The miRNA Transcriptome directly Reflect the Physiological and Biochemical Differences between Red, White and Intermediate Muscle Fiber Types
Ontology highlight
ABSTRACT:
ORGANISM(S): Sus scrofa
PROVIDER: GSE64523 | GEO | 2015/12/23
SECONDARY ACCESSION(S): PRJNA271218
REPOSITORIES: GEO
Similar Datasets
Project description:MicroRNAs (miRNAs) are small non-coding RNAs that can regulate the expression of their target genes at post-transcriptional level. Skeletal muscle comprises different �ber types that can be broadly classified as red, intermediate and white fiber types. Recently, a set of miRNAs were identified to be expressed on a fiber type-specific manner between red and white fiber types. Nonetheless, an integral explanation of the miRNA transcriptome differences in all three fiber types is long overdue. Herein, we collected 15 kinds of porcine skeletal muscles from different anatomic locations, which were then clearly divided into red, white and intermediate fiber type based on the hierarchical clustering analysis for the ratios of myosin heavy chain (MHC) isoforms. We further illustrated that three muscles, which typically represented each muscle fiber type (i.e. red: peroneal longus (PL), intermediate: psoas major muscle (PMM), white: longissimus dorsi muscle (LDM)), have distinct metabolic patterns of mitochondrial and glycolytic enzyme levels. In addition, we constructed the small RNA libraries for PL, PMM and LDM using deep sequencing approach. Results showed that, the differentially expressed miRNAs were mainly enriched in PL and played a vital role in myogenesis and energy metabolism. Overall, this comprehensive analysis will contribute to a better understanding of the miRNA regulatory mechanism for the phenotypic diversity of skeletal muscles. 3 sample
2015-12-23 | E-GEOD-64523 | biostudies-arrayexpress
Project description:The physiological, biochemical and functional difference of oxidative and glycolytic muscles play important roles in human metabolic health as well as in meat quality of animal. To explore this aspect, we firstly provided a genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA transcriptome for PMM (psoas major muscle; oxidative) and LDM (longissimus dorsi muscle; glycotic) in this study. We observed hypomethylation of subtelomeric regions and high mitochondria content contributed to fast replicative senescence in PMM. The DMRs in promoter (478) and gene bodies (5718) were main enriched in GTPase regulator activity and signaling cascade mediated pathway. Integration analysis revealed methylation status within gene promoter (or gene body) and miRNA promoter have significant negative correlation with mRNA and miRNA expression, respectively. Which included numerous genes were closely related to distinct phenotypic traits between LDM and PMM. For instance, the hypermethylation and down-expression of HK-2 and PFKFB4 decreased the glycolytic potential in PMM. In addition, we validated the promoter hypomethylation and up-expression of miR-378 results in silencing the target gene expression and inducing promoted capillaries biosynthesis in PMM. Together, these results provide a thorough understanding of muscle metabolism and development from an genomic and epigenetic perspective.
2016-05-24 | GSE81759 | GEO
Project description:The physiological, biochemical and functional difference of oxidative and glycolytic muscles play important roles in human metabolic health as well as in meat quality of animal. To explore this aspect, we firstly provided a genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA transcriptome for PMM (psoas major muscle; oxidative) and LDM (longissimus dorsi muscle; glycotic) in this study. We observed hypomethylation of subtelomeric regions and high mitochondria content contributed to fast replicative senescence in PMM. The DMRs in promoter (478) and gene bodies (5718) were main enriched in GTPase regulator activity and signaling cascade mediated pathway. Integration analysis revealed methylation status within gene promoter (or gene body) and miRNA promoter have significant negative correlation with mRNA and miRNA expression, respectively. Which included numerous genes were closely related to distinct phenotypic traits between LDM and PMM. For instance, the hypermethylation and down-expression of HK-2 and PFKFB4 decreased the glycolytic potential in PMM. In addition, we validated the promoter hypomethylation and up-expression of miR-378 results in silencing the target gene expression and inducing promoted capillaries biosynthesis in PMM. Together, these results provide a thorough understanding of muscle metabolism and development from an genomic and epigenetic perspective.
