Identification and temporal expression of putative circadian clock transcripts in the amphipod crustaceanTalitrus saltator

BackgroundTalitrus saltatoris an amphipod crustacean that inhabits the supralittoral zone on sandy beaches in the Northeast Atlantic and Mediterranean.T. saltatorexhibits endogenous locomotor activity rhythms and time-compensated sun and moon orientation, both of which necessitate at least one chronometric mechanism. Whilst their behaviour is well studied, currently there are no descriptions of the underlying molecular components of a biological clock in this animal, and very few in other crustacean species.MethodsWe harvested brain tissue from animals expressing robust circadian activity rhythms and used homology cloning and Illumina RNAseq approaches to sequence and identify the core circadian clock and clock-related genes in these samples. We assessed the temporal expression of these genes in time-course samples from rhythmic animals using RNAseq.ResultsWe identified a comprehensive suite of circadian clock gene homologues inT. saltatorincluding the ‘core’ clock genesperiod(Talper),cryptochrome 2(Talcry2),timeless(Taltim),clock(Talclk), andbmal1(Talbmal1). In addition we describe the sequence and putative structures of 23 clock-associated genes including two unusual, extended isoforms of pigment dispersing hormone (Talpdh). We examined time-course RNAseq expression data, derived from tissues harvested from behaviourally rhythmic animals, to reveal rhythmic expression of these genes with approximately circadian period inTalperandTalbmal1. Of the clock-related genes,casein kinase IIβ(TalckIIβ),ebony(Talebony),jetlag(Taljetlag),pigment dispensing hormone(Talpdh),protein phosphatase 1(Talpp1),shaggy(Talshaggy),sirt1(Talsirt1), sirt7 (Talsirt7) and supernumerary limbs (Talslimb) show temporal changes in expression.DiscussionWe report the sequences of principle genes that comprise the circadian clock ofT. saltatorand highlight the conserved structural and functional domains of their deduced cognate proteins. Our sequencing data contribute to the growing inventory of described comparative clocks. Expression profiling of the identified clock genes illuminates tantalising targets for experimental manipulation to elucidate the molecular and cellular control of clock-driven phenotypes in this crustacean.

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Achilles-Mediated and Sex-Specific Regulation of Circadian mRNA Rhythms in Drosophila

Journal of Biological Rhythms ◽

10.1177/0748730419830845 ◽

2019 ◽

Vol 34 (2) ◽

pp. 131-143 ◽

Cited By ~ 3

Author(s):

Jiajia Li ◽

Renee Yin Yu ◽

Farida Emran ◽

Brian E. Chen ◽

Michael E. Hughes

Keyword(s):

Circadian Clock ◽

Molecular Mechanisms ◽

Rna Binding ◽

Clock Genes ◽

Peripheral Tissues ◽

Knock Down ◽

Rhythmic Expression ◽

The Core ◽

Physiological Processes ◽

Specific Regulation

The circadian clock is an evolutionarily conserved mechanism that generates the rhythmic expression of downstream genes. The core circadian clock drives the expression of clock-controlled genes, which in turn play critical roles in carrying out many rhythmic physiological processes. Nevertheless, the molecular mechanisms by which clock output genes orchestrate rhythmic signals from the brain to peripheral tissues are largely unknown. Here we explored the role of one rhythmic gene, Achilles, in regulating the rhythmic transcriptome in the fly head. Achilles is a clock-controlled gene in Drosophila that encodes a putative RNA-binding protein. Achilles expression is found in neurons throughout the fly brain using fluorescence in situ hybridization (FISH), and legacy data suggest it is not expressed in core clock neurons. Together, these observations argue against a role for Achilles in regulating the core clock. To assess its impact on circadian mRNA rhythms, we performed RNA sequencing (RNAseq) to compare the rhythmic transcriptomes of control flies and those with diminished Achilles expression in all neurons. Consistent with previous studies, we observe dramatic upregulation of immune response genes upon knock-down of Achilles. Furthermore, many circadian mRNAs lose their rhythmicity in Achilles knock-down flies, suggesting that a subset of the rhythmic transcriptome is regulated either directly or indirectly by Achilles. These Achilles-mediated rhythms are observed in genes involved in immune function and in neuronal signaling, including Prosap, Nemy and Jhl-21. A comparison of RNAseq data from control flies reveals that only 42.7% of clock-controlled genes in the fly brain are rhythmic in both males and females. As mRNA rhythms of core clock genes are largely invariant between the sexes, this observation suggests that sex-specific mechanisms are an important, and heretofore under-appreciated, regulator of the rhythmic transcriptome.

