Regulation of gene expression mediating indeterminate muscle growth in teleosts

Transcriptomic Insights into Post-Spawning Death and Muscle Atrophy in Ayu (Plecoglossus altivelis)

In semelparous species like the ayu (Plecoglossus altivelis), spawning is followed by rapid physiological decline and death; yet, the underlying molecular mechanisms remain largely unexplored. This study examines transcriptomic changes in ayu skeletal muscle before and after spawning, with a focus on key genes and pathways contributing to muscle atrophy and metabolic dysfunction. Through RNA sequencing and DEG analysis, we identified over 3000 DEGs, and GSEA and KEGG pathway analysis revealed significant downregulation of energy metabolism and protein degradation. In post-spawning ayu, a rapid decrease in body weight was observed, accompanied by a decline in the expression of myosin heavy chain genes, which are major muscle protein genes, and gene expression changes indicative of muscle atrophy. Decreased expression of AP-1 transcription factors associated with muscle development and aging was also evident. PPI network analysis identified carbohydrate catabolism protein gapdh may be the key factor that led to muscle atrophy and accelerated aging in ayu. Our study revealed that after spawning, the ayu muscle tissue undergoes strong metabolic disorders and cellular stress responses, providing special insights into the mechanisms through the post-spawning death of ayu.

Short communication: Differential expression of piwi1 and piwi2 genes in tissues of tambacu and zebrafish: A possible relationship with the indeterminate muscle growth

Fish skeletal muscle is a component of the human diet, and understanding the mechanisms that control muscle growth can contribute to improving production in this sector and benefits the human health. In this sense, fish such as tambacu can represent a valuable source for exploring muscle growth regulators due to the indeterminate muscle growth pattern. In this context, the genes responsible for the indeterminate and determinate muscle growth pattern of fish are little explored, with piwi genes being possible candidates involved with these growth patterns. Piwi genes are associated with the proliferation and self-renewal of germ cells, and there are descriptions of these same functions in somatic cells from different tissues. However, little is known about the function of these genes in fish somatic cells. Considering this, our objective was to analyze the expression pattern of piwi 1 and 2 genes in cardiac muscle, skeletal muscle, liver, and gonad of zebrafish (species with determinate growth) and tambacu (species with indeterminate growth). We observed a distinct expression of piwi1 and piwi2 between tambacu and zebrafish, with both genes more expressed in tambacu in all tissues evaluated. Piwi genes can represent potential candidates involved with indeterminate muscle growth control.

Review: Understanding fish muscle biology in the indeterminate growth species pacu (Piaractus mesopotamicus)

The muscle phenotype of fish is regulated by numerous factors that, although widely explored, still need to be fully understood. In this context, several studies aimed to unravel how internal and external stimuli affect the muscle growth of these vertebrates. The pacu (Piaractus mesopotamicus) is a species of indeterminate muscular growth that quickly reaches high body weight. For this reason, it adds great importance to the productive sector, along with other round fish. In this context, we aimed to compile studies on fish biology and skeletal muscle growth, focusing on studies by our research group that used pacu as an experimental model along with other species. Based on these studies, new muscle phenotype regulators were identified and explored in vivo, in vitro, and in silico studies, which strongly contribute to advances in understanding muscle growth mechanisms with future applications in the productive sector.

Identification, Characterization and Functional Analysis of Fibroblast Growth Factors in Black Rockfish (Sebastes schlegelii)

Fibroblast growth factors (FGFs) are short polypeptides that play essential roles in various cellular biological processes, including cell migration, proliferation, and differentiation, as well as tissue regeneration, immune response, and organogenesis. However, studies focusing on the characterization and function of FGF genes in teleost fishes are still limited. In this study, we identified and characterized expression patterns of 24 FGF genes in various tissues of embryonic and adult specimens of the black rockfish (Sebates schlegelii). Nine FGF genes were found to play essential roles in myoblast differentiation, as well as muscle development and recovery in juvelines of S. schlegelii. Moreover, sex-biased expression pattern of multiple FGF genes was recorded in the species' gonads during its development. Among them, expression of the FGF1 gene was recorded in interstitial and sertoli cells of testes, promoting germ-cell proliferation and differentiation. In sum, the obtained results enabled systematic and functional characterization of FGF genes in S. schlegelii, laying a foundation for further studies on FGF genes in other large teleost fishes.

