Integrated miRNA-mRNA Analysis Reveals Regulatory Mechanisms of Muscle Fiber Transformation Underlying Meat Quality Variation in Chicken
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ABSTRACT:
ORGANISM(S): Gallus gallus
PROVIDER: GSE299746 | GEO | 2026/06/13
REPOSITORIES: GEO
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Project description:Skeletal muscle fiber composition influences meat quality and metabolic regulation in poultry, yet fiber-type–specific responses to high-fat diet (HFD) remain poorly understood. This study examined the effects of short-term (SHFD) and long-term (LHFD) HFD feeding on fast/glycolytic (pectoralis major, PEM) and slow/oxidative (soleus, SOL) muscles in Guangyuan grey chickens. Histological analysis showed SOL fibers underwent oxidative-to-glycolytic transition under LHFD, accompanied by mitochondrial disruption. PEM accumulated more lipids and showed early metabolic stress. Transcriptome profiling revealed 3840 differentially expressed genes between PEM and SOL, with 1761 constitutively different. Under SHFD, SOL activated protective pathways including PPAR and autophagy, while PEM showed limited adaptation. LHFD induced further downregulation of fatty acid metabolism and structural genes (e.g., ALPK1, CA12, PM20D2, SLC27A1, and GADD45G) in PEM, but SOL maintained or enhanced expression of genes (e.g., NR4A3, PRKAG2, NOCT, PPARA, and SLC6A6) involved in muscle organization and lipid processing. Temporal clustering highlighted progressive divergence in transcriptional responses. These results suggest SOL fibers exhibit greater resilience to lipid overload than PEM fibers. Our findings provide insight into the molecular basis of muscle-type–specific adaptations to dietary fat and offer targets for improving metabolic health and meat quality in poultry.
2025-12-02 | GSE304154 | GEO
Project description:The phenotypic characteristics and meat quality of skeletal muscle are collectively determined by the muscle cells, other cellular groups within it, and their intricate interactions with the extracellular microenvironment. Exosomes have the capacity to influence the development and microenvironment of skeletal muscle, thus playing a crucial role in its differentiation and maturation. In this study, we conducted an initial evaluation of the muscle fiber phenotypes in glycolytic skeletal muscle (Longissimus dorsi, HC-L) and oxidative skeletal muscle (Psoas major, HC-P) of Hechuan black pigs. The results revealed significant differences in terms of muscle fiber diameter, density, and type phenotypes (P<0.05). Subsequently, we isolated and identified exosomes derived from skeletal muscle (SKM-Exos). Co-culture experiments with myoblasts demonstrated that SKM-Exos can promote both myoblast proliferation and differentiation. Furthermore, sequencing analysis confirmed that miRNAs present in SKM-Exos are selectively coated miRNAs. It is noteworthy that the expression of miR-4331-3p was notably higher in SKM-Exos compared to its derived skeletal muscles. It was significantly elevated in the SKM-Exos of HC-L when compared to those of HC-P, and have interactions with the differentially expressed genes between HC-L and HC-P. Interestingly enough, miR-4331-3p has been shown to enhance myoblast proliferation while inhibiting the differentiation process. By investigating the interaction between SKM-Exos, their derived miRNAs, and myoblasts, this study elucidated the molecular mechanism underlying the regulation of muscle fiber differentiation by SKM-Exos and provided valuable insights into the intricate molecular processes involved in meat formation.
2026-06-07 | GSE269386 | GEO
Project description:We used phosphoproteomic profiling of slow-twitch (soleus, SOL) and fast-twitch (biceps femoris, BF) muscle to identify differences between these muscle types.
2022-08-16 | PXD036066 |
Project description:succinate (SUC), as a feed additive, can regulate muscle fiber structure and fat deposition, and has a positive effect on meat quality. In this study, 30 male Tan sheep lambs were selected to investigate the effects of SUC in diet on Tan sheep production performance, lamb quality, muscle fiber structure, liver and longissimus' muscle entities (LT) transcriptomes. Different levels of SUC were fed (0%, 1.0%, 2.0%, respectively) and the experiment lasted for 60 days. Compared with CON group, 2% SUC group significantly increased average daily gain from 1 to 15 days and 46 to 60 days during the experiment period, and significantly increased dry matter intake from 1 to 15 days, 16 to 30 days and 46 to 60 days during the experiment period (P<0.05). Both 1% SUC group and 2% SUC group could decrease feed to gain ratio and increase carcass weight (P<0.05). The slaughter rate of 2% SUC group was significantly increased (P=0.012). In both 1% SUC and 2% SUC groups, shear force and cooking loss were decreased, intramuscular fat was increased, and a* of LT muscle was increased (P=0.036). In addition, the muscle fiber structure of Tan sheep LT muscle in 1% SUC group and 2% SUC group was changed, the diameter of muscle fiber was decreased, the cross-sectional area of type Ⅰ and type Ⅱa muscle fiber was decreased, and the density of type Ⅰ muscle fiber was increased (P<0.05). Transcriptomic results showed that the addition of SUC can change the expression of muscle development and muscle fiber type transformation genes. Differential genes are mainly involved in various pathways related to lipid metabolism, energy metabolism and muscle development, improve muscle glucose uptake capacity, and improve meat quality in circadian rhythm. In conclusion, SUC can regulate the nutritional metabolism of Tan Sheep, change the muscle fiber structure of Tan Sheep, and improve the production performance and meat quality. Our results show that adding 1% SUC to the Tan sheep diet is productively more beneficial.