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The Plant Circadian Clock and Chromatin Modifications

Genes ◽

10.3390/genes9110561 ◽

2018 ◽

Vol 9 (11) ◽

pp. 561 ◽

Cited By ~ 6

Author(s):

Ping Yang ◽

Jianhao Wang ◽

Fu-Yu Huang ◽

Songguang Yang ◽

Keqiang Wu

Keyword(s):

Circadian Clock ◽

Clock Genes ◽

Feedback Regulation ◽

Chromatin Modifications ◽

Environmental Signals ◽

The Core ◽

Physiological Processes ◽

Circadian Clock Genes ◽

Rhythmic Gene ◽

Transcriptional Feedback

The circadian clock is an endogenous timekeeping network that integrates environmental signals with internal cues to coordinate diverse physiological processes. The circadian function depends on the precise regulation of rhythmic gene expression at the core of the oscillators. In addition to the well-characterized transcriptional feedback regulation of several clock components, additional regulatory mechanisms, such as alternative splicing, regulation of protein stability, and chromatin modifications are beginning to emerge. In this review, we discuss recent findings in the regulation of the circadian clock function in Arabidopsis thaliana. The involvement of chromatin modifications in the regulation of the core circadian clock genes is also discussed.

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Genetic redundancy strengthens the circadian clock leading to a narrow entrainment range

Journal of The Royal Society Interface ◽

10.1098/rsif.2013.0221 ◽

2013 ◽

Vol 10 (84) ◽

pp. 20130221 ◽

Cited By ~ 33

Author(s):

A. Erzberger ◽

G. Hampp ◽

A. E. Granada ◽

U. Albrecht ◽

H. Herzel

Keyword(s):

Circadian Clock ◽

Clock Genes ◽

Genetic Network ◽

Circadian Clocks ◽

Mutant Mice ◽

Nonlinear Phenomena ◽

Genetic Redundancy ◽

Activity Rhythms ◽

Almost All ◽

External Signals

Circadian clocks are internal timekeepers present in almost all organisms. Driven by a genetic network of highly conserved structure, they generate self-sustained oscillations that entrain to periodic external signals such as the 24 h light–dark cycle. Vertebrates possess multiple, functionally overlapping homologues of the core clock genes. Furthermore, vertebrate clocks entrain to a range of periods three times as narrow as that of other organisms. We asked whether genetic redundancies play a role in governing entrainment properties and analysed locomotor activity rhythms of genetically modified mice lacking one set of clock homologues. Exposing them to non-24 h light–dark cycles, we found that the mutant mice have a wider entrainment range than the wild types. Spectral analysis furthermore revealed nonlinear phenomena of periodically forced self-sustained oscillators for which the entrainment range relates inversely to oscillator amplitude. Using the forced oscillator model to explain the observed differences in entrainment range between mutant and wild-type mice, we sought to quantify the overall oscillator amplitude of their clocks from the activity rhythms and found that mutant mice have weaker circadian clocks than wild types. Our results suggest that genetic redundancy strengthens the circadian clock leading to a narrow entrainment range in vertebrates.

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Nyctinastic thallus movement in the liverwort Marchantia polymorpha is regulated by a circadian clock

10.1101/2020.02.09.940403 ◽

2020 ◽

Author(s):

Ulf Lagercrantz ◽

Anja Billhardt ◽

Sabine N. Rousku ◽

D. Magnus Eklund

Keyword(s):

Circadian Clock ◽

Feedback Loop ◽

Clock Genes ◽

Marchantia Polymorpha ◽

Leaf Position ◽

Rhythmic Movements ◽

The Core ◽

Growth Development ◽

Rhythmic Growth ◽

Transcriptional Feedback

ABSTRACTThe circadian clock coordinates an organism’s growth, development and physiology with environmental factors. One illuminating example is the rhythmic growth of hypocotyls and cotyledons in Arabidopsis thaliana. Such daily oscillations in leaf position are often referred to as sleep movements or nyctinasty. Here, we report that plantlets of the liverwort Marchantia polymorpha show analogous rhythmic movements of thallus lobes, and that the circadian clock controls this rhythm, with auxin a likely meditator. The mechanisms of this circadian clock are partly conserved as compared to angiosperms, with homologs to the core clock genes PRR, RVE and TOC1 forming a core transcriptional feedback loop also in M. polymorpha.