2016-05-24 | GSE81757 | GEO
Project description:The physiological, biochemical and functional difference of oxidative and glycolytic muscles play important roles in human metabolic health as well as in meat quality of animal. To explore this aspect, we firstly provided a genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA transcriptome for PMM (psoas major muscle; oxidative) and LDM (longissimus dorsi muscle; glycotic) in this study. We observed hypomethylation of subtelomeric regions and high mitochondria content contributed to fast replicative senescence in PMM. The DMRs in promoter (478) and gene bodies (5718) were main enriched in GTPase regulator activity and signaling cascade mediated pathway. Integration analysis revealed methylation status within gene promoter (or gene body) and miRNA promoter have significant negative correlation with mRNA and miRNA expression, respectively. Which included numerous genes were closely related to distinct phenotypic traits between LDM and PMM. For instance, the hypermethylation and down-expression of HK-2 and PFKFB4 decreased the glycolytic potential in PMM. In addition, we validated the promoter hypomethylation and up-expression of miR-378 results in silencing the target gene expression and inducing promoted capillaries biosynthesis in PMM. Together, these results provide a thorough understanding of muscle metabolism and development from an genomic and epigenetic perspective.
2016-05-24 | GSE81755 | GEO
Project description:The introduction of long oligonucleotide-based probes has led to many comparative studies of these two platforms in mammals, but remains to be performed for pig. Further, the characteristics of global gene expression in diverse porcine muscle tissues have not been yet been fully established. This is the first global gene expression study of a collection of nine porcine muscle tissues consisting of cardiac and various skeletal muscle types using both cDNA-based and long oligonucleotide-based microarray platforms. The expression profiles from the two platforms agree in differentiating between cardiac, skeletal red, skeletal intermediate and skeletal white muscle types by producing almost identical hierarchical expression clusters. The clusters from both platforms also reveal that gene expression profiles of the skeletal intermediate type are more similar to the red type than to the white type. Analysis of the ability to identify differentially expressed genes based on gene set analysis and GO term integration show a platform overlap of at least 80% for the cardiac-skeletal comparisons and a platform overlap of at least 58% for the skeletal red-white comparisons. Interestingly, the oligonucleotide platform was always able to identify more GO terms associated with differential expression than the cDNA platform. We further examined the skeletal red-white expression differences and found many GO biological processes that are known to be associated with these phenotypes including calcium ion transport, glycolysis, fatty acid beta-oxidation and muscle contraction. In addition, the expression of genes involved in differentiation between slow (red) and fast (white) muscle types such as MYBPC1, TNNI1, TNNT3 and ATP2A1 is highly regulated between red and white type muscles. Not previously shown to be associated with this tissue difference we found the biological process post-Golgi vesicle-mediated transport. Similar results were obtained with GO classes cellular components and molecular functions. Using the gene expression profiles from the oligonucleotide platform we presented and applied an approach for predicting alternatively spliced transcripts across cardiac and skeletal type muscles. One of the predicted transcripts from the gene named UBE2C has been shown to have six transcript variants in human, but they are not expressed in a cardiac-skeletal specific manner as we have observed here. We speculate that one of our oligonucleotide probes for this gene is able to detect only three of these variants whereas the other detects all six variants and that these variants are expressed in a cardiac-skeletal muscle specific manner. These results supports some of the advantages of using oligonucleotide-based microarray platforms for global gene expression profiling and the observed differences in gene expression among muscle tissues contribute to the understanding of the molecular processes behind porcine muscle biology. Keywords: tissue comparison, platform comparison
2012-10-30 | GSE10597 | GEO