2025-12-26 | GSE285317 | GEO
Project description:This experiment was conducted to identify target genes of the microRNA-499 in skeletal muscle of transgenic mice that overexpressed miR-499. The following abstract from the submitted manuscript describes the major findings of this work. Coupling of mitochondrial function and skeletal muscle fiber type by a miR-499/Fnip1/AMPK circuit. Jing Liu, Xijun Liang, Danxia Zhou, Ling Lai, Tingting Fu, Yan Kong, Qian Zhou, Rick B. Vega, Min-Sheng Zhu, Daniel P. Kelly, Xiang Gao, and Zhenji Gan. Upon adaption of skeletal muscle to physiological and pathophysiological stimuli, muscle fiber type and mitochondrial function are coordinately regulated. Recent studies have identified pathways involved in control of contractile proteins of oxidative type fibers. However, the mechanism for coupling of mitochondrial function to muscle contractile machinery during fiber type transition remains unknown. Here, we show that the expression of the genes encoding type I myosins, Myh7/Myh7b and their intronic miR-208b/miR-499 parallels mitochondrial function during fiber type transitions. Using in vivo approaches in mice, we found that miR-499 drives a PGC-1a-dependent mitochondrial oxidative metabolism program to match shifts in slow-twitch muscle fiber composition. Mechanistically, miR-499 directly targets Fnip1, a known AMP-activated protein kinase (AMPK)-interacting protein that negatively regulates AMPK, a known activator of PGC-1a. Inhibition of Fnip1 reactivated AMPK/PGC-1a signaling and mitochondrial function in myocytes. Restoration of the expression of miR-499 in the mdx mouse model of Duchenne muscular dystrophy (DMD) reduced the severity of DMD. Thus, we have identified a miR-499/Fnip1/AMPK circuit that can serve as a mechanism to couple muscle fiber type and mitochondrial function. Keywords: muscle, contractile fiber type, mitochondrial function, microRNA, gene regulation RNA from three wild-type (non-transgenic (NTG)) and three miR-499 overexpressing (MCK-miR-499) mice was analyzed. three replicates of each are provided.
2016-09-03 | E-GEOD-72581 | biostudies-arrayexpress
Project description:Amyotrophic lateral sclerosis (ALS) is a lethal motor neuron disease that progressively debilitates neuronal cells that control voluntary muscle activity. In a mouse model of ALS that expresses mutated human superoxide dismutase 1 (SOD1-G93A) skeletal muscle is one of the tissues affected early by mutant SOD1 toxicity. Fast-twitch and slow-twitch muscles are differentially affected in ALS patients and in the SOD1-G93A model, fast-twitch muscles being more vulnerable. We used miRNA microarrays to investigate miRNA alterations in fast-twitch (EDL) and slow-twitch (soleus) skeletal muscles of symptomatic SOD1-G93A animals and their age-matched wild type littermates. At age of 90 days RNA was extracted from extensor digitorum longus (EDL) and soleus (SOL) muscles of male SOD1-G93A animals and their age-matched wild type male littermates. RNA was hybridized on Affymetrix Multispecies miRNA-2_0 Array.
