Search Results (195)

Circular RNA (CircRNA) can regulate gene expression through acting as a competitive endogenous RNA (ceRNA), thus becoming involved in various biological processes. However, little was known about the role of circRNA in the formation of meat quality in pigs. Here, circRNAs were first characterized in muscles with differential meat quality and myofiber composition, longissimus thoracis, and semitendinosus muscles, with RNA-sequencing (RNA-seq). A total of 1126 differentially expressed circRNAs were identified. Among them, Circ-06958 is highly expressed in both muscles. Circ-06958 originated from Long-chain acyl-CoA synthetase 1 (ACSL1), a gene involved in muscle development. Circ-06958 was then characterized experimentally for the first time. Next, it was revealed that Circ-06958 increased proliferation of muscle cells, including porcine skeletal muscle satellite cells (PMSCs) and C2C12 myoblasts, by promoting cell cycle progression. Circ-06958 was mainly localized in cytoplasm, indicating it can function as a ceRNA. A regulatory axis Circ-06958/miR-31-5p/Adenylate Kinase 4 (AK4) axis was constructed with molecular biology techniques. Afterward, it was shown that miR-31-5p inhibited cell proliferation by affecting cell cycle progression in the two cells, while AK4 increased it. We made it clear that Circ-06958 promoted muscle cell proliferation via the miR-31-5p/AK4 axis. The results will contribute to further revealing the mechanisms through which meat quality generates. Full article

Skeletal muscle development is a critical economic trait in livestock, governed by myogenic satellite cell regulation. Integrins mediate mechanical anchorage to the ECM and enable ECM–intracellular signaling. CIB2, as an EF-hand-domain protein involved in mechanotransduction, shows significant developmental regulation in goat muscle. Although the role of CIB2 in skeletal muscle growth is poorly characterized, we observed pronounced developmental upregulation of IB2 in postnatal goat muscle. CIB2 expression increased >20-fold by postnatal day 90 (P90) compared to P1, sustaining elevation through P180 (p < 0.05). Functional investigations indicated that siRNA-mediated knockdown of CIB2 could inhibit myoblast proliferation by inducing S-phase arrest (p < 0.05) and downregulating the expression of CDK4/Cyclin D/E. Simultaneously, CIB2 interference treatment was found to decrease the proliferative activity of goat myogenic satellite cells, yet it significantly promoted differentiation by upregulating the expression of MyoD/MyoG/MyHC (p < 0.01). Mechanistically, CTCF was identified as a transcriptional repressor binding to an intragenic region of the CIB2 gene locus (ChIP enrichment: 2.3-fold, p < 0.05). Knockdown of CTCF induced upregulation of CIB2 (p < 0.05). RNA-seq analysis established CIB2 as a calcium signaling hub: its interference activated IL-17/TNF and complement cascades, while overexpression suppressed focal adhesion/ECM–receptor interactions and enriched neuroendocrine pathways. Collectively, this study identifies the CTCF-CIB2–integrin α7β1–PI3K/AKT axis as a novel molecular mechanism that regulates the balance of myogenic fate in goats. These findings offer promising targets for genomic selection and precision breeding strategies aimed at enhancing muscle productivity in ruminants. Full article

Prolonged high-dose administration of synthetic glucocorticoids (GCs) leads to limb muscle atrophy and weakness, yet its underlying mechanisms remain incompletely understood. Muscle fibers and muscle satellite cells (MSCs) are essential for skeletal muscle development and associated pathologies. This study demonstrates that dexamethasone (Dex) induced MSC-derived extracellular vesicles (EVs) impair myogenesis in muscle fiber-like cells (MFLCs) via inducible nitric oxide synthase (iNOS) suppression. High-throughput sequencing revealed a marked upregulation of miR-335-5p in MSC-derived EVs following Dex treatment. Mechanistically, EV miR-335-5p targeted MAPK11, leading to iNOS downregulation and subsequent UPS activation in MFLCs, which directly promoted muscle protein degradation. Collectively, our findings identify the EV miR-335-5p/MAPK11/iNOS axis as a critical mediator of GC-induced muscle atrophy, offering novel insights into therapeutic strategies targeting EV-mediated signaling in muscle wasting disorders. Full article