Project description:The introduction of long oligonucleotide-based probes has led to many comparative studies of these two platforms in mammals, but remains to be performed for pig. Further, the characteristics of global gene expression in diverse porcine muscle tissues have not been yet been fully established. This is the first global gene expression study of a collection of nine porcine muscle tissues consisting of cardiac and various skeletal muscle types using both cDNA-based and long oligonucleotide-based microarray platforms. The expression profiles from the two platforms agree in differentiating between cardiac, skeletal red, skeletal intermediate and skeletal white muscle types by producing almost identical hierarchical expression clusters. The clusters from both platforms also reveal that gene expression profiles of the skeletal intermediate type are more similar to the red type than to the white type. Analysis of the ability to identify differentially expressed genes based on gene set analysis and GO term integration show a platform overlap of at least 80% for the cardiac-skeletal comparisons and a platform overlap of at least 58% for the skeletal red-white comparisons. Interestingly, the oligonucleotide platform was always able to identify more GO terms associated with differential expression than the cDNA platform. We further examined the skeletal red-white expression differences and found many GO biological processes that are known to be associated with these phenotypes including calcium ion transport, glycolysis, fatty acid beta-oxidation and muscle contraction. In addition, the expression of genes involved in differentiation between slow (red) and fast (white) muscle types such as MYBPC1, TNNI1, TNNT3 and ATP2A1 is highly regulated between red and white type muscles. Not previously shown to be associated with this tissue difference we found the biological process post-Golgi vesicle-mediated transport. Similar results were obtained with GO classes cellular components and molecular functions. Using the gene expression profiles from the oligonucleotide platform we presented and applied an approach for predicting alternatively spliced transcripts across cardiac and skeletal type muscles. One of the predicted transcripts from the gene named UBE2C has been shown to have six transcript variants in human, but they are not expressed in a cardiac-skeletal specific manner as we have observed here. We speculate that one of our oligonucleotide probes for this gene is able to detect only three of these variants whereas the other detects all six variants and that these variants are expressed in a cardiac-skeletal muscle specific manner. These results supports some of the advantages of using oligonucleotide-based microarray platforms for global gene expression profiling and the observed differences in gene expression among muscle tissues contribute to the understanding of the molecular processes behind porcine muscle biology. Keywords: tissue comparison, platform comparison Muscle tissue samples from heart (HEA), Vastus intermedius (VIN), Infraspinatus (ISP), Supraspinatus (SSP), Biceps femoris (BFE), Longissimus dorsi (LDO), Semimembranosus (SME), Semitendinosus (STE) and Triceps brachii (TBR). A common reference sample was constructed by combining all samples. The exact same tissue samples were used for expression profiling with cDNA microarrays and 70-mer long oligonucleotide microarrays.
2012-10-30 | E-GEOD-10597 | biostudies-arrayexpress
Project description:Melatonin has been reported to play crucial roles in regulating meat quality, improving reproductive properties and maintaining intestinal health in animal production, but whether it regulates skeletal muscle development in weaned piglet is rarely studied. This study was conducted to investigate the effects of melatonin on growth performance, skeletal muscle development and lipid metabolism in animals by intragastric administration of melatonin solution. Twelve 28-day-old DLY (Duroc × Landrace × Yorkshire) weaned piglets with similar body weight were randomly divided into two groups: control group and melatonin group. The results showed that melatonin supplementation for 23 days had no effect on growth performance, but significantly reduced serum glucose content (P<0.05). Remarkably, melatonin increased longissimus dorsi muscle (LDM) weight, eye muscle area and decreased the liver weight in weaned piglets (P<0.05). In addition, the cross-sectional area of muscle fibers was increased (P<0.05), while triglyceride (TG) levels were decreased in LDM and psoas major muscle (PMM) by melatonin treatment (P<0.05). Transcriptome sequencing showed melatonin induced the expression of genes related to skeletal muscle hypertrophy and fatty acid oxidation. Enrichment analysis indicated that melatonin regulated cholesterol metabolism, protein digestion and absorption and mitophagy signaling pathways in muscle. Gene set enrichment analysis (GSEA) also confirmed the effects of melatonin on skeletal muscle development and mitochondrial structure and function. Moreover, quantitative real-time polymerase chain reaction (qPCR) analysis revealed that melatonin supplementation elevated the gene expression of cell differentiation and muscle fiber development, including paired box 7 (PAX7), myogenin (MYOG), myosin heavy chain (MYHC) ⅡA and MYHC ⅡB (P<0.05), which was accompanied by increased insulin like growth factor 1 (IGF1) and insulin like growth factor binding protein 5 (IGFBP5) expression in LDM (P<0.05). Additionally, melatonin regulated lipid metabolism and activated mitochondrial function in muscle by increasing the mRNA abundance of cytochrome c oxidase subunit 6A (COX6A), COX5B and carnitine palmitoyltransferase 2 (CPT2) and decreasing the mRNA expression of peroxisome proliferator activated receptor gamma (PPARG), Acetyl-CoA carboxylase (ACC) and fatty acid binding protein 4 (FABP4) (P<0.05). Together, our results suggest that melatonin could promote skeletal muscle growth and muscle fiber hypertrophy, improve mitochondrial function and decrease fat deposition in muscle.
