Roles of lncRNAs and circRNAs in regulating skeletal muscle development

Identification and functional analysis of circpdlim5a generated from pdlim5a gene splicing in the skeletal muscle of Japanese flounder (Paralichthys olivaceus)

Circular RNAs (circRNAs) are non-coding RNAs with endogenous regulatory functions, including regulating skeletal muscle development. However, its role in the development of skeletal muscle in Japanese flounder (Paralichthys olivaceus) is not clear. Therefore we screened a candidate circpdlim5a, which is derived from the gene pdlim5a, from the skeletal muscle transcriptome of Japanese flounder. We characterized circpdlim5a, which was more stable compared to the linear RNA pdlim5a. Distributional characterization of circpdlim5a showed that circpdlim5a was predominantly distributed in the nucleus and was highly expressed in the skeletal muscle of adult Japanese flounder (24 months). When we further studied the circpdlim5a function, we found that it inhibited the expression of proliferation and differentiation genes according to the over-expression experiment of circpdlim5a in myoblasts. We concluded that circpdlim5a may inhibit the proliferation and differentiation of myoblasts and thereby inhibit skeletal muscle development in Japanese flounder. This experiment provides information for the study of circRNAs by identifying circpdlim5a and exploring its function, and offers clues for molecular breeding from an epigenetic perspective.

Genome-wide characteristics and potential functions of circular RNAs from the embryo muscle development in Chengkou mountain chicken

The Chengkou mountain chicken, a native Chinese poultry breed, holds significant importance in the country's poultry sector due to its delectable meat and robust stress tolerance. Muscle growth and development are pivotal characteristics in poultry breeding, with muscle fiber development during the embryonic period crucial for determining inherent muscle growth potential. Extensive evidence indicates that non-coding RNAs (ncRNAs) play a regulatory role in muscle growth and development. Among ncRNAs, circular RNAs (circRNAs), characterized by a closed-loop structure, have been shown to modulate biological processes through the regulation of microRNAs (miRNAs). This study seeks to identify and characterize the spatiotemporal-specific expression of circRNAs during embryonic muscle development in Chengkou mountain chicken, and to construct the potential regulatory network of circRNAs-miRNA-mRNAs. The muscle fibers of HE-stained sections became more distinct, and their boundaries were more defined over time. Subsequent RNA sequencing of 12 samples from four periods generated 9,904 novel circRNAs, including 917 differentially expressed circRNAs. The weighted gene co-expression network analysis (WGCNA)-identified circRNA source genes significantly enriched pathways related to cell fraction, cell growth, and muscle fiber growth regulation. Furthermore, a competitive endogenous RNA (ceRNA) network constructed using combined data of present and previous differentially expressed circRNAs, miRNA, and mRNA revealed that several circRNA transcripts regulate MYH1D, MYH1B, CAPZA1, and PERM1 proteins. These findings provide insight into the potential pathways and mechanisms through which circRNAs regulate embryonic muscle development in poultry, a theoretical support for trait improvement in domestic chickens.

Non-coding CGG repeat expansion in LOC642361/NUTM2B-AS1 is associated with a phenotype of oculopharyngodistal myopathy

BACKGROUND

Oculopharyngodistal myopathy (OPDM) is a rare adult-onset neuromuscular disease, associated with CGG repeat expansions in the 5' untranslated region of LRP12, GIPC1, NOTCH2NLC and RILPL1. However, the genetic cause of a proportion of pathoclinically confirmed cases remains unknown.

METHODS

A total of 26 OPDM patients with unknown genetic cause(s) from 4 tertiary referral hospitals were included in this study. Clinical data and laboratory findings were collected. Muscle samples were observed by histological and immunofluorescent staining. Long-read sequencing was initially conducted in six patients with OPDM. Repeat-primed PCR was used to screen the CGG repeat expansions in LOC642361/NUTM2B-AS1 in all 26 patients.

RESULTS

We identified CGG repeat expansion in the non-coding transcripts of LOC642361/NUTM2B-AS1 in another two unrelated Chinese cases with typical pathoclinical features of OPDM. The repeat expansion was more than 70 times in the patients but less than 40 times in the normal controls. Both patients showed no leucoencephalopathy but one showed mild cognitive impairment detected by Montreal Cognitive Assessment. Rimmed vacuoles and p62-positive intranuclear inclusions (INIs) were identified in muscle pathology, and colocalisation of CGG RNA foci with p62 was also found in the INIs of patient-derived fibroblasts.

CONCLUSIONS

We identified another two unrelated cases with CGG repeat expansion in the long non-coding RNA of the LOC642361/NUTM2B-AS1 gene, presenting with a phenotype of OPDM. Our cases broadened the recognised phenotypic spectrum and pathogenesis in the disease associated with CGG repeat expansion in LOC642361/NUTM2B-AS1.