Prenatal and postnatal skeletal muscle development in ruminants is coordinated by interactions between genetic, nutritional, epigenetic, and endocrine factors. This review focuses on the influence of maternal nutrition during gestation on fetal myogenesis, satellite cell dynamics, and myogenic regulatory factors expression, including MYF5, MYOD1, and MYOG. Studies in sheep and cattle indicate that nutrient restriction or overnutrition alters muscle fiber number, the cross-sectional area, and the transcriptional regulation of myogenic genes in offspring. Postnatally, muscle hypertrophy is primarily mediated by satellite cells, which are activated via PAX7, MYOD, and MYF5, and regulated through mechanisms such as CARM1-induced chromatin remodeling and miR-31-mediated mRNA expression. Hormonal signaling via the GH–IGF1 axis and thyroid hormones further modulate satellite cell proliferation and protein accretion. Genetic variants, such as myostatin mutations in Texel sheep and Belgian Blue cattle, enhance muscle mass but may compromise reproductive efficiency. Nutritional interventions, including the plane of nutrition, supplementation strategies, and environmental stressors such as heat and stocking density, significantly influence muscle fiber composition and carcass traits. This review provides a comprehensive overview of skeletal muscle programming in ruminants, tracing the developmental trajectory from progenitor cell differentiation to postnatal growth and maturation. These insights underscore the need for integrated approaches combining maternal diet optimization, molecular breeding, and precision livestock management to enhance muscle growth, meat quality, and production sustainability in ruminant systems. Full article

Investigations of endogenous plant circular RNAs (circRNAs) in several plant species have revealed changes in their circular RNA profiles in response to biotic and abiotic stresses. Recently, circRNAs have emerged as critical regulators of gene expression. The destructive impacts on agriculture due to plant viral infections necessitate better discernment of the involvement of plant circRNAs during viral infection. However, few such studies have been conducted hitherto. Sobemoviruses cause great economic impacts on important crops such as rice, turnip, alfalfa, and wheat. Our current study investigates the dynamics of plant circRNA profiles in the host Arabidopsis thaliana (A. thaliana) during infections with the sobemoviruses Turnip rosette virus (TRoV) and Rice yellow mottle virus (RYMV), as well as the small circular satellite RNA of the Lucerne transient streak virus (scLTSV), focusing on circRNA dysregulation in the host plants and its potential implications in triggering plant cellular defense responses. Towards this, two rounds of deep sequencing were conducted on the RNA samples obtained from infected and uninfected plants followed by the analysis of circular RNA profiles using RNA-seq and extensive bioinformatic analyses. We identified 760 circRNAs, predominantly encoded in exonic regions and enriched in the chloroplast chromosome, suggesting them as key sites for circRNA generation during viral stress. Gene ontology (GO) analysis indicated that these circRNAs are mostly associated with plant development and protein binding, potentially influencing the expression of their host genes. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed photosynthesis as the most affected pathway. Interestingly, the non-coding exogenous scLTSV specifically induced several circRNAs, some of which contain open reading frames (ORFs) capable of encoding proteins. Our biochemical assays demonstrated that transgenic expression of scLTSV in A. thaliana enhanced resistance to TRoV, suggesting a novel strategy for improving plant viral resistance. Our results highlight the complexity of circRNA dynamics in plant–virus interactions and offer novel insights into potential circRNA-based strategies for enhancing plant disease resistance by modulating the differential expression of circRNAs. Full article

Background: Duchenne muscular dystrophy (DMD), which affects 1 in 3500 to 5000 newborn boys worldwide, is characterized by progressive skeletal muscle weakness and degeneration. The reduced muscle regeneration capacity presented by patients is associated with increased fibrosis. Satellite cells (SCs) are skeletal muscle stem cells that play an important role in adult muscle maintenance and regeneration. The absence or mutation of dystrophin in DMD is hypothesized to impair SC asymmetric division, leading to cell cycle arrest. Methods: To overcome the limited availability of biopsies from DMD patients, we used our 3D skeletal muscle organoid (SMO) system, which delivers a stable population of myogenic progenitors (MPs) in dormant, activated, and committed stages, to perform SMO cultures using three DMD patient-derived iPSC lines. Results: The results of scRNA-seq analysis of three DMD SMO cultures versus two healthy, non-isogenic, SMO cultures indicate reduced MP populations with constant activation and differentiation, trending toward embryonic and immature myotubes. Mapping our data onto the human myogenic reference atlas, together with primary SC scRNA-seq data, indicated a more immature developmental stage of DMD organoid-derived MPs. DMD fibro-adipogenic progenitors (FAPs) appear to be activated in SMOs. Conclusions: Our organoid system provides a promising model for studying muscular dystrophies in vitro, especially in the case of early developmental onset, and a methodology for overcoming the bottleneck of limited patient material for skeletal muscle disease modeling. Full article