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GUN4 Affects the Circadian Clock and Seedlings Adaptation to Changing Light Conditions

International Journal of Molecular Sciences ◽

10.3390/ijms23010194 ◽

2021 ◽

Vol 23 (1) ◽

pp. 194

Author(s):

Tao Li ◽

Rui Wu ◽

Zhixin Liu ◽

Jiajing Wang ◽

Chenxi Guo ◽

...

Keyword(s):

Circadian Clock ◽

Clock Genes ◽

Response Regulator ◽

Signal Recognition Particle ◽

Biological Clock ◽

Chlorophyll Synthesis ◽

Light Conditions ◽

Strong Light ◽

Expression Of Genes ◽

Changing Light

The chloroplast is a key organelle for photosynthesis and perceiving environmental information. GENOME UNCOUPLED 4 (GUN4) has been shown to be required for the regulation of both chlorophyll synthesis, reactive oxygen species (ROS) homeostasis and plastid retrograde signaling. In this study, we found that growth of the gun4 mutant was significantly improved under medium strong light (200 μmol photons m−2s−1) compared to normal light (100 μmol photons m−2s−1), in marked contrast to wild-type (WT). Further analysis revealed that GUN4 interacts with SIGNAL RECOGNITION PARTICLE 54 KDA SUBUNIT (SRP43) and SRP54. RNA-seq analysis indicated that the expression of genes for light signaling and the circadian clock is altered in gun4 compared with (WT). qPCR analysis confirmed that the expression of the clock genes CLOCK-RELATED 1 (CCA1), LATE ELONGATION HYPOCOTYL (LHY), TIMING OF CAB EXPRESSION 1 (TOC1) and PSEUDO RESPONSE REGULATOR 7 (PRR7) is significantly changed in the gun4 and srp54 mutants under normal and medium strong light conditions. These results suggest that GUN4 may coordinate the adaptation of plants to changing light conditions by regulating the biological clock, although it is not clear whether the effect is direct or indirect.

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Prognostic values of the core components of the mammalian circadian clock in prostate cancer

PeerJ ◽

10.7717/peerj.12539 ◽

2021 ◽

Vol 9 ◽

pp. e12539

Author(s):

Wenchang Yue ◽

Xiao Du ◽

Xuhong Wang ◽

Niu Gui ◽

Weijie Zhang ◽

...

Keyword(s):

Circadian Clock ◽

Risk Score ◽

Clock Genes ◽

Predictive Performance ◽

Lymph Node Status ◽

Free Survival ◽

The Core ◽

Circadian Clock Genes ◽

Core Components ◽

Score Model

Background Prostate cancer (PC) is one of the most common malignancies in males. Extensive and complex connections between circadian rhythm and cancer were found. Nonetheless, in PC, the potential role of the core components of the mammalian circadian clock (CCMCCs) in prognosis prediction has not been fully clarified. Methods We firstly collected 605 patients with PC from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. Survival analysis was carried out for each CCMCC. Then, we investigated the prognostic ability of CCMCCs by Cox regression analysis. Independent prognostic signatures were extracted for the establishment of the circadian clock-based risk score model. We explored the predictive performance of the risk score model in the TCGA training cohort and the independent GEO dataset. Finally, the relationships between risk score and clinicopathological parameters, biological processes, and signaling pathways were evaluated. Results The expression levels of CCMCCs were widely correlated with age, tumor status, lymph node status, disease-free survival (DFS), progression-free survival (PFS), and overall survival (OS). Nine circadian clock genes, including CSNK1D, BTRC, CLOCK, CSNK1E, FBXL3, PRKAA2, DBP, NR1D2, and RORB, were identified as vital prognostic factors in PC and were used to construct the circadian clock-based risk score model. For DFS, the area under the 3-year or 5-year receiver operating characteristic curves ranged from 0.728 to 0.821, suggesting better predictive performance. When compared with T3-4N1 stage, PC patients at T2N0 stage might be benefited more from the circadian clock-based risk score model. Furthermore, a high circadian clock-based risk score indicated shorter DFS (p < 0.0001), early progression (p < 0.0001), and higher 5-year death rate (p = 0.007) in PC. The risk score was related to tumor status (p < 0.001), lymph node status (p < 0.001), and ribosome-related biogenesis and pathways. Conclusions The vital roles of circadian clock genes in clinical outcomes were fully depicted. The circadian clock-based risk score model could reflect and predict the prognosis of patients with PC.

