Circadian rhythmicity and photic plasticity of myosin gene transcription in fast skeletal muscle of Atlantic cod (Gadus morhua)

Transcriptomic landscape of Atlantic salmon (Salmo salar L.) skin

In this study, we present the first spatial transcriptomic atlas of Atlantic salmon skin using the Visium Spatial Gene Expression protocol. We utilized frozen skin tissue from 4 distinct sites, namely the operculum, pectoral and caudal fins, and scaly skin at the flank of the fish close to the lateral line, obtained from 2 Atlantic salmon (150 g). High-quality frozen tissue sections were obtained by embedding tissue in optimal cutting temperature media prior to freezing and sectioning. Further, we generated libraries and spatial transcriptomic maps, achieving a minimum of 80 million reads per sample with mapping efficiencies ranging from 79.3 to 89.4%. Our analysis revealed the detection of over 80,000 transcripts and nearly 30,000 genes in each sample. Among the tissue types observed in the skin, the epithelial tissues exhibited the highest number of transcripts (unique molecular identifier counts), followed by muscle tissue, loose and fibrous connective tissue, and bone. Notably, the widest nodes in the transcriptome network were shared among the epithelial clusters, while dermal tissues showed less consistency, which is likely attributable to the presence of multiple cell types at different body locations. Additionally, we identified collagen type 1 as the most prominent gene family in the skin, while keratins were found to be abundant in the epithelial tissue. Furthermore, we successfully identified gene markers specific to epithelial tissue, bone, and mesenchyme. To validate their expression patterns, we conducted a meta-analysis of the microarray database, which confirmed high expression levels of these markers in mucosal organs, skin, gills, and the olfactory rosette.

Daily Rhythmicity of Muscle-Related and Rhythm Genes Expression in Mackerel Tuna (Euthynnus affinis)

The aim of this study was to investigate the circadian rhythm of muscle-related gene expression in mackerel tuna under different weather conditions. The experiment was carried out under two weather conditions at four sampling times (6:00, 12:00, 18:00, and 24:00) to determine the expression of growth, function, and rhythm genes: white muscle rhythm genes were rhythmic on sunny and cloudy days, except for PER3 and RORA; all functional genes had daily rhythmicity. Red muscle had daily rhythmicity on both sunny and cloudy days; functional genes had daily rhythmicity except for MBNL. The expression levels of the rhythm gene PER1 were determined to be significantly different by independent t-test samples in white muscle at 6:00, 12:00, 18:00, and 24:00 under different weather conditions; the expression levels of the functional genes MBNL and MSTN were both significantly different. In the red muscle, the expression of the rhythm genes PER3, REVERBA, and BMAL1 was determined by independent t-test samples at 6:00, 12:00, 18:00, and 24:00 on cloudy and sunny days; the functional gene MBNL was significantly different. The present study showed that mackerel tuna muscle rhythm genes and functional genes varied significantly in expression levels depending on weather, time of day, and light intensity and that the expression levels of myogenic genes were closely related to clock gene expression. The fish were also able to adapt to changes in light intensity in different weather conditions through positive physiological regulation.

Building a model for predicting metabolic syndrome using artificial intelligence based on an investigation of whole-genome sequencing

Background

The circadian system is responsible for regulating various physiological activities and behaviors and has been gaining recognition. The circadian rhythm is adjusted in a 24-h cycle and has transcriptional–translational feedback loops. When the circadian rhythm is interrupted, affecting the expression of circadian genes, the phenotypes of diseases could amplify. For example, the importance of maintaining the internal temporal homeostasis conferred by the circadian system is revealed as mutations in genes coding for core components of the clock result in diseases. This study will investigate the association between circadian genes and metabolic syndromes in a Taiwanese population.

Methods

We performed analysis using whole-genome sequencing, read vcf files and set target circadian genes to determine if there were variants on target genes. In this study, we have investigated genetic contribution of circadian-related diseases using population-based next generation whole genome sequencing. We also used significant SNPs to create a metabolic syndrome prediction model. Logistic regression, random forest, adaboost, and neural network were used to predict metabolic syndrome. In addition, we used random forest model variables importance matrix to select 40 more significant SNPs, which were subsequently incorporated to create new prediction models and to compare with previous models. The data was then utilized for training set and testing set using five-fold cross validation. Each model was evaluated with the following criteria: area under the receiver operating characteristics curve (AUC), precision, F1 score, and average precision (the area under the precision recall curve).

Results

After searching significant variants, we used Chi-Square tests to find some variants. We found 186 significant SNPs, and four predicting models which used 186 SNPs (logistic regression, random forest, adaboost and neural network), AUC were 0.68, 0.8, 0.82, 0.81 respectively. The F1 scores were 0.412, 0.078, 0.295, 0.552, respectively. The other three models which used the 40 SNPs (logistic regression, adaboost and neural network), AUC were 0.82, 0.81, 0.81 respectively. The F1 scores were 0.584, 0.395, 0.574, respectively.