Growth regulation in brook charr Salvelinus fontinalis

Fish growth can be modulated through genetic selection. However, it is not known whether growth regulatory mechanisms modulated by genetic selection can provide information about phenotypic growth variations among families or populations. Following a five-generation breeding program that selected for the absence of early sexual maturity and increased growth in brook charr we aimed to understand how the genetic selection process modifies the growth regulatory pathway of brook charr at the molecular level. To achieve this, we studied the regulation of growth traits at three different levels: 1) between lines-one under selection, the other not, 2) among-families expressing differences in average growth phenotypes, which we termed family performance, and 3) among individuals within families that expressed extreme growth phenotypes, which we termed slow- and fast-growing. At age 1+, individuals from four of the highest performing and four of the lowest performing families in terms of growth were sampled in both the control and selected lines. The gene expression levels of three reference and ten target genes were analyzed by real-time PCR. Results showed that better growth performance (in terms of weight and length at age) in the selected line was associated with an upregulation in the expression of genes involved in the growth hormone (GH)/insulin growth factor-1 (IGF-1) axis, including the igf-1 receptor in pituitary; the gh-1 receptor and igf-1 in liver; and ghr and igf-1r in white muscle. When looking at gene expression within families, family performance and individual phenotypes were associated with upregulations of the leptin receptor and neuropeptid Y-genes related to appetite regulation-in the slower-growing phenotypes. However, other genes related to appetite (ghrelin, somatostatin) or involved in muscle growth (myosin heavy chain, myogenin) were not differentially expressed. This study highlights how transcriptomics may improve our understanding of the roles of different key endocrine steps that regulate physiological performance. Large variations in growth still exist in the selected line, indicating that the full genetic selection potential has not been reached.

Age-Associated Different Transcriptome Profiling in Zebrafish and Rats: an Insight into the Diversity of Vertebrate Aging

Most mammals, including humans, show obvious aging phenotypes, for example, loss of tissue plasticity and sarcopenia. In this regard, fish can be attractive models to study senescence because of their unique aging characteristics. The lifespan of fish varies widely, and several species can live for over 200 years. Moreover, some fish show anti-aging features and indeterminate growth throughout their life. Therefore, exploring the aging mechanism in fish could provide new insights into vertebrate aging. To this end, we conducted RNA sequencing (RNA-seq) assays for various organs and growth stages of zebrafish and compared the data with previously published RNA-seq data of rats. Age-associated differentially expressed genes (DEGs) for all zebrafish tissue samples reveal the upregulation of circadian genes and downregulation of hmgb3a. On one hand, a comparative analysis of DEG profiles associated with aging between zebrafish and rats identifies upregulation of circadian genes and downregulation of collagen genes as conserved transcriptome changes. On the other hand, in zebrafish, upregulation of autophagy-related genes in muscles and AP-1 transcription factor genes in various tissues is observed, which may imply fish-specific anti-aging characteristics. Consistent with our knowledge of mammalian aging, DEG profiles related to tissue senescence are observed in rats. We also detect age-associated downregulation of muscle homeostasis and differentiation-related genes in zebrafish gills, indicating a fish-specific senescence phenotype. Our results indicate both common and different aging profiles between fish and mammals, which could be used for future translational research.

The functional verification and analysis of Fugu promoter of cardiac gene tnni1a in zebrafish

Troponin I type 1b (Tnni1b) is thought to be a novel isoform that is expressed only in the zebrafish heart. Knocking down of tnni1b can lead to cardiac defects in zebrafish. Although both the zebrafish tnni1b and human troponin I1 (TNNI1) genes are thought to be closely associated with fatal cardiac development, the regulatory molecular mechanisms of these genes are poorly understood. Analyzing the functionally conserved sequence, especially in the noncoding regulatory region involved in gene expression, clarified these mechanisms. In this study, we isolated a 3 kb fragment upstream of Fugu tnni1a that can regulate green fluorescence protein (GFP) expression in a heart-specific manner, similar to the pattern of zebrafish homologue expression. Three evolutionarily conserved regions (ECRs) in the 5'-flanking sequence of Fugu tnni1a were identified by sequence alignment. Deletion analysis led to the identification of ECR2 as a core sequence that affects the heart-specific expression function of the Fugu tnni1a promoter. Interestingly, both the Fugu tnni1a promoter and ECR2 sequence were functionally conserved in zebrafish, although they shared no sequence similarity. Together, the findings of our study provided further evidence for the important role of tnni1a homologous in cardiac development and demonstrated that two functionally conserved sequences in the zebrafish and Fugu genomes may be ECRs, despite their lack of similarity.