Begomoviruses infect many crops and weeds globally, especially in the tropical and subtropical regions, where there are waves of epidemics. These begomovirus epidemics are frequently associated with three DNA satellites: betasatellites, alphasatellites, and deltasatellites. Except for the origin of replication, these satellites show no sequence identity with the helper begomovirus. Alphasatellites and betasatellites encode the $\mathsf{\alpha }$-Rep and βC1 proteins, respectively, while deltasatellites encode no proteins. $\mathsf{\alpha }$-Rep, which functions like the Rep of the helper begomoviruses, ensures alphasatellite replication autonomy, while betasatellites and deltasatellites depend wholly on the helper virus for replication. The betasatellite βC1 protein is a pathogenicity determinant and suppressor of RNA silencing. The associations between satellites and helper viruses vary, depending on the virus and the host, and the roles of these satellites in disease development are an active area of investigation. This review highlights current information on the role of DNA satellites in begomovirus diseases and examines commonalities and differences between and within these satellites under prevailing conditions. Furthermore, two episomes, SEGS-1 and SEGS-2, associated with cassava mosaic geminiviruses, and their possible status as DNA satellites are discussed. DNA satellites are a major factor in begomovirus infections, which are a major constraint to crop production, especially in tropical and subtropical regions. Thus, areas for future research efforts, as well as implications in the biotechnological management of these viruses, are discussed in this review. Full article

Recent studies on myogenic satellite cells (SCs) in Duchenne muscular dystrophy (DMD) documented altered division capacities and impaired regeneration potential of SCs in DMD patients and animal models. It remains unknown, however, if SC-intrinsic effects trigger these deficiencies at pre-contractile stages of myogenesis rather than resulting from the pathologic environment. In this study, we isolated SCs from a porcine DMD model and age-matched wild-type (WT) piglets for comprehensive analysis. Using immunofluorescence, differentiation assays, traction force microscopy (TFM), RNA-seq, and label-free proteomic measurements, SCs behavior was characterized, and molecular changes were investigated. TFM revealed significantly higher average traction forces in DMD than WT SCs (90.4 ± 10.5 Pa vs. 66.9 ± 8.9 Pa; p = 0.0018). We identified 1390 differentially expressed genes and 1261 proteins with altered abundance in DMD vs. WT SCs. Dysregulated pathways uncovered by gene ontology (GO) enrichment analysis included sarcomere organization, focal adhesion, and response to hypoxia. Multi-omics factor analysis (MOFA) integrating transcriptomic and proteomic data, identified five factors accounting for the observed variance with an overall higher contribution of the transcriptomic data. Our findings suggest that SC impairments result from their inherent genetic abnormality rather than from environmental influences. The observed biological changes are intrinsic and not reactive to the pathological surrounding of DMD muscle. Full article

Phlox are ornamentals of great decorative value, grown throughout the world for their attractive flowers. Phlox cultivar collections at the Tsitsin Main Botanical Garden and the Botanical Garden of Lomonosov Moscow State University (both Moscow, Russia) were surveyed for virus diseases. Tobacco streak ilarvirus (TSV), beet ringspot nepovirus (BRSV), and BRSV satellite RNA (satRNA) were first detected in phlox when viromes of symptomatic Phlox paniculata plants were studied using high-throughput sequencing. The nearly complete genomes of three TSV and BRSV isolates and two BRSV satRNAs were assembled and characterized. TSV isolates shared 96.9–99.7% nucleotide sequence identity and were 82.2–89.1% identical to their closest relatives from broad bean, dahlia, and echinacea. BRSV isolates were distantly related to each other (83.7–89.3% identity) and were closest to those from oxalis and potato. BRSV satRNAs shared 90.6% identity and were 87.8–94.1% identical to satRNAs associated with tomato black ring virus L and S serotypes. Thus, TSV, BRSV, and BRSV satRNA were for the first time detected in a new natural host P. paniculata in Russia, adding to the list of known phlox viruses and expanding information on the host range, geographic distribution, and genetic diversity of these viruses. Full article