Conclusions

Circadian gene defect may also contribute to metabolic syndrome. Our study found several related genes and building a simple model to predict metabolic syndrome.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-022-03379-7.

Genome-Wide Identification, Characterization and Expression Profiling of myosin Family Genes in Sebastes schlegelii

Myosins are important eukaryotic motor proteins that bind actin and utilize the energy of ATP hydrolysis to perform a broad range of functions such as muscle contraction, cell migration, cytokinesis, and intracellular trafficking. However, the characterization and function of myosin is poorly studied in teleost fish. In this study, we identified 60 myosin family genes in a marine teleost, black rockfish (Sebastes schlegelii), and further characterized their expression patterns. myosin showed divergent expression patterns in adult tissues, indicating they are involved in different types and compositions of muscle fibers. Among 12 subfamilies, S. schlegelii myo2 subfamily was significantly expanded, which was driven by tandem duplication events. The up-regulation of five representative genes of myo2 in the skeletal muscle during fast-growth stages of juvenile and adult S. schlegelii revealed their active role in skeletal muscle fiber synthesis. Moreover, the expression regulation of myosin during the process of myoblast differentiation in vitro suggested that they contribute to skeletal muscle growth by involvement of both myoblast proliferation and differentiation. Taken together, our work characterized myosin genes systemically and demonstrated their diverse functions in a marine teleost species. This lays foundation for the further studies of muscle growth regulation and molecular mechanisms of indeterminate skeletal muscle growth of large teleost fishes.

Myosin XVIII

Class XVIII myosins represent a branch of the myosin family tree characterized by the presence of large N- and C-terminal extensions flanking a generic myosin core. These myosins display the highest sequence similarity to conventional class II muscle myosins and are compatible with but not restricted to myosin-2 contractile structures. Instead, they fulfill their functions at diverse localities, such as lamella, actomyosin bundles, the Golgi apparatus, focal adhesions, the cell membrane, and within sarcomeres. Sequence comparison of active-site residues and biochemical data available thus far indicate that this myosin class lacks active ATPase-driven motor activity, suggesting that its members function as structural myosins. An emerging body of evidence indicates that this structural capability is essential for the organization, maturation, and regulation of the contractile machinery in both muscle and nonmuscle cells. This is supported by the clear association of myosin-18A (Myo18A) and myosin-18B (Myo18B) dysregulation with diseases such as cancer and various myopathies.

The Influence of Short-term Fasting on Muscle Growth and Fiber Hypotrophy Regulated by the Rhythmic Expression of Clock Genes and Myogenic Factors in Nile Tilapia

Circadian clock genes and myogenic factors are tightly integrated to influence muscle growth upon dietary deprivation in animals. In this study, we reported that upon short-term fasting of Nile tilapia juveniles for 7 and 15 days, the growth of the fish stagnated and the size of muscle fibers decreased. To reveal the molecular mechanisms of how starvation affects fish muscle growth, we analyzed the rhythmic expression of circadian clock genes and myogenic factors. After 7 and 15 days of fasting treatment, the muscle tissues were collected for 24 h (at zeitgeber times ZT0, ZT3, ZT6, ZT9, ZT12, ZT18, ZT21, and ZT24) from tilapia juveniles. Among the 27 clock genes, the expression of cyr1b, nr1d1, per1, clocka, clockb, ciarta, and aanat2 displayed a daily rhythmicity in normal daily cycle, while arntl2, cry1a, cry1b, npas2, nr1d2b, per2, per3, rorαb, clocka, clockb, nfil3, cipca, and cipcb exhibited daily rhythmicity in the fasting fish muscles. The transcript levels of clockb showed moderate positive correlation with the aanat2, ciarta, cry1b, and nr1d1 in the muscle tissue of normally fed Nile tilapia juvenile. In comparison of the two treatment modes, the expression levels of clocka, clockb, and cry1b showed the rhythmicity, but clockb expression was significantly decreased and the acrophase had shifted. The transcript levels of fbxo32 and pdk4 had either moderate or strong positive correlations with other daily expression of clock genes except arntl2 in the muscle after 7-day fasting. The expressions of myogenic regulatory factors were also either upregulated or downregulated. These observations demonstrated that dietary starvation might affect fish muscle growth by modulating the differential expression of circadian clock genes and myogenic factors. Thus, our work provides a better understanding of the molecular mechanism of dietary starvation on fish growth and may provide dietary administration in aquiculture.

Daily rhythmicity of clock gene transcript levels in fast and slow muscle fibers from Chinese perch (Siniperca chuatsi)

Background

Clock genes are considered to be the molecular core of biological clock in vertebrates and they are directly involved in the regulation of daily rhythms in vertebrate tissues such as skeletal muscles. Fish myotomes are composed of anatomically segregated fast and slow muscle fibers that possess different metabolic and contractile properties. To date, there is no report on the characterization of the circadian clock system components of slow muscles in fish.