Zebrafish Danio rerio myotomal muscle structure and growth from a spatial transcriptomics perspective

Fish exhibit different muscle structures and growth characteristics compared with mammals. We used a spatial transcriptomics approach and examined myotomal muscle sections from zebrafish. Adult muscles were divided into eight regions according to spatial gene expression characteristics. Slow muscle was located in the wedge-shaped region near the lateral line and at the base of the dorsal fin, intermediate muscle was located in a ribbon-shaped region adjacent to slow muscle, and fast muscle was located in the deep region of the trunk, surrounded by intermediate muscle; the interior of fast muscle was further divided into 6 parts by their transcriptomic features. Combined analysis of adult and larval data revealed that adult muscles contain specific regions similar to larval muscles. These regions showed active myogenesis and a high expression of genes associated with muscle hyperplasia. This is the first study to apply spatial transcriptomics to fish myotomal muscle structure and growth.

Diallel Cross Application and Histomolecular Characterization: An Attempt to Develop Reference Stock of Labeo ariza

The objective of the present study was to evaluate the growth performance and genetic variation in diallel crosses of Ariza labeo (Labeo ariza) originating from three geographically separated rivers (Atrai, Jamuna and Kangsha) in Bangladesh. Intra (G1K♀K♂, G2J♀J♂, and G3A♀A♂) and inter (G4K♀A♂, G5K♀J♂, G6A♀K♂, G7A♀J♂, G8J♀K♂, and G9J♀A♂) stocks were produced following diallel cross (sex ratio-1:1 and n = 48; 16 from each river). Reproductive and growth performance, muscle cellularity and genetic variation following genotyping of eight microsatellite markers (Lr1, Lr2, Lr3, Lr22, Lr24, Lr27, Lr28 and Lr29) and analysis of all crossbreeds was performed. The fertilization (95% ± 2.11%), hatching (88% ± 1.03%), and survival rates (82% ± 1.88%) of G4K♀A♂ were higher compared to other groups. With respect to length and weight gains (2.67 ± 0.4 cm and 3.39 ± 0.2 g), SGR (3.23% ± 0.20%), and heterosis (8.87% and 24.74%) G4K♀A♂ was the superior group. A higher number of hyperplastic muscle fibers, mean number of alleles (2.75) and mean observed heterozygosity (0.417) from G4K♀A♂ could be interpreted to mean that G4K♀A♂ comprise better performance efficiency compared to others and are considered for continuing the L. ariza stock improvement program.

The miRNA expression profile directly reflects the energy metabolic differences between slow and fast muscle with nutritional regulation of the Chinese perch (Siniperca chuatsi)

Fish skeletal muscles are composed of two distinct types, slow and fast muscles, and they play important roles in maintaining the body's movement and energy metabolism. The two types of muscle are easy to separate, so they are often used as the model system for studies on their physiological and functional characteristics. In this study, we revealed that the carbohydrate and lipid metabolic KEGG pathways are different between slow and fast muscles of Chinese perch with transcriptome analysis. In fast muscle, glucose metabolism was catabolic with higher glycolysis capacity, while in slow muscle, glucose metabolism was anabolic with more glycogen synthesis. In addition, oxidative metabolism in slow muscle was stronger than that in fast muscle. By analyzing the expression levels of 40 miRNAs involved in metabolism in the muscles of Chinese perch, 18 miRNAs were significantly upregulated and 7 were significantly downregulated in slow muscle compared with fast muscle. Based on functional enrichment analysis of their target genes, the differential expression levels of 17 miRNAs in slow and fast muscles were reflected in their carbohydrate and lipid metabolism. Among these, 15 miRNAs were associated with carbohydrate metabolism, and 6 miRNAs were associated with lipid metabolism. After 3 days of starvation, the expression levels of 15 miRNAs involved in glucose metabolism in fast and slow muscles increased. However, after 7 days of starvation, the mRNA levels of miR-22a, miR-23a, miR-133a-3p, miR-139, miR-143, miR-144, miR-181a and miR-206 decreased to basal levels. Our data suggest that the possible reason for the difference in glucose and lipid metabolism is that more miRNAs inhibit the expression of target genes in slow muscle.

