A Luciferase-Based Assay to Test Whether Gene Expression Responses to Environmental Inputs Are Temporally Restricted by the Circadian Clock

2016 ◽  
pp. 93-106
Author(s):  
Amaury de Montaigu ◽  
Markus Christian Berns ◽  
George Coupland
Keyword(s):  
Gene Expression ◽  
Circadian Clock

scholarly journals Transcriptomal dissection of soybean circadian rhythmicity in two geographically, phenotypically and genetically distinct cultivars

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yanlei Yue ◽  
Ze Jiang ◽  
Enoch Sapey ◽  
Tingting Wu ◽  
Shi Sun ◽  
...  
Keyword(s):  
Gene Expression ◽  
Circadian Clock ◽  
Chromosome Structure ◽  
Clock Genes ◽  
Expression Profiles ◽  
Circadian Rhythmicity ◽  
Rna Seq ◽  
Night Time ◽  
Time Points ◽  
Circadian Clock Genes

Abstract Background In soybean, some circadian clock genes have been identified as loci for maturity traits. However, the effects of these genes on soybean circadian rhythmicity and their impacts on maturity are unclear. Results We used two geographically, phenotypically and genetically distinct cultivars, conventional juvenile Zhonghuang 24 (with functional J/GmELF3a, a homolog of the circadian clock indispensable component EARLY FLOWERING 3) and long juvenile Huaxia 3 (with dysfunctional j/Gmelf3a) to dissect the soybean circadian clock with time-series transcriptomal RNA-Seq analysis of unifoliate leaves on a day scale. The results showed that several known circadian clock components, including RVE1, GI, LUX and TOC1, phase differently in soybean than in Arabidopsis, demonstrating that the soybean circadian clock is obviously different from the canonical model in Arabidopsis. In contrast to the observation that ELF3 dysfunction results in clock arrhythmia in Arabidopsis, the circadian clock is conserved in soybean regardless of the functional status of J/GmELF3a. Soybean exhibits a circadian rhythmicity in both gene expression and alternative splicing. Genes can be grouped into six clusters, C1-C6, with different expression profiles. Many more genes are grouped into the night clusters (C4-C6) than in the day cluster (C2), showing that night is essential for gene expression and regulation. Moreover, soybean chromosomes are activated with a circadian rhythmicity, indicating that high-order chromosome structure might impact circadian rhythmicity. Interestingly, night time points were clustered in one group, while day time points were separated into two groups, morning and afternoon, demonstrating that morning and afternoon are representative of different environments for soybean growth and development. However, no genes were consistently differentially expressed over different time-points, indicating that it is necessary to perform a circadian rhythmicity analysis to more thoroughly dissect the function of a gene. Moreover, the analysis of the circadian rhythmicity of the GmFT family showed that GmELF3a might phase- and amplitude-modulate the GmFT family to regulate the juvenility and maturity traits of soybean. Conclusions These results and the resultant RNA-seq data should be helpful in understanding the soybean circadian clock and elucidating the connection between the circadian clock and soybean maturity.

scholarly journals Influence of the period-dependent circadian clock on diurnal, circadian, and aperiodic gene expression in Drosophila melanogaster

2002 ◽  
Vol 99 (14) ◽  
pp. 9562-9567 ◽  
Author(s):  
Y. Lin ◽  
M. Han ◽  
B. Shimada ◽  
L. Wang ◽  
T. M. Gibler ◽  
...  
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Circadian Clock

scholarly journals Circadian Clock Gene Expression in the Coral Favia fragum over Diel and Lunar Reproductive Cycles

PLoS ONE ◽  
2011 ◽  
Vol 6 (5) ◽  
pp. e19755 ◽  
Author(s):  
Kenneth D. Hoadley ◽  
Alina M. Szmant ◽  
Sonja J. Pyott
Keyword(s):  
Gene Expression ◽  
Circadian Clock ◽  
Clock Gene ◽  
Circadian Clock Gene ◽  
Clock Gene Expression ◽  
Favia Fragum ◽  
Reproductive Cycles

scholarly journals Correction to: Low-Grade Inflammation Aggravates Rotenone Neurotoxicity and Disrupts Circadian Clock Gene Expression in Rats

2018 ◽  
Vol 35 (4) ◽  
pp. 999-1000 ◽  
Author(s):  
Huan Li ◽  
Sheng Song ◽  
Yuan Wang ◽  
Chun Huang ◽  
Feng Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Circadian Clock ◽  
Clock Gene ◽  
Low Grade ◽  
Circadian Clock Gene ◽  
Clock Gene Expression ◽  
Low Grade Inflammation

scholarly journals Peripheral Sensory Organs Contribute to Temperature Synchronization of the Circadian Clock in Drosophila melanogaster

2021 ◽  
Vol 12 ◽  
Author(s):  
Rebekah George ◽  
Ralf Stanewsky
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Circadian Clock ◽  
Temperature Fluctuations ◽  
Fruit Fly ◽  
Circadian Clocks ◽  
Sensory Cells ◽  
Clock Gene Expression ◽  
External Time ◽  
Peripheral Sensory

Circadian clocks are cell-autonomous endogenous oscillators, generated and maintained by self-sustained 24-h rhythms of clock gene expression. In the fruit fly Drosophila melanogaster, these daily rhythms of gene expression regulate the activity of approximately 150 clock neurons in the fly brain, which are responsible for driving the daily rest/activity cycles of these insects. Despite their endogenous character, circadian clocks communicate with the environment in order to synchronize their self-sustained molecular oscillations and neuronal activity rhythms (internal time) with the daily changes of light and temperature dictated by the Earth’s rotation around its axis (external time). Light and temperature changes are reliable time cues (Zeitgeber) used by many organisms to synchronize their circadian clock to the external time. In Drosophila, both light and temperature fluctuations robustly synchronize the circadian clock in the absence of the other Zeitgeber. The complex mechanisms for synchronization to the daily light–dark cycles are understood with impressive detail. In contrast, our knowledge about how the daily temperature fluctuations synchronize the fly clock is rather limited. Whereas light synchronization relies on peripheral and clock-cell autonomous photoreceptors, temperature input to the clock appears to rely mainly on sensory cells located in the peripheral nervous system of the fly. Recent studies suggest that sensory structures located in body and head appendages are able to detect temperature fluctuations and to signal this information to the brain clock. This review will summarize these studies and their implications about the mechanisms underlying temperature synchronization.