Bovine enhancer-regulated circSGCB acts as a ceRNA to regulate skeletal muscle development via enhancing KLF3 expression

Skeletal muscle growth and development in livestock and poultry play a pivotal role in determining the quality and yield of meat production. However, the mechanisms of myogenesis are remained unclear due to it finely regulated by a complex network of biological macromolecules. In this study, leveraging previous sequencing data, we investigated a differentially expressed circular RNA (circSGCB) present in fetal and adult muscle tissues among various ruminant species, including cattle, goat, and sheep. Our analysis revealed that circSGCB is a single exon circRNA, potentially regulated by an adjacent bovine enhancer. Functional analysis through loss-of-function tests demonstrated that circSGCB exerts inhibitory effects on bovine myoblast proliferation while promoting myocytes generation. Furthermore, we discovered that circSGCB primarily localizes to the cytoplasm, where it functions as a molecular sponge by binding to bta-miR-27a-3p. This interaction releases the mRNAs of KLF3 gene and further activates downstream functional pathways. In vivo, studies provided evidence that up-regulation of KLF3 contributes to muscle regeneration. These findings collectively suggest that circSGCB operates via a competing endogenous RNA (ceRNA) mechanism to regulate KLF3, thereby influencing myogenesis in ruminants and highlights it may as potential molecular targets for enhancing meat production in livestock and poultry industries.

A Circular RNA Generated from Nebulin (NEB) Gene Splicing Promotes Skeletal Muscle Myogenesis in Cattle as Detected by a Multi-Omics Approach

Cattle and the draught force provided by its skeletal muscle have been integral to agro-ecosystems of agricultural civilization for millennia. However, relatively little is known about the cattle muscle functional genomics (including protein coding genes, non-coding RNA, etc.). Circular RNAs (circRNAs), as a new class of non-coding RNAs, can be effectively translated into detectable peptides, which enlightened us on the importance of circRNAs in cattle muscle physiology function. Here, RNA-seq, Ribosome profiling (Ribo-seq), and peptidome data are integrated from cattle skeletal muscle, and detected five encoded peptides from circRNAs. It is further identified and functionally characterize a 907-amino acids muscle-specific peptide that is named circNEB-peptide because derived by the splicing of Nebulin (NEB) gene. This peptide localizes to the nucleus and cytoplasm and directly interacts with SKP1 and TPM1, key factors regulating physiological activities of myoblasts, via ubiquitination and myoblast fusion, respectively. The circNEB-peptide is found to promote myoblasts proliferation and differentiation in vitro, and induce muscle regeneration in vivo. These findings suggest circNEB-peptide is an important regulator of skeletal muscle regeneration and underscore the possibility that more encoding polypeptides derived by RNAs currently annotated as non-coding exist.

The emerging role of circRNAs on skeletal muscle development in economical animals

CircRNAs are a novel type of closed circular molecules formed through a covalent bond lacking a 5'cap and 3' end tail, which mainly arise from mRNA precursor. They are widely distributed in plants and animals and are characterized by stable structure, high conservativeness in cells or tissues, and showed the expression specificity at different stages of development in different tissues. CircRNAs have been gradually attracted wide attention with the development of RNA sequencing, which become a new research hotspot in the field of RNA. CircRNAs play an important role in gene expression regulation. Presently, the related circRNAs research in the regulation of animal muscle development is still at the initial stage. In this review, the formation, properties, biological functions of circRNAs were summarized. The recent research progresses of circRNAs in skeletal muscle growth and development from economic animals including livestock, poultry and fishes were introduced. Finally, we proposed a prospective for further studies of circRNAs in muscle development, and we hope our research could provide new ideas, some theoretical supports and helps for new molecular genetic markers exploitation and animal genetic breeding in future.

Whole-Transcriptome RNA Sequencing Uncovers the Global Expression Changes and RNA Regulatory Networks in Duck Embryonic Myogenesis

Duck meat is pivotal in providing high-quality protein for human nutrition, underscoring the importance of studying duck myogenesis. The regulatory mechanisms governing duck myogenesis involve both coding and non-coding RNAs, yet their specific expression patterns and molecular mechanisms remain elusive. To address this knowledge gap, we performed expression profiling analyses of mRNAs, lncRNAs, circRNAs, and miRNAs involved in duck myogenesis using whole-transcriptome RNA-seq. Our analysis identified 1733 differentially expressed (DE)-mRNAs, 1116 DE-lncRNAs, 54 DE-circRNAs, and 174 DE-miRNAs when comparing myoblasts and myotubes. A GO analysis highlighted the enrichment of DE molecules in the extracellular region, protein binding, and exocyst. A KEGG analysis pinpointed pathways related to ferroptosis, PPAR signaling, nitrogen metabolism, cell cycle, cardiac muscle contraction, glycerolipid metabolism, and actin cytoskeleton. A total of 51 trans-acting lncRNAs, including ENSAPLT00020002101 and ENSAPLT00020012069, were predicted to participate in regulating myoblast proliferation and differentiation. Based on the ceRNAs, we constructed lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA ceRNA networks involving five miRNAs (miR-129-5p, miR-133a-5p, miR-22-3p, miR-27b-3p, and let-7b-5p) that are relevant to myogenesis. Furthermore, the GO and KEGG analyses of the DE-mRNAs within the ceRNA network underscored the significant enrichment of the glycerolipid metabolism pathway. We identified five different DE-mRNAs, specifically ENSAPLG00020001677, ENSAPLG00020002183, ENSAPLG00020005019, ENSAPLG00020010497, and ENSAPLG00020017682, as potential target genes that are crucial for myogenesis in the context of glycerolipid metabolism. These five mRNAs are integral to ceRNA networks, with miR-107_R-2 and miR-1260 emerging as key regulators. In summary, this study provides a valuable resource elucidating the intricate interplay of mRNA-lncRNA-circRNA-miRNA in duck myogenesis, shedding light on the molecular mechanisms that govern this critical biological process.