MSTN has been used as a candidate gene in the genetics, breeding, and improvement of animal breeds. However, the possible mechanism by which the MSTN gene regulates muscle development through PSMA6 is not well understood. Previous methylome and transcriptome sequencing analyses of gluteal muscle tissues from MSTN+/−Luxi cattle and wild-type Luxi cattle identified that the PSMA6 gene exhibited a negative correlation between methylation levels and transcriptional activity. To investigate whether MSTN expression regulates PSMA6 gene expression, we examined the effects of MSTN on DNA methyltransferases (DNMT1, DNMT2, DNMT3A, and DNMT3B) and DNA demethylases (TET1, TET2, and TET3). Additionally, chromatin immunoprecipitation (ChIP) assays were performed to detect the binding interaction between PSMA6 and TET2. In this paper, we first established an MSTN knockdown cellular model to preliminarily validate its regulatory effect on PSMA6 expression. Subsequently, the developmental impact of PSMA6 on bovine skeletal muscle satellite cells was further investigated through both knockdown and overexpression of the PSMA6 gene. Furthermore, we examined changes in the expression of key components of the AKT/mTOR signaling pathway to elucidate the mechanisms underlying the PSMA6-mediated regulation of satellite cell development. The results demonstrate that myostatin (MSTN) inhibition significantly decreased proteasome 20S subunit alpha-6 (PSMA6) gene expression, while increasing demethylase expression, particularly ten-eleven translocation-2 (TET2), which exhibited the most pronounced changes. During the cell proliferation stage, the markers Paired Box 7 (PAX7) and Ki-67 exhibited no significant changes, whereas the PSMA6 gene was either overexpressed or disrupted. Conversely, PSMA6 overexpression altered the myogenic differentiation markers, causing the differential regulation of myosin heavy chain (MyHC) and myogenin (MyoG) expression, with MyHC upregulation and concurrent MyoG downregulation. PSMA6 gene overexpression led to the downregulation of AKT1 and Rac1, as well as the activation of the AKT/mTOR pathway, including key factors such as mTOR, p-mTOR, RPS6, p-RPS6, and RhoA. PSMA6 interference resulted in the downregulation of p-mTOR and the upregulation of p-RPS6. Gene expression profiling in our study revealed that the myostatin (MSTN) knockout model significantly reduced the transcriptional levels of the proteasome α6 subunit (PSMA6) (p < 0.05), with the regulatory intensity showing a significant negative correlation with MSTN expression. This molecular evidence substantiates a negative regulatory axis between MSTN and PSMA6. Functional experiments demonstrated that PSMA6 overexpression specifically enhanced myotube formation rates in bovine skeletal muscle satellite cells, whereas siRNA-mediated PSMA6 knockdown exhibited no significant effects on cellular proliferation, indicating the functional specificity of this gene in myogenic differentiation. Mechanistic investigations further revealed that PSMA6 activates the canonical AKT/mTOR signaling transduction cascade through the phosphorylation of AKT and its downstream effector mTOR, thereby mediating the expression of myogenic regulatory factors MyoD and myogenin. Collectively, these findings demonstrate that MSTN deficiency alleviates the transcriptional repression of PSMA6, remodels skeletal muscle differentiation-associated signaling networks, and ultimately drives the directional differentiation of satellite cells toward myofiber specification. Full article

Tandemly repeated DNA fragments are major components of centromeres and pericentromeric heterochromatin, which is responsible for chromosomal stability and segregation. Recent evidence suggests that transcripts from these repeats play a key role in heterochromatin maintenance, and these repeats can be highly dynamic with various copy numbers. Here, we developed a mathematical model for human satellite repeats, which tracks the silenced and desilenced repeats, lncRNA, and copy number. Our model shows that chromatin factors for silencing and RNA stability can facilitate copy gain in satellites. Also, the system can be bistable, and cells with different copy numbers, silenced repeats with a small copy number, and desilenced repeats with a large copy number may coexist. To incorporate the cooperative methylation by neighboring repeats and the local chromatin environment, we also developed a spatial model where the local chromatin environment facilitates methylation locally. This model suggests that a local domain of silenced repeats may be an important feature of copy number regulation. Our models suggest that pericentromeric repeats are highly dynamic, and small changes in chromatin regulation can lead to large changes in satellite copy numbers. Full article

Muscle satellite (stem) cells (MSCs) reside in skeletal muscle and are essential for myogenesis. Thus, MSCs are widely used in cultured meat research. This study aimed to identify substances that promote MSC proliferation and differentiation while maintaining their intrinsic properties, with the long-term goal of replacing fetal bovine serum (FBS) for bovine MSC cultivation. Therefore, this study evaluated the effects of six growth factors (TGF-β, HGF, PDGF, insulin, IGF-1, and EGF) and the cytokine IL-2 on bovine MSCs. Each factor was applied during the proliferation and differentiation of MSCs, and the proliferation rate, differentiation rate, and expression of relevant mRNA and proteins were analyzed. Insulin most effectively promoted MSC proliferation and differentiation. Specifically, insulin increased cell proliferation rates, proliferation markers Ki67 and PCNA expressions, and markers of differentiation, such as myotube formation and creatine kinase activity, alongside the expressions of MYOD, MYOG, and MYH. Furthermore, insulin suppressed low FBS-induced reductions in proliferation and differentiation markers. This study suggests insulin can promote MSC proliferation and differentiation and reduce FBS usage. Thus, this study provides a potential means of cultivating MSCs on a large scale for cultured meat production. Full article

