacterized mechanism in certain brain oscillator neurons and carries out a dual role as a photoreceptor and transcription factor in other tissues. Here, I review how transcriptional feedback loops function to keep time in Drosophila, how they impose delays to maintain a 24-h cycle, and how they maintain synchrony with environmental light:dark cycles. The transcriptional feedback loops that keep time in Drosophila are well conserved in other animals, thus what we learn about these loops in Drosophila should continue to provide insight into the operation of analogous transcriptional feedback loops in other animals.