MicroRNA-3906 regulates fast muscle differentiation through modulating the target gene homer-1b in zebrafish embryos

Transcriptome integration analysis revealed that miR-103-3p regulates goat myoblast proliferation by targeting FGF18

BACKGROUND

Myoblasts serve as the fundamental building blocks of muscle fibers, and there is a positive correlation between the diameter of myofibers during the juvenile phase and the rate of muscle growth, which does not change in adulthood. However, the molecular mechanisms governing myofiber diameter across various developmental stages in goats remain largely unclear.

RESULTS

In this study, we examined miRNA expression in the longissimus dorsi muscle tissue of goats at two distinct ages: one month, a period characterized by robust muscle growth, and nine months, when muscle development plateaus in adulthood. A total of 408 known miRNAs and 86 novel miRNAs were identified, with 32 miRNAs exhibiting differential expression between the two groups. A functional enrichment analysis of these targeted genes revealed significant enrichment in pathways closely correlated with skeletal muscle growth, development, and senescence. Notably, chi-miR-103-3p was identified among the DE miRNAs and appeared to play an important role in skeletal myoblast proliferation. Bioinformatics analysis, complemented by dual luciferase activity assays revealed that chi-miR-103-3p specifically targets the 3'UTR of FGF18. Subsequent cell transfection experiments demonstrated that chi-miR-103-3p suppresses the expression of FGF18 in goat myoblasts, thereby inhibiting cell proliferation. Moreover, FGF18 was observed to enhance the proliferation of goat myoblasts.

CONCLUSIONS

Collectively, our data indicated that the elevated expression of chi-miR-103-3p in adult goat myoblasts significantly repressed FGF18 expression, thereby limiting rapid muscle growth. Proliferation and differentiation of myoblasts can affect myofiber number and cell volume expansion. These findings lay the foundation for further elucidation of the molecular mechanisms underlying muscle growth and development across different life stages of goats. Additionally, it could be a potential molecular marker for improving muscle production in goats.

Genome-wide association study for growth traits with 1066 individuals in largemouth bass (Micropterus salmoides)

The largemouth bass is a native species of North America that was first introduced to mainland China in the 1980s. In recent years, it has been extensively farmed in China due to its high meat quality and broad adaptability. In this study, we collected growth trait data from 1,066 largemouth bass individuals across two populations. We generated an average of approximately 7× sequencing coverage for these fish using Illumina sequencers. From the samples, we identified 2,695,687 SNPs and retained 1,809,116 SNPs for further analysis after filtering. To estimate the number of genome-wide effective SNPs, we performed LD pruning with PLINK software and identified 77,935 SNPs. Our GWAS revealed 15 SNPs associated with six growth traits. We identified a total of 24 genes related to growth, with three genes-igf1, myf5, and myf6-directly associated with skeletal muscle development and growth, located near the leading SNP on chromosome 23. Other candidate genes are involved in the development of tissues and organs or other physiological processes. These findings provide a valuable set of SNPs and genes that could be useful for genetic breeding programs aimed at enhancing growth in largemouth bass.

Skeletal muscle feature of different populations in large yellow croaker (Larimichthys crocea): from an epigenetic point of view

Fish skeletal muscle is composed of well-defined fiber types. In order to identify potential candidate genes affecting muscle growth and development under epigenetic regulation. Bisulfite sequencing was utilized to analyze and compare the muscle DNA methylation profiles of Larimichthys crocea inhabiting different environments. The results revealed that DNA methylation in L. crocea was predominantly CG methylation, with 2,396 differentially methylated regions (DMRs) identified through comparisons among different populations. The largest difference in methylation was observed between the ZhouShan and JinMen wild populations, suggesting that L. crocea may have undergone selection and domestication. Additionally, GO and KEGG enrichment analysis of differentially methylated genes (DMGs) revealed 626 enriched GO functional categories, including various muscle-related genes such as myh10, myf5, myf6, ndufv1, klhl31, map3k4, syn2b, sostdc1a, bag4, and hsp90ab. However, significant enrichment in KEGG pathways was observed only in the JinMen and XiangShan populations of L. crocea. Therefore, this study provides a theoretical foundation for a better understanding of the epigenetic regulation of skeletal muscle growth and development in L. crocea under different environmental conditions.