Striated myosin heavy chain gene is a crucial regulator of larval myogenesis in the pacific oyster Crassostrea gigas

Pacific oyster (Crassostrea gigas), the most productive economical bivalve mollusc, is identified as an attractive model for developmental studies due to its classical mosaic developmental pattern. Myosin heavy chain is a structural and functional component of myosin, the key muscle protein of thick filament. Here, full length cDNA of striated myosin heavy chains in C. gigas (CgSmhc) was obtained, and the expression profiles were examined in different development stage. CgSmhc had a high expression level in trochophore and D-shaped stage during embryo-larval stage. In adult, CgSmhc was a muscle-specific gene and primarily expressed in muscle tissues. Then, activity of 5' flanking region of CgSmhc were examined through an reconstructed EGFP vector. The results indicated that 3098 bp 5'-flanking region of CgSmhc owned various conserved binding sites of myogenesis-related regulatory elements, and the 2000 bp 5'-flanking sequence was sufficient to induce the CgSmhc expression. Subsequently, the CRISPR/Cas9-mediated target disruption of CgSmhc was generated by co-injection of Cas9mRNA and CgSmhc-sgRNAs into one-cell stage embryos of C. gigas. Loss of CgSmhc had a visible effect on the sarcomeric organization of thin filaments in larval musculature, indicating that CgSmhc was required during larval myogenesis to regulate the correct assembly of sarcomere.

Identifying the Related Genes of Muscle Growth and Exploring the Functions by Compensatory Growth in Mandarin Fish (Siniperca chuatsi)

How organisms display many different biochemical, physiological processes through genes expression and regulatory mechanisms affecting muscle growth is a central issue in growth and development. In Siniperca chuatsi, the growth-related genes and underlying relevant mechanisms are poorly understood, especially for difference of body sizes and compensatory growth performance. Muscle from 3-month old individuals of different sizes was used for transcriptome analysis. Results showed that 8,942 different expression genes (DEGs) were identified after calculating the RPKM. The DEGs involved in GH-IGF pathways, protein synthesis, ribosome synthesis and energy metabolisms, which were expressed significantly higher in small individuals (S) than large fish (L). In repletion feeding and compensatory growth experiments, eight more significant DEGs were used for further research (GHR2, IGFR1, 4ebp, Mhc, Mlc, Myf6, MyoD, troponin). When food was plentiful, eight genes participated in and promoted growth and muscle synthesis, respectively. Starvation can be shown to inhibit the expression of Mhc, Mlc and troponin, and high expression of GHR2, IGFR1, and 4ebp inhibited growth. Fasting promoted the metabolic actions of GHR2, IGFR1, and 4ebp rather than the growth-promoting actions. MyoD can sense and regulate the hunger, which also worked with Mhc and Mlc to accelerate the compensatory growth of S. chuatsi. This study is helpful to understand the regulation mechanisms of muscle growth-related genes. The elected genes will contribute to the selective breeding in future as candidate genes.

Satellite cell division and fiber hypertrophy alternate with new fiber formation during indeterminate muscle growth in juvenile lake sturgeon (Acipenser fulvescens)

Age-dependent changes in muscle fiber size, myonuclear domain volume, fiber-end-terminal configuration, fiber and fish growth, and stem cell or satellite cell (SC) number and proliferation were investigated in developing lake sturgeon (Acipenser fulvescens Rafinesque, 1817) to characterize indeterminate muscle growth during early life. We hypothesized that up to 29 months post hatch (MPH), SC numbers and mitotic activity, the mitotic cycle duration of SCs, fiber morphology, and the volume of cytoplasmic domains around fiber nuclei would change during periods of fiber hypertrophy and hyperplasia. Single-fiber cultures were used in pulse-chase studies of SC division and the Pax7+ SC population. The number of SCs per fiber increased until 17 MPH, peaking as a proportion of fiber nuclei at 3 and 17 MPH. SC cycle time decreased in duration with age after peaks at 3 and 5 MPH. Domain volume was high at 1 and 29 MPH and low from 2 to 6 MPH. Fibers with uniformly tapered ends were most frequent at 4 MPH. Results suggest 3 and 6–17 MPH as intervals for both SC proliferation and fiber hypertrophy, and that fiber growth alternated with new fiber formation (termed fiber hyperplasia) from 4 to 5 MPH and from 17 to 29 MPH. These patterns of cellular dynamics in lake sturgeon muscle growth advance our understanding of indeterminate growth.