2014-03-04 | E-GEOD-55507 | biostudies-arrayexpress
Project description:<p>Skeletal muscles, accounting for 40% of mammalian body mass, exhibit pronounced heterogeneity due to distinct anatomical locations. Animal husbandry excessively focuses on longissimus dorsi (LDM) development, while neglecting other muscles. In this study, we integrated Bulk RNA Sequencing (bulk RNA-seq) and Liquid Chromatography-Mass Spectrometery (LC-MS) analyses of Soleus (SOL), Gastrocnemius (GAS), and Psoas major (PMM) across three key stages in Duroc pigs. As a result, we identified 9 critical genes (S100A1, MBOAT2, CA3, GYG2, ACTN3, ENO3, SLC3A2, SLC16A10, and GAPDH) and 8 metabolites potentially involved in regulating both skeletal muscle development and fiber-type transformation. The heterogeneity between SOL and GAS was low at birth but increased gradually during development. In contrast, PMM exhibited high heterogeneity compared to SOL and GAS from birth. Notably, expression levels of MYH7, MYH1, and MYH4 displayed stage-specific and muscle type-dependent variations. Moreover, we observed a developmental shift from the MAPK signaling pathway (1-21 d) to the regulation of actin cytoskeleton (21-120 d). Pairwise comparisons between SOL, GAS, and PMM revealed signaling pathways enriched in muscle fiber-type switching. Collectively, through the integration of bulk RNA-seq and LC-MS data, this study provides novel molecular breeding strategies for genetic improvement in meat-producing animals.</p>
2025-09-09 | MTBLS12963 | MetaboLights
Project description:To investigate the impact of adding succinate to the diet on the production performance, meat quality, muscle fiber characteristics, and transcriptome of the longissimus dorsi muscle in Tan sheep, 36 Tan sheep were selected and fed with different levels of succinate (0%, 0.5%, 1.0%, 2.0%) for a 60-day trial period. Overall, compared to the control group, the addition of succinate to the diet improved the production performance, slaughter performance, and meat quality of Tan sheep. It significantly increased dry matter intake, carcass weight, eye muscle area, and the GR value while significantly reducing the shear force and cooking loss of the longissimus dorsi muscle (p<0.05). Furthermore, the addition of succinate to the diet altered the muscle fiber characteristics of the longissimus dorsi muscle in Tan sheep, significantly increasing the fiber diameter and cross-sectional area of type I and type IIa muscle fibers (p<0.05). The addition of 1.0% succinate to the diet altered the transcriptome of the longissimus dorsi muscle in Tan sheep, with 741 differentially expressed genes identified compared to the control group. These differentially expressed genes were involved in various pathways related to lipid metabolism, energy metabolism, and muscle development, such as insulin secretion, insulin resistance, cAMP signaling pathway, PI3K-Akt signaling pathway, and FoxO signaling, among others. In summary, succinate plays a crucial role in regulating energy metabolism, protein deposition, and glucose and lipid metabolism homeostasis in Tan sheep through insulin signaling pathways and the interaction of muscle cell factors. By modulating the expression of relevant genes, succinate improves the muscle fiber characteristics of Tan sheep, thereby enhancing production performance and meat quality.
2023-11-26 | GSE248353 | GEO
Project description:The biochemical and functional differences between oxidative and glycolytic muscles affect human muscle health and animal meat quality, but the epigenetic regulation with respect to lncRNAs and circRNAs remains largely unknown. Here, we employed porcine oxidative and glycolytic skeletal muscles, at growth curve inflection point, to survey variant global lncRNAs and circRNAs expression using RNA-seq. In total, we obtained 540 million raw reads approximately 81.02 Gb of high quality data. After a strict filtering process, 4,046 lncRNAs were identified, including 911 differentially expressed lncRNAs (p < 0.05). The cis-regulatory analysis identified target genes that were enriched for specific GO terms and pathways (p < 0.05), including oxidation-reduction process, glycolytic process, fatty acid metabolic, PPAR signaling pathway, which are closely related to the different phenotypes between oxidative and glycolytic muscles. Additional, we also identified 810 circRNAs, 137 of them were differentially expressed (p < 0.05). The host genes of circRNAs were related to motor activity, transition between fast and slow fiber and ATP metabolic process by function enrichment analysis. Interestingly, we found circRNA290-miR27b-Foxj3 and circRNA9210-miR-23a-MEF2C taken as two competing endogenous network, which was closely linked to muscle fiber-type switching. circRNA41-miR-217-SIRT1 network was connected with mitochondria biogenesis in muscle. Furthermore, we found 44.69%, 39.19% and 54.01% of differentially expressed mRNAs, lncRNAs and circRNAs were siginificantly enriched pig QTL regions (traits of meat quality and growing development), respectively. Togeter, this study reveals a mass of candidate lncRNAs and circRNAs involved in muscle physiological function, which improve understanding of muscle metabolism and development from epigenetic perspectives.
2018-08-30 | GSE119137 | GEO
Project description:This experiment was conducted to identify target microRNAs of the peroxisome proliferator-activated receptor (PPAR) in skeletal muscle of transgenic mice that overexpressed PPARalpha or PPARbeta. We have recently demonstrated that skeletal muscle-specific PPARb transgenic (MCK-PPARb) mice exhibit increased exercise endurance, whereas MCK-PPARa mice have reduced exercise performance. Accordingly, we sought to determine whether PPARb and PPARa drive distinct programs involved in muscle fiber type determination. Myosin heavy chain (MHC) immunohistochemical staining of soleus muscle revealed a marked increase in type 1 fibers in the MCK-PPARb muscle compared to non-transgenic (NTG) littermates but a profound reduction in MCK-PPARa muscle. miRNA profiling revealed that levels of miR-208b and miR-499 were increased in MCK-PPARb muscle but reduced in MCK-PPARa muscle. miR-208b and miR-499, which are embedded in the Myh7 and Myh7b genes, respectively, have been shown previously to regulate slow-twitch muscle genes. Lastly, combined inhibition of miR-208b and miR-499 abolished the enhancing effects of PPARb on MHC1 expression in skeletal myotubes, while forced expression of miR-499 in MCK-PPARa muscle completely reversed the type 1 fiber program and exercise capacity. Taken together, these findings demonstrate that miR-208b and miR-499 are necessary to mediate the effects of PPARb and PPARa on muscle fiber type determination.
2013-05-09 | GSE36498 | GEO