A Role of Multi-Omics Technologies in Sheep and Goat Meats: Progress and Way Ahead

Sheep and goat meats are increasingly popular worldwide due to their superior nutritional properties and distinctive flavor profiles. In recent decades, substantial progress in meat science has facilitated in-depth examinations of ovine and caprine muscle development during the antemortem phase, as well as post-mortem changes influencing meat attributes. To elucidate the intrinsic molecular mechanisms and identify potential biomarkers associated with meat quality, the methodologies employed have evolved from traditional physicochemical parameters (such as color, tenderness, water holding capacity, flavor, and pH) to some cutting-edge omics technologies, including transcriptomics, proteomics, and metabolomics approaches. This review provides a comprehensive analysis of multi-omics techniques and their applications in unraveling sheep and goat meat quality attributes. In addition, the challenges and future perspectives associated with implementing multi-omics technologies in this area of study are discussed. Multi-omics tools can contribute to deciphering the molecular mechanism responsible for the altered the meat quality of sheep and goats across transcriptomic, proteomic, and metabolomic dimensions. The application of multi-omics technologies holds great potential in exploring and identifying biomarkers for meat quality and quality control, thereby promoting the optimization of production processes in the sheep and goat meat industry.

Functional role of circRNAs in osteogenesis: A review

The extracellular matrixes (ECM), as well as the microenvironmental signals, play an essential role in osteogenesis by regulating intercellular pathways. Recently, it has been demonstrated that a newly identified RNA, circular RNA, contributes to the osteogenesis process. Circular RNA (circRNA), the most recently identified RNA, is involved in the regulation of gene expression at transcription to translation levels. The dysregulation of circRNAs has been observed in several tumors and diseases. Also, various studies have shown that circRNAs expression is changed during osteogenic differentiation of progenitor cells. Therefore, understanding the role of circRNAs in osteogenesis might help the diagnosis as well as treatment of bone diseases such as bone defects and osteoporosis. In this review, circRNA functions and the related pathways in osteogenesis have been discussed.

Circular Intronic RNA circTTN Inhibits Host Gene Transcription and Myogenesis by Recruiting PURB Proteins to form Heterotypic Complexes

Muscle cell growth plays an important role in skeletal muscle development. Circular RNAs (circRNAs) have been proven to be involved in the regulation of skeletal muscle growth and development. In this study, we explored the effect of circTTN on myoblast growth and its possible molecular mechanism. Using C2C12 cells as a functional model, the authenticity of circTTN was confirmed by RNase R digestion and Sanger sequencing. Previous functional studies have showed that the overexpression of circTTN inhibits myoblast proliferation and differentiation. Mechanistically, circTTN recruits the PURB protein on the Titin (TTN) promoter to inhibit the expression of the TTN gene. Moreover, PURB inhibits myoblast proliferation and differentiation, which is consistent with circTTN function. In summary, our results indicate that circTTN inhibits the transcription and myogenesis of the host gene TTN by recruiting PURB proteins to form heterotypic complexes. This work may act as a reference for further research on the role of circRNA in skeletal muscle growth and development.

Biological functions of circRNAs and their advance on skeletal muscle development in bovine

The development of skeletal muscle in animals is a complex biological process, which are strictly and precisely regulated by many genes and non-coding RNAs. Circular RNA (circRNA) was found as a novel class of functional non-coding RNA with ring structure in recent years, which appears in the process of transcription and is formed by covalent binding of single-stranded RNA molecules. With the development of sequencing and bioinformatics analysis technology, the functions and regulation mechanisms of circRNAs have attracted great attention due to its high stability characteristics. The role of circRNAs in skeletal muscle development have been gradually revealed, where circRNAs were involved in various biological processes, such as proliferation, differentiation, and apoptosis of skeletal muscle cells. In this review, we summarized the current studies advance of circRNAs involved in skeletal muscle development in bovine, and hope to gain a deeper understanding of the functional roles of the circRNAs in muscle growth. Our results will provide some theoretical supports and great helps for the genetic breeding of this species, and aiming at improving bovine growth and development and preventing muscle diseases.