Intramuscular fat (IMF) content is a key factor influencing meat properties including tenderness, flavor, and marbling. However, the complex molecular mechanisms regulating IMF deposition, especially the interactions between intramuscular preadipocytes (IMAdCs) and skeletal muscle satellite cells (SMSCs), remain unclear. In this study, a direct co-culture system of sheep IMAdCs and SMSCs was used to elucidate their intercellular interactions. RNA sequencing and bioinformatics analyses were performed under monoculture and co-culture conditions for later stages of differentiation. The obtained results showed that SMSCs significantly inhibited the adipogenic capacity of IMAdCs. This was reflected in the co-culture markedly altered gene expression and observations of lipid droplets in our studies, i.e., the PPARG, ACOX2, PIK3R1, FABP5, FYN, ALDOC, PFKM, PFKL, HADH, and HADHB genes were down-regulated in the co-cultured IMAdCs in association with the inhibition of fat deposition, whereas ACSL3, ACSL4, ATF3, EGR1, and IGF1R within the genes upregulated in co-culture IMAdCs were associated with the promotion of lipid metabolism. In addition, GO, KEGG, and ligand–receptor pairing analyses further elucidated the molecular mechanisms of intercellular communication. These findings emphasize the regulatory role of SMSCs on intramuscular preadipocyte differentiation and lipid metabolism, providing a theoretical framework for targeted molecular strategies to improve sheep meat quality. Full article

Diabetic peripheral neuropathy (DPN) is a prevalent and disabling complication of diabetes, with painful diabetic peripheral neuropathy (PDPN) being its most severe subtype due to chronic pain and resistance to treatment. Satellite glial cells (SGCs), critical for maintaining dorsal root ganglion (DRG) homeostasis, undergo significant structural and functional changes under pathological conditions. This study investigated the role of galactosylceramide (GalCer), a key sphingolipid, in SGC dysfunction and neuron–glia interactions during DPN progression. Using a rat model of PDPN, we employed single-cell RNA sequencing (scRNA-seq), targeted mass spectrometry, and immunofluorescence analysis. The PDPN group exhibited transcriptional activation and structural reorganization of SGCs, characterized by increased SGC abundance and glial activation, evidenced by elevated Gfap expression. Functional enrichment analyses revealed disruptions in sphingolipid metabolism, including marked reductions in GalCer levels. Subclustering identified vulnerable SGC subsets, such as Cluster a, with dysregulated lipid metabolism. The depletion of GalCer impaired SGC-neuron communication, destabilizing DRG homeostasis and amplifying neurodegeneration and neuropathic pain. These findings demonstrate that GalCer depletion is a central mediator of SGC dysfunction in PDPN, disrupting neuron–glia interactions and exacerbating neuropathic pain. This study provides novel insights into the molecular mechanisms of DPN progression and identifies GalCer metabolism as a potential therapeutic target. Full article

Cultured meat (CM) is derived from the in vitro myogenesis of muscle satellite (stem) cells (MSCs) and offers a promising alternative protein source. However, the development of a cost-effective media formulation that promotes cell growth has yet to be achieved. In this study, laxogenin (LAX) and 5-alpha-hydroxy-laxogenin (5HLAX) were computationally screened against myostatin (MSTN), a negative regulator of muscle mass, because of their antioxidant properties and dual roles as MSTN inhibitors and enhancers of myogenesis regulatory factors. In silico analysis showed LXG and 5HLXG bound to MSTN with binding free energies of −7.90 and −8.50 kcal/mol, respectively. At a concentration of 10 nM, LAX and 5HLAX effectively inhibited the mRNA and protein expressions of MSTN, promoted myogenesis, and enhanced myotube formation and maturation. In addition, by acting as agonists of ROS downregulating factors, they exhibited antioxidative effects. This study shows that supplementation with LAX or 5HLAX at 10 nM in CM production improves texture, quality, and nutritional value. We believe this study fills a research gap on media development for myotube formation and maturation, which are important factors for large-scale in vitro CM production that improve product quality, nutritional value, and efficacy. Full article