Congenital Splay Leg Syndrome in Piglets-Current Knowledge and a New Approach to Etiology

The porcine congenital splay leg syndrome (PCS), even though being of transient nature, is still one of the most important causes for piglet losses due to its high incidence and mortality. Although, described decades ago, the pathogenetic mechanism is still elusive. Numerous, mostly descriptive studies characterized the syndrome at clinical, histological and cellular levels but resulted in a highly diverse picture of the syndrome. Broad variability in phenotypical expression and, in case of proper care, the rapid recovery of affected animals complicated a systematical analysis of the underlying pathogenesis. Although, several environmental factors were discussed as potential causes of PCS, most of the evidence points to a hereditary basis of PCS. Nevertheless, only few of the suggested candidate genes from transcriptome and mapping analyses, like F-box protein 32 (FBXO32), could be confirmed so far. Only recently, a genome wide association study revealed genomic regions on five porcine chromosomes and named a number of potential candidate genes, among them homer scaffold protein 1 (HOMER1). This new candidate-a cellular scaffold protein-plays a role in a plethora of cellular signaling cascades, and is not only involved in skeletal muscle differentiation but also critical for muscular function. In this review, we critically elucidate the current state of knowledge in the field and evaluate current achievements in the identification of the pathogenetic mechanism for the syndrome.

Functional Non-coding RNA During Embryonic Myogenesis and Postnatal Muscle Development and Disease

Skeletal muscle is a highly heterogeneous tissue that plays a crucial role in mammalian metabolism and motion maintenance. Myogenesis is a complex biological process that includes embryonic and postnatal development, which is regulated by specific signaling pathways and transcription factors. Various non-coding RNAs (ncRNAs) account for the majority of total RNA in cells and have an important regulatory role in myogenesis. In this review, we introduced the research progress in miRNAs, circRNAs, and lncRNAs related to embryonic and postnatal muscle development. We mainly focused on ncRNAs that regulate myoblast proliferation, differentiation, and postnatal muscle development through multiple mechanisms. Finally, challenges and future perspectives related to the identification and verification of functional ncRNAs are discussed. The identification and elucidation of ncRNAs related to myogenesis will enrich the myogenic regulatory network, and the effective application of ncRNAs will enhance the function of skeletal muscle.

Molecular Mechanisms Regulating Muscle Plasticity in Fish

Growth rates in fish are largely dependent on genetic and environmental factors, of which the latter can be highly variable throughout development. For this reason, muscle growth in fish is particularly dynamic as muscle structure and function can be altered by environmental conditions, a concept referred to as muscle plasticity. Myogenic regulatory factors (MRFs) like Myogenin, MyoD, and Pax7 control the myogenic mechanisms regulating quiescent muscle cell maintenance, proliferation, and differentiation, critical processes central for muscle plasticity. This review focuses on recent advancements in molecular mechanisms involving microRNAs (miRNAs) and DNA methylation that regulate the expression and activity of MRFs in fish. Findings provide overwhelming support that these mechanisms are significant regulators of muscle plasticity, particularly in response to environmental factors like temperature and nutritional challenges. Genetic variation in DNA methylation and miRNA expression also correlate with variation in body weight and growth, suggesting that genetic markers related to these mechanisms may be useful for genomic selection strategies. Collectively, this knowledge improves the understanding of mechanisms regulating muscle plasticity and can contribute to the development of husbandry and breeding strategies that improve growth performance and the ability of the fish to respond to environmental challenges.