Recent advances and application value of circRNA in neuroblastoma

Neuroblastoma (NB) is children’s most prevalent solid malignant tumor, accounting for 15% of childhood cancer mortality. Non-coding RNA is important in NB pathogenesis. As a newly identified non-coding RNA, abnormal regulation (abnormal up-regulation or down-regulation) of the circRNAs expression is implicated in the tumorigenesis of various tumors, including NB. CircRNAs primarily regulate the expression of microRNA (miRNA) target genes by microRNA (miRNA) sponge adsorption. Clinical evidence suggests that the expression of certain circRNAs is associated with the prognosis and clinical features of NB and hence may be exploited as a biomarker or therapeutic target. This review examines circRNAs that have been demonstrated to play a function in NB.

Roles of super enhancers and enhancer RNAs in skeletal muscle development and disease

Skeletal muscle development is a multistep biological process regulated by a variety of myogenic regulatory factors, including MyoG, MyoD, Myf5, and Myf6 (also known as MRF4), as well as members of the FoxO subfamily. Differentiation and regeneration during skeletal muscle myogenesis contribute to the physiological function of muscles. Super enhancers (SEs) and enhancer RNAs (eRNAs) are involved in the regulation of development and diseases. Few studies have identified the roles of SEs and eRNAs in muscle development and pathophysiology. To develop approaches to enhance skeletal muscle mass and function, a more comprehensive understanding of the key processes underlying muscular diseases is needed. In this review, we summarize the roles of SEs and eRNAs in muscle development and disease through affecting of DNA methylation, FoxO subfamily, RAS-MEK signaling, chromatin modifications and accessibility, MyoD and cis regulating target genes. The summary could inform strategies to increase muscle mass and treat muscle-related diseases.

Circular RNAs in neuroblastoma: Pathogenesis, potential biomarker, and therapeutic target

Neuroblastoma (NB) is a common cancer in childhood responsible for 15 % of fatalities by pediatric cancers. Epigenetic factors play an important role in the pathogenesis of NB. Recently, it has been demonstrated that circular RNAs (circRNAs, ciRNAs), a newly identified class of non-coding RNAs, are also dysregulated in NB. CircRNAs mediate their functions by regulating gene expression mainly through microRNA (miRNA) sponging. The dysregulation (abnormal upregulation or downregulation) of circRNAs is involved in tumorigenesis of a variety of tumors including NB. It seems that the expression of some circRNAs is correlated with NB prognosis and clinical features. CircRNAs might be favorable as a diagnostic/prognostic biomarker and therapeutic target. However, due to the lack of studies, it is difficult to make a conclusion regarding the clinical benefits of circRNAs. In this review, we discussed the circRNAs that experimentally have been proved to be dysregulated in NB tissues and cancer cells.

Regulation of Non-Coding RNA in the Growth and Development of Skeletal Muscle in Domestic Chickens

Chicken is the most widely consumed meat product worldwide and is a high-quality source of protein for humans. The skeletal muscle, which accounts for the majority of chicken products and contains the most valuable components, is tightly correlated to meat product yield and quality. In domestic chickens, skeletal muscle growth is regulated by a complex network of molecules that includes some non-coding RNAs (ncRNAs). As a regulator of muscle growth and development, ncRNAs play a significant function in the development of skeletal muscle in domestic chickens. Recent advances in sequencing technology have contributed to the identification and characterization of more ncRNAs (mainly microRNAs (miRNAs), long non-coding RNAs (LncRNAs), and circular RNAs (CircRNAs)) involved in the development of domestic chicken skeletal muscle, where they are widely involved in proliferation, differentiation, fusion, and apoptosis of myoblasts and satellite cells, and the specification of muscle fiber type. In this review, we summarize the ncRNAs involved in the skeletal muscle growth and development of domestic chickens and discuss the potential limitations and challenges. It will provide a theoretical foundation for future comprehensive studies on ncRNA participation in the regulation of skeletal muscle growth and development in domestic chickens.

Identification and functional analysis of circRNAs in the skeletal muscle of juvenile and adult largemouth bass (Micropterus salmoides)