Results

In the present study, the molecular clock components (clock, arntl1/2, cry1/2/3, cry-dash, npas2, nr1d1/2, per1/2/3, rorα and tim genes) and their daily transcription levels were characterized in slow and fast muscles of Chinese perch (Siniperca chuatsi). Among the 15 clock genes, nrld2 and per3 had no daily rhythmicity in slow muscles, and cry2/3 and tim displayed no daily rhythmicity in fast muscles of the adult fish. In the slow muscles, the highest expression of the most clock paralogs occurred at the dark period except arntl1, nr1d1, nr1d2 and tim. With the exception of nr1d2 and tim, the other clock genes had an acrophase at the light period in fast muscles. The circadian expression of the myogenic regulatory factors (mrf4 and myf5), mstn and pnca showed either a positive or a negative correlation with the transcription pattern of the clock genes in both types of muscles.

Conclusions

It was the first report to unravel the molecular clock components of the slow and fast muscles in vertebrates. The expressional pattern differences of the clock genes between the two types of muscle fibers suggest that the clock system may play key roles on muscle type-specific tissue maintenance and function.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3373-z) contains supplementary material, which is available to authorized users.

Temporal regulation of proteome profile in the fruit fly, Drosophila melanogaster

Background. Diurnal rhythms of protein synthesis controlled by the biological clock underlie the rhythmic physiology in the fruit fly, Drosophila melanogaster. In this study, we conducted a proteome-wide investigation of rhythmic protein accumulation in D. melanogaster.

Materials and Methods. Total protein collected from fly samples harvested at 4 h intervals over the 24 h period were subjected to two-dimensional gel electrophoresis, trypsin digestion and MS/MS analysis. Protein spots/clusters were identified with MASCOT search engine and Swiss-Prot database. Expression of proteins was documented as percentage of volume contribution using the Image Master 2D Platinum software.

Results. A total of 124 protein spots/clusters were identified using MS/MS analysis. Significant variation in the expression of 88 proteins over the 24-h period was observed. A relatively higher number of proteins was upregulated during the night compared to the daytime. The complexity of temporal regulation of the D. melanogaster proteome was further reflected from functional annotations of the differently expressed proteins, with those that were upregulated at night being restricted to the heat shock proteins and proteins involved in metabolism, muscle activity, protein synthesis/folding/degradation and apoptosis, whilst those that were overexpressed in the daytime were apparently involved in metabolism, muscle activity, ion-channel/cellular transport, protein synthesis/folding/degradation, redox homeostasis, development and transcription.

Conclusion. Our data suggests that a wide range of proteins synthesized by the fruit fly, D. melanogaster, is under the regulation of the biological clock.

In vitro and ex vivo models indicate that the molecular clock in fast skeletal muscle of Atlantic cod is not autonomous

The notion that the circadian rhythm is exclusively regulated by a central clock has been challenged by the discovery of peripheral oscillators. These peripheral clocks are known to have a direct influence on the biological processes in a tissue or cell. In fish, several peripheral clocks respond directly to light, thus raising the hypothesis of autonomous regulation. Several clock genes are expressed with daily rhythmicity in Atlantic cod (Gadus morhua) fast skeletal muscle. In the present study, myosatellite cell culture and short-term cultured fast skeletal muscle explant models were developed and characterized, in order to investigate the autonomy of the clock system in skeletal muscle of Atlantic cod. Myosatellite cells proliferated and differentiated in vitro, as shown by the changes in cellular and myogenic gene markers. The high expression of myogenic differentiation 1 during the early days post-isolation implied the commitment to myogenic lineage and the increasing mRNA levels of proliferating cell nuclear antigen (pcna) indicated the proliferation of the cells in vitro. Transcript levels of myogenic marker genes such as pcna and myogenin increased during 5 days in culture of skeletal muscle explants, indicating that the muscle cells were proliferating and differentiating under ex vivo conditions. Transcript levels of the clock gene aryl hydrocarbon receptor nuclear translocator-like 2 (arntl2) in myosatellite cells showed no daily oscillation regardless of photoperiod manipulation. On the other hand, mRNA levels of the clock gene circadian locomotor output cycles kaput (clock) showed circadian rhythmicity in 5-day-old skeletal muscle explant under different photoperiod regimes. The expression of arntl2, cryptochrome2 (cry2), period 2a (per2a) and nuclear receptor subfamily 1, group D, member 1 was not rhythmic in muscle explants but photoperiod manipulation had a significant effect on mRNA levels of cry2 and per2a. Taken together, the lack of rhythmicity of molecular clocks in vitro and ex vivo indicate that the putative peripheral clock in Atlantic cod fast skeletal muscle is not likely to be autonomous.