2023-10-02 | GSE237322 | GEO
Project description:Training at sustainable swimming speeds can produce changes in fish skeletal muscle that are important for aquaculture due to their growth-potentiating effects. Such changes may be even more relevant when fish are fed diets containing an increasing proportion of carbohydrates as an energy source. We evaluated the effects of moderate-intensity sustained swimming on the transcriptomic response of red and white muscle in rainbow trout fed a carbohydrate-rich diet using microarray and qPCR. Analysis of the red and white muscle transcriptome revealed significant changes in the expression of a large number of genes (395 and 597, respectively), with a total of 218 differentially expressed genes (DEGs) common for both muscles. A large number of the genes involved in glucose use and energy generation, contraction, development, synthesis and catabolism of proteins were up-regulated in red and white muscle. Additionally, DEGs in both muscles were involved in processes of defense response and apoptosis. Skeletal muscle contraction activates a transcriptional program required for the successful adaptation of both muscles to the changing demands imposed by swimming conditions. Future studies should further clarify the mechanisms involved in the adaptation of both tissues to exercise and assess possible benefits of such conditions for cultured fish.
2014-05-01 | GSE47141 | GEO
Project description:Training at sustainable swimming speeds can produce changes in fish skeletal muscle that are important for aquaculture due to their growth-potentiating effects. Such changes may be even more relevant when fish are fed diets containing an increasing proportion of carbohydrates as an energy source. We evaluated the effects of moderate-intensity sustained swimming on the transcriptomic response of red and white muscle in rainbow trout fed a carbohydrate-rich diet using microarray and qPCR. Analysis of the red and white muscle transcriptome revealed significant changes in the expression of a large number of genes (395 and 597, respectively), with a total of 218 differentially expressed genes (DEGs) common for both muscles. A large number of the genes involved in glucose use and energy generation, contraction, development, synthesis and catabolism of proteins were up-regulated in red and white muscle. Additionally, DEGs in both muscles were involved in processes of defense response and apoptosis. Skeletal muscle contraction activates a transcriptional program required for the successful adaptation of both muscles to the changing demands imposed by swimming conditions. Future studies should further clarify the mechanisms involved in the adaptation of both tissues to exercise and assess possible benefits of such conditions for cultured fish. Total RNA from pooled red and white skeletal muscle samples of individual rainbow trout from each group (resting fish, n=8; swimming fish, n=8) was labeled with Cy3-dUTP and Cy5-dUTP (GE Healthcare, Barcelona, Spain). We used a dye swap experimental design and each cDNA from a pooled RNA sample was hybridized to two microarrays. For the first slide, cDNAs from resting and swimming fish were labeled with Cy5 and Cy3, respectively, and for the second array dye assignment was reversed. Therefore, samples from individual fish within each group were pooled and expression values shown represent the means of 6 M-CM-^W 2 = 12 technical replicates. A total of four slides were used in this study
2014-05-01 | E-GEOD-47141 | biostudies-arrayexpress
Project description:Because of its high plasticity and rapid growth rate, turkey skeletal muscle is an important model for studying mechanisms responsible for vertebrate skeletal muscle development and function. Skeletal muscle is composed of metabolically heterogeneous myofibers that exhibit high plasticity at both the morphological and transcriptional levels. The objective of this study was to employ microarray analysis to elucidate the differential gene expression between the tonic- “red” Anterior latissimus dorsi (ALD) muscle, the phasic- “white” Posterior latissimus dorsi (PLD), and “mixed”-phenotype Biceps femoris (BF) in 1-week and 19-week old male turkeys. A total of 170 differentially expressed genes were identified in the analyzed muscle samples (P<0.05). Gene Go analysis software was utilized to identify top gene networks and metabolic pathways involving differentially expressed genes. The largest differences were observed between ALD and PLD muscles, where 32 genes were over-expressed and 82 genes were under-expressed in ALD1-PLD1 comparison; and 70 genes were over-expressed and 70 under-expressed in ALD19-PLD19 comparison. The largest number of genes over-expressed in ALD muscles as compared to other muscles, code for extracellular matrix proteins such as dystroglycan and collagen. Furthermore, a number of genes involved in glycolytic metabolism were under-expressed in ALD muscles as compared to BF and PLD muscles. The gene analysis revealed that phenotypically “red” BF muscle has high expression of glycolytic genes usually associated with “white” muscle phenotype. Muscle-specific differences were observed in expression levels of genes coding for proteins involved in mRNA processing and translation regulation, proteosomal degradation, apoptosis, and insulin resistance.
2011-01-13 | GSE23354 | GEO