Circular RNA (circRNA) is a novel emerging type of endogenous regulatory non-coding RNA molecules with a covalent closed-loop configuration, which exerts important functions in multiple biological processes. CircRNAs are known to regulate gene expression as functional regulators interacting with miRNAs by sponge, which have been reported to regulate skeletal muscle development. Nevertheless, the information of circRNAs involved in regulating muscle growth and development in fish is largely unknown. Here, we first identified 312 and 511 circRNAs in skeletal muscle of juvenile and adult largemouth bass (LMB) using RNA sequencing, respectively. The differentially expressed circRNAs (DE-circRNAs) analysis showed that there are 44 DE-circRNAs at two different skeletal muscle growth stages. Six circRNAs were chosen randomly and their relative expression levels in juvenile and adult LMB were confirmed by real-time PCR, indicating that these circRNAs were existed authenticity. In addition, Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis showed that these hose genes (their linear mRNAs) of DE-circRNAs were mainly enriched in the regulation of actin cytoskeleton signaling pathways. The circRNA-miRNA interaction regulatory networks indicated that one circRNA can regulate one or more miRNA. For instance, more than 30 miRNAs were regulated by two circRNAs (circRNA389 and circRNA399). Of them, the muscle-related miRNAs including the let-7 family, miR-133 and miR-26 and so on were found acting as miRNAs sponge regulated by circRNAs, indicating the roles of circRNAs in regulating muscle growth-related genes expression. Overall, these findings will not only broaden our understanding of circRNAs regulation mechanisms underlying muscle growth and development in LMB but also provides a novel clue for further functional research in carnivorous fish genetic breeding.

LncR-133a Suppresses Myoblast Differentiation by Sponging miR-133a-3p to Activate the FGFR1/ERK1/2 Signaling Pathway in Goats

Long noncoding RNAs (lncRNAs) are involved in a variety of biological processes and illnesses. While a considerable number of lncRNAs have been discovered in skeletal muscle to far, their role and underlying processes during myogenesis remain mostly unclear. In this study, we described a new functional lncRNA named lncR-133a. Gene overexpression and interference studies in goat skeletal muscle satellite cells (MuSCs) were used to establish its function. The molecular mechanism by which lncR-133a governs muscle differentiation was elucidated primarily using quantitative real-time PCR (qRT-PCR), Western blotting, dual-luciferase activity assays, RNA immunoprecipitation, biotin-labeled probe, and RNA fluorescence in situ hybridization analyses. LncR-133a was found to be substantially expressed in longissimus thoracis et lumborum muscle, and its expression levels changed during MuSC differentiation in goats. We validated that lncR-133a suppresses MuSC differentiation in vitro. Dual-luciferase reporter screening, Argonaute 2 (AGO2) RNA immunoprecipitation assays, biotin-labeled lncR-133a capture, and fluorescence in situ hybridization showed that lncR-133a interacted with miR-133a-3p. Additionally, miR-133a-3p facilitated MuSC differentiation, but lncR-133a reversed this effect. The luciferase reporter assay and functional analyses established that miR-133a-3p directly targets fibroblast growth factor receptor 1 (FGFR1). Moreover, lncR-133a directly reduced miR-133a-3p’s capacity to suppress FGFR1 expression, and positively regulated the phosphorylation of extracellular signal-regulated kinase 1/2 (ERK1/2). In summary, our results suggested that lncR-133a suppresses goat muscle differentiation by targeting miR-133a-3p and activating FGFR1/ERK1/2 signaling pathway.

CircUBE2Q2 promotes differentiation of cattle muscle stem cells and is a potential regulatory molecule of skeletal muscle development

Background

The growth and development of muscle stem cells (MuSCs) are significant events known to affect muscle plasticity, disease, meat production, and meat quality, which involves the types and functions of mRNA and non-coding RNA. Here, MuSCs were cultured from Guangxi fetal cattle. RNA sequencing was used to analyze the RNA expression of mRNA and non-coding RNAs during the cell proliferation and differentiation phases.

Results

Two thousand one hundred forty-eight mRNAs and 888 non-coding RNAs were differentially expressed between cell proliferation and differentiation phases, including 113 miRNAs, 662 lncRNAs, and 113 circRNAs. RT-qPCR verified the differential expression levels of mRNAs and non-coding RNAs, and the differentially expressed circUBE2Q2 was subsequently characterized. Expression profile analysis revealed that circUBE2Q2 was abundant in muscle tissues and intramuscular fat. The expression of cricUBE2Q2 was also significantly upregulated during MuSCs myogenic differentiation and SVFs adipogenic differentiation and decreased with age in cattle muscle tissue. Finally, the molecular mechanism of circUBE2Q2 regulating MuSCs function that affects skeletal muscle development was investigated. The results showed that circUBE2Q2 could serve as a sponge for miR-133a, significantly promoting differentiation and apoptosis of cultured MuSCs, and inhibiting proliferation of MuSCs.

Conclusions

CircUBE2Q2 is associated with muscle growth and development and induces MuSCs myogenic differentiation through sponging miR-133a. This study will provide new clues for the mechanisms by which mRNAs and non-coding RNAs regulate skeletal muscle growth and development, affecting muscle quality and diseases.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08518-4.

circPTPN4 regulates myogenesis via the miR-499-3p/NAMPT axis

Background

Circular RNAs (circRNAs) are a novel class of endogenous ncRNA, which widely exist in the transcriptomes of different species and tissues. Recent studies indicate important roles for circRNAs in the regulation of gene expression by acting as competing endogenous RNAs (ceRNAs). However, the specific role of circRNAs in myogenesis is still poorly understood. In this study, we attempted to systematically identify the circRNAs involved in myogenesis and analyze the biological functions of circRNAs in chicken skeletal muscle development.