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Changing planetary rotation rescues the biological clock mutantlhy cca1ofArabidopsis thaliana

10.1101/034629 ◽

2015 ◽

Author(s):

Andrew J. Millar ◽

Jamie T. Carrington ◽

Wei Ven Tee ◽

Sarah K. Hodge

Keyword(s):

Gene Expression ◽

Circadian Clock ◽

Double Mutant ◽

Clock Genes ◽

Biological Clock ◽

Laboratory Model ◽

Wild Type ◽

Planetary Rotation ◽

Short Period ◽

Clock Mechanism

Background: Pervasive, 24-hour rhythms from the biological clock affect diverse biological processes in metabolism and behaviour, including the human cell division cycle and sleep-wake cycle, nightly transpiration and energy balance in plants, and seasonal breeding in both plants and animals. The clock mechanism in the laboratory model plant species Arabidopsis thaliana is complex, in part due to the multiple interlocking, negative feedback loops that link the clock genes. Clock gene mutants are powerful tools to manipulate and understand the clock mechanism and its effects on physiology. The LATE ELONGATED HYPOCOTYL and CIRCADIAN CLOCK ASSOCIATED 1 genes encode dawn-expressed, Myb-related repressor proteins that delay the expression of other clock genes until late in the day. Double mutant plants (lhy cca1) have low-amplitude, short-period rhythms that have been used in multiple studies of the plant circadian clock. Results: We used in vivo imaging of several luciferase (LUC) reporter genes to test how the rhythmic gene expression of wild-type and lhy cca1 mutant plants responded to light:dark cycles. Red, blue and red+blue light were similarly able to entrain these gene expression rhythms. The timing of expression rhythms in double mutant plants showed little or no response to the duration of light under 24h light:dark cycles (dusk sensitivity), in contrast to the wild type. As the period of the mutant clock is about 18h, we tested light:dark cycles of different duration (T cycles), simulating altered rotation of planet Earth. lhy cca1 double mutants regained as much dusk sensitivity in 20h T cycles as the wild type in 24h cycles, though the phase of the rhythm in the mutants was much earlier than wild type. The severe, triple lhy cca1 gi mutants also regained dusk sensitivity in 20h cycles. The double mutant showed some dusk sensitivity under 28h cycles. lhy cca1 double mutants under 28h cycles with short photoperiods, however, had the same apparent phase as wild-type plants. Conclusion: Simulating altered planetary rotation with light:dark cycles can reveal normal circadian performance in clock mutants that have been described as arrhythmic under standard conditions. The features rescued here comprise a dynamic behaviour (apparent phase under 28h cycles) and a dynamic property (dusk sensitivity under 20h cycles). These conditional clock phenotypes indicate that parts of the clock mechanism continue to function independently of LHY and CCA1, despite the major role of these genes in wild-type plants under standard conditions. Accessibility: Most results here will be published only in this format, citable by the DOI. Data and analysis are publicly accessible on the BioDare resource (www.biodare.ed.ac.uk), as detailed in the links below. Transgenic lines are linked to Stock Centre IDs below (Table 7).

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Cyclic uniaxial mechanical load enhances chondrogenesis through entraining the molecular circadian clock

10.1101/2021.10.26.465847 ◽

2021 ◽

Author(s):

Judit Vago ◽

Eva Katona ◽

Roland A. Takacs ◽

Roza Zakany ◽

Daan Van Der Veen ◽

...

Keyword(s):