scholarly journals Daily rhythms in gene expression of the human parasite Schistosoma mansoni

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Kate A. Rawlinson ◽  
Adam J. Reid ◽  
Zhigang Lu ◽  
Patrick Driguez ◽  
Anna Wawer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Schistosoma Mansoni ◽  
Circadian Clock ◽  
Drug Targets ◽  
Clock Genes ◽  
Biological Rhythms ◽  
Active Phase ◽  
Egg Laying ◽  
Daily Rhythms ◽  
Metazoan Parasites

Abstract Background The consequences of the earth’s daily rotation have led to 24-h biological rhythms in most organisms. Even some parasites are known to have daily rhythms, which, when in synchrony with host rhythms, can optimise their fitness. Understanding these rhythms may enable the development of control strategies that take advantage of rhythmic vulnerabilities. Recent work on protozoan parasites has revealed 24-h rhythms in gene expression, drug sensitivity and the presence of an intrinsic circadian clock; however, similar studies on metazoan parasites are lacking. To address this, we investigated if a metazoan parasite has daily molecular oscillations, whether they reveal how these longer-lived organisms can survive host daily cycles over a lifespan of many years and if animal circadian clock genes are present and rhythmic. We addressed these questions using the human blood fluke Schistosoma mansoni that lives in the vasculature for decades and causes the tropical disease schistosomiasis. Results Using round-the-clock transcriptomics of male and female adult worms collected from experimentally infected mice, we discovered that ~ 2% of its genes followed a daily pattern of expression. Rhythmic processes included a stress response during the host’s active phase and a ‘peak in metabolic activity’ during the host’s resting phase. Transcriptional profiles in the female reproductive system were mirrored by daily patterns in egg laying (eggs are the main drivers of the host pathology). Genes cycling with the highest amplitudes include predicted drug targets and a vaccine candidate. These 24-h rhythms may be driven by host rhythms and/or generated by a circadian clock; however, orthologs of core clock genes are missing and secondary clock genes show no 24-h rhythmicity. Conclusions There are daily rhythms in the transcriptomes of adult S. mansoni, but they appear less pronounced than in other organisms. The rhythms reveal temporally compartmentalised internal processes and host interactions relevant to within-host survival and between-host transmission. Our findings suggest that if these daily rhythms are generated by an intrinsic circadian clock then the oscillatory mechanism must be distinct from that in other animals. We have shown which transcripts oscillate at this temporal scale and this will benefit the development and delivery of treatments against schistosomiasis.

scholarly journals Artificial light at night shifts the circadian system but still leads to physiological disruption in a wild bird

2020 ◽  
Author(s):  
Davide M. Dominoni ◽  
Maaike de Jong ◽  
Kees van Oers ◽  
Peter O’Shaughnessy ◽  
Gavin Blackburn ◽  
...  
Keyword(s):  
Gene Expression ◽  
Circadian Clock ◽  
Candidate Genes ◽  
Clock Gene ◽  
Circadian Disruption ◽  
Artificial Light ◽  
Wild Animals ◽  
Light At Night ◽  
Internal Desynchronization ◽  
Physiological Pathways

AbstractGlobally increasing levels of artificial light at night (ALAN) have been associated with shifts in behavioral rhythms of many wild organisms. It is however unknown to what extent this change in behavior is due to shifts in the circadian clock, and, importantly, whether the physiological pathways orchestrated by the circadian clock are desynchronized by ALAN. Such circadian disruption could have severe consequences for wildlife health, as shown for humans. Here, we analyze the effects of experimental ALAN on rhythmic behavior, gene expression and metabolomic profiles in a wild songbird, the great tit (Parus major). We exposed 34 captive males to three ALAN intensities or to dark nights and recorded their activity rhythms. After three weeks, we collected mid-day and midnight samples of hypothalamus, hippocampus, liver, spleen and plasma. ALAN advanced wake-up time, and this shift was paralleled by an advance in hypothalamic expression of the clock gene BMAL1, which is key to integrating physiological pathways. BMAL1 advances were remarkably consistent across tissues, suggesting close links of brain and peripheral clock gene expression with activity rhythms. However, only a minority of other candidate genes (4 out of 12) paralleled the shifted BMAL1 expression. Moreover, metabolomic profiling showed that only 9.7% of the 755 analyzed metabolites followed the circadian shift. Thus, despite the shifted timing of key clock functions under ALAN, birds suffered internal desynchronization. We thus suggest circadian disruption to be a key link between ALAN and health impacts, in birds and humans alike.Significance StatementShifts in daily activity are a common consequence of artificial light at night (ALAN). In humans, shifted activity cycles often become desynchronized from internal physiological rhythms, with serious health implications. To what extent a similar desynchronization occurs in wild animals experiencing ALAN is currently unknown. We exposed captive great tits to increasing levels of LAN, and found that activity patterns and a core clock gene, BMAL1, shifted in concert. However, only a minority of additional candidate genes and less than 10% of the metabolites followed this circadian shift, suggesting internal desynchronization of physiological rhythms. Our study emphasizes the massive potential for ALAN to impact the health of wild animals through circadian disruption.

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