Results

In total, 532 circRNAs were identified as being differentially expressed between pectoralis major (PEM) and soleus (SOL) in 7-week-old Xinghua chicken. Among them, a novel circRNA (novel_circ_002621), generated by PTPN4 gene, was named circPTPN4 and identified. circPTPN4 is highly expressed in skeletal muscle, and its expression level is upregulated during myoblast differentiation. circPTPN4 facilitates the proliferation and differentiation of myoblast. Moreover, circPTPN4 suppresses mitochondria biogenesis and activates fast-twitch muscle phenotype. Mechanistically, circPTPN4 can function as a ceRNA to regulate NAMPT expression by sponging miR-499-3p, thus participating in AMPK signaling.

Conclusions

circPTPN4 functions as a ceRNA to regulate NAMPT expression by sponging miR-499-3p, thus promoting the proliferation and differentiation of myoblast, as well as activating fast-twitch muscle phenotype.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-021-00664-1.

Circular RNA hsa_circ_0000073 Enhances Osteosarcoma Cells Malignant Behavior by Sponging miR-1252-5p and Modulating CCNE2 and MDM2

Objective: An increasing number of studies have demonstrated that circular RNAs (circRNAs) are involved in tumor progression. However, the role of hsa_circ_0000073 in osteosarcoma (OS) is still not fully elucidated.

Methods: Quantitative reverse transcription-polymerase chain reaction or Western blot was used to detect the gene expression. GeneChip analysis, bioinformatics, luciferase reporter, and RNA immunoprecipitation assays were adopted to predict and verify the relationships between genes. Counting Kit-8 Assay, clone formation assay, wound-healing assay, transwell assays, cell cycle assays, and in vivo tumorigenesis were used to evaluate cell function.

Results: hsa_circ_0000073 was highly expressed in OS cell lines and could promote OS progression, including proliferation, migration, invasion, and cell cycle in vitro as well as tumorigenesis in vivo. Mechanically, hsa_circ_0000073 could readily downregulate the expression of CCNE2 and MDM2 through miR-1252-5p. Rescue experiments validated miR-1252-5p mimics, or CCNE2/MDM2 short hairpin RNA could reverse the hsa_circ_0000073 overexpressing-induced impairment of malignant tumor behavior.

Conclusion: hsa_circ_0000073 functions as a tumor promoter in OS to increase malignant tumor behavior through sponging miR-1252-5p and regulating CCNE2 and MDM2 expression, which could be a novel target for OS therapy.

LncRNAs as a new regulator of chronic musculoskeletal disorder

Objectives

In recent years, long non‐coding RNAs (lncRNAs) have been found to play a role in the occurrence, progression and prognosis of chronic musculoskeletal disorders.

Design and methods

Literature exploring on PubMed was conducted using the combination of keywords 'LncRNA' and each of the following: 'osteoarthritis', 'rheumatoid arthritis', 'osteoporosis', 'osteogenesis', 'osteoclastogenesis', 'gout arthritis', 'Kashin‐Beck disease', 'ankylosing spondylitis', 'cervical spondylotic myelopathy', 'intervertebral disc degeneration', 'human muscle disease' and 'muscle hypertrophy and atrophy'. For each disorder, we focused on the publications in the last five years (5/1/2016‐2021/5/1, except for Kashin‐Beck disease). Finally, we excluded publications that had been reported in reviews of various musculoskeletal disorders during the last three years. Here, we summarized the progress of research on the role of lncRNA in multiple pathological processes during musculoskeletal disorders.

Results

LncRNAs play a crucial role in regulating downstream gene expression and maintaining function and homeostasis of cells, especially in chondrocytes, synovial cells, osteoblasts, osteoclasts and skeletal muscle cells.

Conclusions

Understanding the mechanisms of lncRNAs in musculoskeletal disorders may provide promising strategies for clinical practice.

The Expression Profiles of mRNAs and lncRNAs in Buffalo Muscle Stem Cells Driving Myogenic Differentiation

Buffalo breeding has become an important branch of the beef cattle industry. Hence, it is of great significance to study buffalo meat production and meat quality. However, the expression profiles of mRNA and long non-coding RNAs (lncRNA) molecules in muscle stem cells (MuSCs) development in buffalo have not been explored fully. We, therefore, performed mRNA and lncRNA expression profiling analysis during the proliferation and differentiation phases of MuSCs in buffalo. The results showed that there were 4,820 differentially expressed genes as well as 12,227 mRNAs and 1,352 lncRNAs. These genes were shown to be enriched in essential biological processes such as cell cycle, p53 signaling pathway, RNA transport and calcium signaling pathway. We also identified a number of functionally important genes, such as MCMC4, SERDINE1, ISLR, LOC102394806, and LOC102403551, and found that interference with MYLPF expression significantly inhibited the differentiation of MuSCs. In conclusion, our research revealed the characteristics of mRNA and lncRNA expression during the differentiation of buffalo MuSCs. This study can be used as an important reference for the study of RNA regulation during muscle development in buffalo.