Altered miRNA and mRNA Expression in Sika Deer Skeletal Muscle with Age

Studies of the gene and miRNA expression profiles associated with the postnatal late growth, development, and aging of skeletal muscle are lacking in sika deer. To understand the molecular mechanisms of the growth and development of sika deer skeletal muscle, we used de novo RNA sequencing (RNA-seq) and microRNA sequencing (miRNA-seq) analyses to determine the differentially expressed (DE) unigenes and miRNAs from skeletal muscle tissues at 1, 3, 5, and 10 years in sika deer. A total of 51,716 unigenes, 171 known miRNAs, and 60 novel miRNAs were identified based on four mRNA and small RNA libraries. A total of 2,044 unigenes and 11 miRNAs were differentially expressed between adolescence and juvenile sika deer, 1,946 unigenes and 4 miRNAs were differentially expressed between adult and adolescent sika deer, and 2,209 unigenes and 1 miRNAs were differentially expressed between aged and adult sika deer. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that DE unigenes and miRNA were mainly related to energy and substance metabolism, processes that are closely associate with the growth, development, and aging of skeletal muscle. We also constructed mRNA–mRNA and miRNA–mRNA interaction networks related to the growth, development, and aging of skeletal muscle. The results show that mRNA (Myh1, Myh2, Myh7, ACTN3, etc.) and miRNAs (miR-133a, miR-133c, miR-192, miR-151-3p, etc.) may play important roles in muscle growth and development, and mRNA (WWP1, DEK, UCP3, FUS, etc.) and miRNAs (miR-17-5p, miR-378b, miR-199a-5p, miR-7, etc.) may have key roles in muscle aging. In this study, we determined the dynamic miRNA and unigenes transcriptome in muscle tissue for the first time in sika deer. The age-dependent miRNAs and unigenes identified will offer insights into the molecular mechanism underlying muscle development, growth, and maintenance and will also provide valuable information for sika deer genetic breeding.

Calcium Imaging in the Zebrafish

The zebrafish (Danio rerio) has emerged as a widely used model system during the last four decades. The fact that the zebrafish larva is transparent enables sophisticated in vivo imaging, including calcium imaging of intracellular transients in many different tissues. While being a vertebrate, the reduced complexity of its nervous system and small size make it possible to follow large-scale activity in the whole brain. Its genome is sequenced and many genetic and molecular tools have been developed that simplify the study of gene function in health and disease. Since the mid 90's, the development and neuronal function of the embryonic, larval, and later, adult zebrafish have been studied using calcium imaging methods. This updated chapter is reviewing the advances in methods and research findings of zebrafish calcium imaging during the last decade. The choice of calcium indicator depends on the desired number of cells to study and cell accessibility. Synthetic calcium indicators, conjugated to dextrans and acetoxymethyl (AM) esters, are still used to label specific neuronal cell types in the hindbrain and the olfactory system. However, genetically encoded calcium indicators, such as aequorin and the GCaMP family of indicators, expressed in various tissues by the use of cell-specific promoters, are now the choice for most applications, including brain-wide imaging. Calcium imaging in the zebrafish has contributed greatly to our understanding of basic biological principles during development and adulthood, and the function of disease-related genes in a vertebrate system.

microRNA-206 modulates an Rtn4a/Cxcr4a/Thbs3a axis in newly forming somites to maintain and stabilize the somite boundary formation of zebrafish embryos

Although microRNA-206 (miR-206) is known to regulate proliferation and differentiation of muscle fibroblasts, the role of miR-206 in early-stage somite development is still unknown. During somitogenesis of zebrafish embryos, reticulon4a (rtn4a) is specifically repressed by miR-206. The somite boundary was defective, and actin filaments were crossing over the boundary in either miR-206-knockdown or rtn4a-overexpressed embryos. In these treated embryos, C-X-C motif chemokine receptor 4a (cxcr4a) was reduced, while thrombospondin 3a (thbs3a) was increased. The defective boundary was phenocopied in either cxcr4a-knockdown or thbs3a-overexpressed embryos. Repression of thbs3a expression by cxcr4a reduced the occurrence of the boundary defect. We demonstrated that cxcr4a is an upstream regulator of thbs3a and that defective boundary cells could not process epithelialization in the absence of intracellular accumulation of the phosphorylated focal adhesion kinase (p-FAK) in boundary cells. Therefore, in the newly forming somites, miR-206-mediated downregulation of rtn4a increases cxcr4a. This activity largely decreases thbs3a expression in the epithelial cells of the somite boundary, which causes epithelialization of boundary cells through mesenchymal-epithelial transition (MET) and eventually leads to somite boundary formation. Collectively, we suggest that miR-206 mediates a novel pathway, the Rtn4a/Cxcr4a/Thbs3a axis, that allows boundary cells to undergo MET and form somite boundaries in the newly forming somites of zebrafish embryos.