Circadian Clock ◽

Clock Genes ◽

Mechanical Load ◽

Marker Gene ◽

Cartilage Matrix ◽

Limb Bud ◽

Mechanical Stimuli ◽

Rhythmic Expression ◽

The Core ◽

Chondroprogenitor Cells

Objective: The biomechanical environment plays a key role in regulating cartilage formation, but current understanding of mechanotransduction pathways in chondrogenic cells is still incomplete. Amongst the combination of external factors that control chondrogenesis are temporal cues that are governed by the cell-autonomous circadian clock. However, mechanical stimulation has not yet directly been proven to modulate chondrogenesis via entraining the circadian clock in chondroprogenitor cells. Design: The purpose of this study was to establish whether mechanical stimuli entrain the core clock in chondrogenic cells, and whether augmented chondrogenesis caused by mechanical loading was at least partially mediated by the synchronised, rhythmic expression of the core circadian clock genes, chondrogenic transcription factors, and cartilage matrix constituents. Results: We report here, for the first time, that cyclic uniaxial mechanical load applied for 1 hour for a period of 6 days entrains the molecular clockwork in chondroprogenitor cells during chondrogenesis in limb bud-derived micromass cultures. In addition to the several core clock genes, the chondrogenic markers SOX9, ACAN, and COL2A1 also followed a robust sinusoidal rhythmic expression pattern. These rhythmic conditions significantly enhanced cartilage matrix production and upregulated marker gene expression. The observed chondrogenesis-promoting effect of the mechanical environment was at least partially attributable to its entraining effect on the molecular clockwork, as co-application of the small molecule clock modulator longdaysin attenuated the stimulatory effects of mechanical load. Conclusions: Results from this study suggest that an optimal biomechanical environment enhances tissue homeostasis and histogenesis during early chondrogenesis through entraining the molecular clockwork.

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The Core-Clock Gene NR1D1 Impacts Cell Motility In Vitro and Invasiveness in a Zebrafish Xenograft Colon Cancer Model

Cancers ◽

10.3390/cancers12040853 ◽

2020 ◽

Vol 12 (4) ◽

pp. 853 ◽

Cited By ~ 2

Author(s):

Alireza Basti ◽

Rita Fior ◽

Müge Yalҫin ◽

Vanda Póvoa ◽

Rosario Astaburuaga ◽

...

Keyword(s):

Cell Migration ◽

Circadian Clock ◽

Cell Motility ◽

Clock Genes ◽

Xenograft Model ◽

Migration And Invasion ◽

Altered Expression ◽

The Core

Malfunctions of circadian clock trigger abnormal cellular processes and influence tumorigenesis. Using an in vitro and in vivo xenograft model, we show that circadian clock disruption via the downregulation of the core-clock genes BMAL1, PER2, and NR1D1 impacts the circadian phenotype of MYC, WEE1, and TP53, and affects proliferation, apoptosis, and cell migration. In particular, both our in vitro and in vivo results suggest an impairment of cell motility and a reduction in micrometastasis formation upon knockdown of NR1D1, accompanied by altered expression levels of SNAI1 and CD44. Interestingly we show that differential proliferation and reduced tumour growth in vivo may be due to the additional influence of the host-clock and/or to the 3D tumour architecture. Our results raise new questions concerning host–tumour interaction and show that core-clock genes are involved in key cancer properties, including the regulation of cell migration and invasion by NR1D1 in zebrafish xenografts.

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Identification of the suprachiasmatic nucleus in birds

AJP Regulatory Integrative and Comparative Physiology ◽

10.1152/ajpregu.2001.280.4.r1185 ◽

2001 ◽

Vol 280 (4) ◽

pp. R1185-R1189 ◽

Cited By ~ 43

Author(s):

Takashi Yoshimura ◽

Shinobu Yasuo ◽

Yoshikazu Suzuki ◽

Eri Makino ◽

Yuki Yokota ◽

...

Keyword(s):

Locomotor Activity ◽

Circadian Rhythms ◽

Circadian Clock ◽

Suprachiasmatic Nucleus ◽

Japanese Quail ◽

Clock Genes ◽

Biological Clock ◽

Circadian Oscillators ◽

Circadian Clock Genes ◽

Dim Light

Circadian rhythms are generated by an internal biological clock. The suprachiasmatic nucleus (SCN) in the hypothalamus is known to be the dominant biological clock regulating circadian rhythms in mammals. In birds, two nuclei, the so-called medial SCN (mSCN) and the visual SCN (vSCN), have both been proposed to be the avian SCN. However, it remains an unsettled question which nuclei are homologous to the mammalian SCN. We have identified circadian clock genes in Japanese quail and demonstrated that these genes are expressed in known circadian oscillators, the pineal and the retina. Here, we report that these clock genes are expressed in the mSCN but not in the vSCN in Japanese quail, Java sparrow, chicken, and pigeon. In addition, mSCN lesions eliminated or disorganized circadian rhythms of locomotor activity under constant dim light, but did not eliminate entrainment under light-dark (LD) cycles in pigeon. However, the lesioned birds became completely arrhythmic even under LD after the pineal and the eye were removed. These results indicate that the mSCN is a circadian oscillator in birds.

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