Long non-coding RNAs and their involvement in bipolar disorders

Non-coding RNAs (nc-RNAs) can be defined as RNA molecules that are not translated into proteins. Although the functional meaning of many nc-RNAs remains still to be verified, several of these molecules have a clear biological importance, which goes from translation of mRNAs to DNA replication. Indeed, regulatory nc-RNAs can be classified into two groups: short non-coding RNAs (sncRNAs) and long-non coding RNAs (lncRNAs). In the last years, lncRNAs have gained increasing importance in the study of gene regulation, helping authors understand the molecular mechanisms underlying cellular physiology and pathology. LncRNAs are greater than 200 bp and accumulate in nucleus, cytoplasm and exosomes with high tissue specificity, acting in cis or in trans in order to exert enhancer or silencer modulation on gene expression. Such regulatory features, which are widespread in human cells and tissues, can be disrupted in several morbid states. Recent evidences may suggest a disruption of lncRNAs in bipolar disorders, a cluster of severe, chronic and disabling psychiatric diseases, which are characterized by major depressive states cyclically alternating with manic episodes. Here, the authors reviewed genes, classification, biogenesis, structures, functions and databases regarding lncRNAs, and also focused on bipolar disorders, in which some lncRNAs, especially those involved in inflammation and neuronal development, has reported to be dysregulated.

EFFECTS OF PUERARIA LOBATA COMBINED WITH HIGH-INTENSITY INTERMITTENT TRAINING ON SKELETAL MUSCLE QUALITY AND GENE EXPRESSION

ABSTRACT Extraction of effective components from Pueraria lobata has important value for skeletal muscle quality and gene expression. The improvement effect of traditional high-intensity intermittent training on skeletal muscle has not been obvious, and it is difficult to guarantee the properties of some volatiles. Based on this, this paper analyzes the effect of high-intensity intermittent training on skeletal muscle quality and gene expression in Pueraria lobata. Based on a brief summary of extraction of Pueraria lobata, status of research on the pharmaceutical components of Pueraria lobata was summarized. Different specimens of Pueraria lobata were selected as research objects, and the process of high-intensity intermittent training was designed. High-intensity intermittent training, solvent extraction and water solvent extraction were combined together to design the fixed-bed continuous extraction scheme. According to the influence of Pueraria lobata on skeletal muscle quality, the influence of intermittent training on skeletal muscle quality was analyzed. The extraction results showed that Pueraria lobata combined with high-intensity intermittent training can effectively improve the content of skeletal muscle and ensure the effective expression of skeletal muscle gene.

Sp1-Mediated circRNA circHipk2 Regulates Myogenesis by Targeting Ribosomal Protein Rpl7

Circular RNAs (circRNAs) represent a class of covalently closed single-stranded RNA molecules that are emerging as essential regulators of various biological processes. The circRNA circHipk2 originates from exon 2 of the Hipk2 gene in mice and was reported to be involved in acute promyelocytic leukemia and myocardial injury. However, the functions and mechanisms of circHipk2 in myogenesis are largely unknown. Here, to deepen our knowledge about the role of circHipk2, we studied the expression and function of circHipk2 during skeletal myogenesis. We found that circHipk2 was mostly distributed in the cytoplasm, and dynamically and differentially expressed in various myogenesis systems in vitro and in vivo. Functionally, overexpression of circHipk2 inhibited myoblast proliferation and promoted myotube formation in C2C12 cells, whereas the opposite effects were observed after circHipk2 knockdown. Mechanistically, circHipk2 could directly bind to ribosomal protein Rpl7, an essential 60S preribosomal assembly factor, to inhibit ribosome translation. In addition, we verified that transcription factor Sp1 directly bound to the promoter of circHipk2 and affected the expression of Hipk2 and circHipk2 in C2C12 myoblasts. Collectively, these findings identify circHipk2 as a candidate circRNA regulating ribosome biogenesis and myogenesis proliferation and differentiation.

Global transcriptomic analysis reveals Lnc-ADAMTS9 exerting an essential role in myogenesis through modulating the ERK signaling pathway

Background

Long non-coding RNAs (lncRNAs) are emerging key regulators involved in a variety of biological processes such as cell differentiation and development. The balance between myogenesis and adipogenesis is crucial for skeletal muscle homeostasis in humans and meat quality in farm animals. The present study aimed to reveal the global transcriptomic profiles of adipogenic (Adi-) and myogenic (Myo-) precursors derived from porcine skeletal muscle and identify lncRNAs involved in the modulation of myogenesis homeostasis in porcine skeletal muscle.