microRNAs in skeletal muscle development

A fundamental process during both embryo development and stem cell differentiation is the control of cell lineage determination. In developing skeletal muscle, many of the diffusible signaling molecules, transcription factors and more recently non-coding RNAs that contribute to this process have been identified. This has facilitated advances in our understanding of the molecular mechanisms underlying the control of cell fate choice. Here we will review the role of non-coding RNAs, in particular microRNAs (miRNAs), in embryonic muscle development and differentiation, and in satellite cells of adult muscle, which are essential for muscle growth and regeneration. Some of these short post-transcriptional regulators of gene expression are restricted to skeletal muscle, but their expression can also be more widespread. In addition, we discuss a few examples of long non-coding RNAs, which are numerous but much less well understood.

Genome-wide association study identifies candidate genes for piglet splay leg syndrome in different populations

BACKGROUND

Piglet splay leg syndrome (PSL) is one of the most frequent genetic defects, and can cause considerable economic loss in pig production. The present understanding of etiology and pathogenesis of PSL is poor. The current study focused on identifying loci associated with PSL through a genome-wide association study (GWAS) performed with the Illumina Porcine60 SNP Beadchip v2.0. The study was a case/control design with four pig populations (Duroc, Landrace, Yorkshire and one crossbred of Landrace × Yorkshire).

RESULT

After quality control of the genotyping data, 185 animals (73 cases, 112 controls) and 43,495 SNPs were retained for further analysis. Principal components (PCs) identified from the genomic kinship matrix were included in the statistical model for correcting the effect of population structure. Seven chromosome-wide significant SNPs were identified on Sus scrofa chromosome 1 (SSC1), SSC2 (2 SNPs), SSC7, SSC15 (2 SNPs) and SSC16 after strict Bonferroni correction. Four genes (HOMER1 and JMY on SSC2, ITGA1 on SSC16, and RAB32 on SSC1) related to muscle development, glycogen metabolism and mitochondrial dynamics were identified as potential candidate genes for PSL.

CONCLUSIONS

We identified seven chromosome-wide significant SNPs associated with PSL and four potential candidate genes for PSL. To our knowledge, this is the first pilot study aiming to identify the loci associated with PSL using GWAS. Further investigations and validations for those findings are encouraged.

Zebrafish and Medaka: new model organisms for modern biomedical research

Although they are primitive vertebrates, zebrafish (Danio rerio) and medaka (Oryzias latipes) have surpassed other animals as the most used model organisms based on their many advantages. Studies on gene expression patterns, regulatory cis-elements identification, and gene functions can be facilitated by using zebrafish embryos via a number of techniques, including transgenesis, in vivo transient assay, overexpression by injection of mRNAs, knockdown by injection of morpholino oligonucleotides, knockout and gene editing by CRISPR/Cas9 system and mutagenesis. In addition, transgenic lines of model fish harboring a tissue-specific reporter have become a powerful tool for the study of biological sciences, since it is possible to visualize the dynamic expression of a specific gene in the transparent embryos. In particular, some transgenic fish lines and mutants display defective phenotypes similar to those of human diseases. Therefore, a wide variety of fish model not only sheds light on the molecular mechanisms underlying disease pathogenesis in vivo but also provides a living platform for high-throughput screening of drug candidates. Interestingly, transgenic model fish lines can also be applied as biosensors to detect environmental pollutants, and even as pet fish to display beautiful fluorescent colors. Therefore, transgenic model fish possess a broad spectrum of applications in modern biomedical research, as exampled in the following review.