Skeletal Muscle and the Effects of Ammonia Toxicity in Fish, Mammalian, and Avian Species: A Comparative Review Based on Molecular Research

Typically, mammalian and avian models have been used to examine the effects of ammonia on skeletal muscle. Hyperammonemia causes sarcopenia or muscle wasting, in mammals and has been linked to sarcopenia in liver disease patients. Avian models of skeletal muscle have responded positively to hyperammonemia, differing from the mammalian response. Fish skeletal muscle has not been examined as extensively as mammalian and avian muscle. Fish skeletal muscle shares similarities with avian and mammalian muscle but has notable differences in growth, fiber distribution, and response to the environment. The wide array of body sizes and locomotion needs of fish also leads to greater diversity in muscle fiber distribution and growth between different fish species. The response of fish muscle to high levels of ammonia is important for aquaculture and quality food production but has not been extensively studied to date. Understanding the differences between fish, mammalian and avian species’ myogenic response to hyperammonemia could lead to new therapies for muscle wasting due to a greater understanding of the mechanisms behind skeletal muscle regulation and how ammonia effects these mechanisms. This paper provides an overview of fish skeletal muscle and ammonia excretion and toxicity in fish, as well as a comparison to avian and mammalian species.

Multiple transcription factors mediating the expressional regulation of myosin heavy chain gene involved in the indeterminate muscle growth of fish

Torafugu myosin heavy chain gene, MYH_M2528-1, is specifically expressed in neonatal slow and fast muscle fibers, suggesting its functional role in indeterminate muscle growth in fish. However, the transcriptional regulatory mechanisms of MYH_M2528-1 involved in indeterminate muscle growth in fish remained unknown. We previously isolated a 2100 bp 5'- flanking sequence of torafugu MYH_M2528-1 that showed sufficient promoter activity to allow specific gene expression in neonatal muscle fibers of zebrafish. Here, we examined the cis-regulatory mechanism of 2100 bp 5'-flanking region of torafugu MYH_M2528-1 using deletion-mutation analysis in zebrafish embryo. We discovered that myoblast determining factor (MyoD) binding elements play a key role and participate in the transcriptional regulation of MYH_M2528-1 expression in zebrafish embryos. We further discovered that paired box protein (Pax3) are required for promoting MYH_M2528-1 expression and myocyte enhancer factor-2 (MEF2) binding sites participate in the transcriptional regulation of MYH_M2528-1 expression in slow/fast skeletal muscles. Our study also confirmed that the nuclear factor of activated T-cell (NFAT) binding sites take part in the transcriptional regulation of MYH_M2528-1 expression in slow and fast muscles fiber in relation to indeterminate muscle growth. These results obviously confirmed that multiple cis-elements in the 5'-flanking region of MYH_M2528-1 function in the transcriptional regulation of its expression.

Cloning, SNP detection, and growth correlation analysis of the 5' flanking regions of two myosin heavy chain-7 genes in Mandarin fish (Siniperca chuatsi)

Myosin heavy chains (MYHs) play important roles in muscle growth and contraction. In fish, MYHs contribute to hyperplasia and hypertrophy of muscle fibers, which can continue into adult life and thus result in indeterminate growth in some species. We previously identified two MYH genes, MYH-7a and MYH-7b, that are differentially expressed in Mandarin fish (Siniperca chuatsi) and appear to function in early growth. However, the regulatory role of their 5' flanking regions is unknown. To examine the effects of single nucleotide polymorphisms (SNPs) in these regions, we used genome walking to amplify their flanking sequences and analyzed the regulatory elements and binding sites. A single SNP locus was found in the flanking sequence of each gene. These SNP loci are located in the conserved glucocorticoid receptor binding region (MYH-7a: G-614A; Allele frequency: G:A = 94.9:5.1; GG (89.76) and AG (10.24) genotypes) and the LIM homeobox domain transcription factor binding sequence (MYH-7b: C-1933A; Allele frequency: C:A = 54.8:45.2; AA (20.82), AC (48.81), and CC (30.37) genotypes). At the G-614A loci, the GG genotype exhibited more superior growth traits (total length, body length, body height, etc.) than the AG genotype, with the exception of caudal peduncle length. Alternatively, at the C-1933A loci, the AC and AA genotypes showed significant differences in all growth traits, except for head length, with AC exhibiting superior traits. The AA and CC genotypes showed significant differences in caudal peduncle length and height, while no differences were observed between the AC and CC genotypes. Thus, these SNPs in the 5' flanking regions of MYH-7a and MYH-7b are correlated with superior growth and can be used for selecting Mandarin fish during breeding.

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.