Results

In this study, a total of 655 novel individual lncRNAs including differentially expressed 24 lncRNAs, and 755 differentially expressed mRNAs were identified (fold change ≥2 or ≤ 0.5 and adjusted P < 0.05). Integrated results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis accompanied by the variation of intracellular Ca²⁺ concentration highlighted Lnc-ADAMTS9 involved in the modulation of myogenesis homeostasis in porcine skeletal muscle. Although Lnc-ADAMTS9 knock-down did not alter the mRNA expression of ADAMTS9, we demonstrated that Lnc-ADAMTS9 can promote myogenic proliferation and myogenic differentiation of myogenic precursors through inhibiting the ERK/MAPK signaling pathway.

Conclusion

We deciphered a comprehensive catalog of mRNAs and lncRNAs that might be involved in the regulation of myogenesis and adipogenesis homeostasis in the skeletal muscle of pigs. The Lnc-ADAMTS9 exerts an essential role in myogenesis through the ERK signaling pathway.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-020-00524-4.

Circular RNA hsa_circ_0000658 inhibits osteosarcoma cell proliferation and migration via the miR-1227/IRF2 axis

Osteosarcoma (OS) is the most frequently occurring bone cancer. Circular RNAs (circRNAs) have been shown to exert pivotal impact in modulation of gene expression, but their roles in OS are still not fully understood. In this study, we analysed the role of circ‐0000658 in OS. Thereafter, molecular techniques such as Western blot, qRT‐PCR, RNA‐binding protein immunoprecipitation and Dual‐Luciferase reporter assays were implemented to investigate the role of circ‐0000658/miR‐1227/interferon regulatory factor‐2 (IRF2) axis in OS. Eventually, the impact of circ‐0000658 on tumour growth and metastasis was observed in a xenograft mouse model. The results of this study revealed that circ‐0000658 exhibits low levels in OS tissues and cell lines. Moreover, circ‐0000658 repression promoted cell cycle, proliferation, invasion and migration but inhibited the apoptosis of OS cells. Researches have previously shown that circ‐0000658 contains a binding site for miR‐1227 and thus can abundantly sponge miR‐1227 to up‐regulate the expression of its target gene IRF2. Moreover, both inhibition of miR‐1227 and overexpression of IRF2 reversed cell proliferation and invasion, which was triggered by circ‐0000658 repression. Conclusively, circ‐0000658 modulates biological function of OS cells through the miR‐1227/IRF2 axis. Therefore, circ‐0000658 might act as a possible novel therapeutic target for the treatment of OS.

Regulation of Skeletal Muscle Atrophy in Cachexia by MicroRNAs and Long Non-coding RNAs

Skeletal muscle atrophy is a common complication of cachexia, characterized by progressive bodyweight loss and decreased muscle strength, and it significantly increases the risks of morbidity and mortality in the population with atrophy. Numerous complications associated with decreased muscle function can activate catabolism, reduce anabolism, and impair muscle regeneration, leading to muscle wasting. microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), types of non-coding RNAs, are important for regulation of skeletal muscle development. Few studies have specifically identified the roles of miRNAs and lncRNAs in cellular or animal models of muscular atrophy during cachexia, and the pathogenesis of skeletal muscle wasting in cachexia is not entirely understood. To develop potential approaches to improve skeletal muscle mass, strength, and function, a more comprehensive understanding of the known key pathophysiological processes leading to muscular atrophy is needed. In this review, we summarize the known miRNAs, lncRNAs, and corresponding signaling pathways involved in regulating skeletal muscle atrophy in cachexia and other diseases. A comprehensive understanding of the functions and mechanisms of miRNAs and lncRNAs during skeletal muscle wasting in cachexia and other diseases will, therefore, promote therapeutic treatments for muscle atrophy.

Circular RNAs in Embryogenesis and Cell Differentiation With a Focus on Cancer Development

In the recent years thousands of non-coding RNAs have been identified, also thanks to highthroughput sequencing technologies. Among them, circular RNAs (circRNAs) are a well-represented class characterized by the high sequence conservation and cell type specific expression in eukaryotes. They are covalently closed loops formed through back-splicing. Recently, circRNAs were shown to regulate a variety of cellular processes functioning as miRNA sponges, RBP binding molecules, transcriptional regulators, scaffold for protein translation, as well as immune regulators. A growing number of studies are showing that deregulated expression of circRNAs plays important and decisive actions during the development of several human diseases, including cancer. The research on their biogenesis and on the various molecular mechanisms in which they are involved is going very fast, however, there are still few studies that address their involvement in embryogenesis and eukaryotic development. This review has the intent to describe the most recent progress in the study of the biogenesis and molecular activities of circRNAs providing insightful information in the field of embryogenesis and cell differentiation. In addition, we describe the latest research on circRNAs as novel promising biomarkers in diverse types of tumors.