Mesoporous silica-coated upconversion nanocrystals for near infrared light-triggered control of gene expression in zebrafish

AIM

To develop a platform technology for photoactivation of gene expression in deep tissues.

MATERIALS & METHODS

Upconversion nanoparticles (UCNs) were synthesized from rare earth elements like Ytterbium, Yttrium and Thulium. The nanoparticles were then further coated with a layer of mesoporous silica and loaded with photomorpholinos or photocaged plasmids and tested in zebrafish. The UCNs were activated using safe near-infrared (NIR) light which in turn produced UV light locally to enable photoactivation in deep tissues.

RESULTS

Light-controlled gene knockdown was demonstrated in an in vivo model, namely zebrafish. UCNs loaded with photomorpholinos were used to knockdown a gene - ntl, which is essential for notochord formation and mesoderm patterning in zebrafish using NIR light. UCN-mediated light-controlled gene expression was also achieved by expressing GFP in tumor cells transplanted into adult zebrafish by irradiating the fish with NIR light. Apart from the delivery and control of genes, the UCNs were also used as imaging agents to image both zebrafish embryos and adult zebrafish. enabled excellent background-free, fluorescent imaging of both embryos and adult zebrafish.

CONCLUSION

This technique of controlling gene expression/knockdown through NIR using UCNs is a game changer in the field of genetic manipulation and has the potential of being an excellent, safe and easy to implement tool for developmental biologists to investigate the role of specific genes in development. However, this technique is not restricted to be used only in zebrafish and can be extended for use in other animal models and even for clinical use, in various gene therapy applications.

Noncoding RNAs, Emerging Regulators of Skeletal Muscle Development and Diseases

A healthy and independent life requires skeletal muscles to maintain optimal function throughout the lifespan, which is in turn dependent on efficient activation of processes that regulate muscle development, homeostasis, and metabolism. Thus, identifying mechanisms that modulate these processes is of crucial priority. Noncoding RNAs (ncRNAs), including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), have emerged as a class of previously unrecognized transcripts whose importance in a wide range of biological processes and human disease is only starting to be appreciated. In this review, we summarize the roles of recently identified miRNAs and lncRNAs during skeletal muscle development and pathophysiology. We also discuss several molecular mechanisms of these noncoding RNAs. Undoubtedly, further systematic understanding of these noncoding RNAs' functions and mechanisms will not only greatly expand our knowledge of basic skeletal muscle biology, but also significantly facilitate the development of therapies for various muscle diseases, such as muscular dystrophies, cachexia, and sarcopenia.

miR-487b, miR-3963 and miR-6412 delay myogenic differentiation in mouse myoblast-derived C2C12 cells

Background

Skeletal muscle differentiation is a multistep, complex pathway in which several important signaling molecules are involved. Recently, microRNAs (miRNAs), endogenous non-coding small RNAs that regulate mRNAs, have been proposed to be involved in skeletal muscle differentiation. In this study, we identified skeletal muscle differentiation-associated miRNAs by comparing miRNA expression profiles between C2C12 cells and Wnt4 over-expressing C2C12 cells (W4-08), which can spontaneously differentiate into myotubes.

Results

We identified miR-206, miR-133a, and miR-133b as up-regulated miRNAs and miR-487b, miR-3963 and miR-6412 as down-regulated miRNAs in differentiating cells. We focused on the down-regulated miRNAs because their functions were largely unknown. Transfection of mimics of these miRNAs into C2C12 cells resulted in significantly reduced expression of myogenic differentiation markers, including troponin T and myosin heavy chain fast type and slow type, but did not affect the expression of the myogenic transcription factors, MyoD and myogenin.

Conclusions

These miRNAs were characterized as new myogenic differentiation-associated miRNAs which may delay late myogenic differentiation or maturation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12860-015-0061-9) contains supplementary material, which is available to authorized users.