scholarly journals Genome-Wide Expression Profiling of mRNAs, lncRNAs and circRNAs in Skeletal Muscle of Two Different Pig Breeds

Animals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 3169
Author(s):  
Xinhua Hou ◽  
Ligang Wang ◽  
Fuping Zhao ◽  
Xin Liu ◽  
Hongmei Gao ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Fatty Acid ◽  
Fatty Acid Metabolism ◽  
Muscle Development ◽  
Target Genes ◽  
Acid Metabolism ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Skeletal Muscle Development ◽  
Pig Breeds

RNA-Seq technology is widely used to analyze global changes in the transcriptome and investigate the influence on relevant phenotypic traits. Beijing Black pigs show differences in growth rate and meat quality compared to western pig breeds. However, the molecular mechanisms responsible for such phenotypic differences remain unknown. In this study, longissimus dorsi muscles from Beijing Black and Yorkshire pigs were used to construct RNA libraries and perform RNA-seq. Significantly different expressions were observed in 1051 mRNAs, 322 lncRNAs, and 82 circRNAs. GO and KEGG pathway annotation showed that differentially expressed mRNAs participated in skeletal muscle development and fatty acid metabolism, which determined the muscle-related traits. To explore the regulatory role of lncRNAs, the cis and trans-target genes were predicted and these lncRNAswere involved in the biological processes related to skeletal muscle development and fatty acid metabolismvia their target genes. CircRNAs play a ceRNA role by binding to miRNAs. Therefore, the potential miRNAs of differentially expressed circRNAs were predicted and interaction networks among circRNAs, miRNAs, and key regulatory mRNAs were constructed to illustrate the function of circRNAs underlying skeletal muscle development and fatty acid metabolism. This study provides new clues for elucidating muscle phenotypic variation in pigs.

scholarly journals Identification and Characterization of Circular RNAs in Longissimus Dorsi Muscle Tissue from Two Goat Breeds using RNA-Seq

2021 ◽  
Author(s):  
Jiyuan Shen ◽  
Huimin Zhen ◽  
Lu Li ◽  
Yuting Zhang ◽  
Jiqing Wang ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Muscle Fiber ◽  
Muscle Development ◽  
Production Performance ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Longissimus Dorsi ◽  
Rna Seq ◽  
Skeletal Muscle Development ◽  
Fiber Size

Abstract Background: Circular RNAs (circRNAs) are a class of non-coding RNA that play crucial roles in the development of skeletal muscle. However, little is known about the role of circRNAs in caprine skeletal muscle. In this study, the muscle fiber size and expression profiles of circRNAs were compared in Longissimus dorsi muscle of Liaoning cashmere (LC) goats and Ziwuling black (ZB) goats with significant phenotypic differences in meat production performance, using hematoxylin and eosin staining and RNA-Seq, respectively.Results: The muscle fiber size in LC goats were larger than those in ZB goats (P < 0.05). A total of 10,875 circRNAs were identified and 214 of these were differentially expressed between the two caprine breeds. The authentication and expression levels of 20 circRNAs were confirmed using reverse transcriptase-polymerase chain reaction (RT-PCR) and DNA sequencing. The parent genes of differentially expressed circRNAs were mainly enriched in connective tissue development, Rap1, cGMP-PKG, cAMP and Ras signaling pathway. Some miRNAs reportedly associated with skeletal muscle development and intramuscular fat deposition would be targeted by several differentially expressed circRNAs and the most highly expressed circRNA (circ_001086).Conclusion: These results provide an improved understanding of the functions of circRNAs in skeletal muscle development of goats.

scholarly journals Characterization of microRNAs during Embryonic Skeletal Muscle Development in the Shan Ma Duck

Animals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1417
Author(s):  
Chuan Li ◽  
Ting Xiong ◽  
Mingfang Zhou ◽  
Lei Wan ◽  
Suwang Xi ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Muscle Development ◽  
Target Genes ◽  
Mapk Signaling ◽  
Differentially Expressed ◽  
Mitogen Activated Protein Kinase ◽  
Luciferase Reporter ◽  
Meat Production ◽  
Skeletal Muscle Development ◽  
Differentially Expressed Mirnas

Poultry skeletal muscle provides high quality protein for humans. Study of the genetic mechanisms during duck skeletal muscle development contribute to future duck breeding and meat production. In the current study, three breast muscle samples from Shan Ma ducks at embryonic day 13 (E13) and E19 were collected, respectively. We detected microRNA (miRNA) expression using high throughput sequencing following bioinformatic analysis. qRT-PCR validated the reliability of sequencing results. We also identified target prediction results using the luciferase reporter assay. A total of 812 known miRNAs and 279 novel miRNAs were detected in six samples; as a result, 61 up-regulated and 48 down-regulated differentially expressed miRNAs were identified between E13 and E19 (|log2 fold change| ≥ 1 and p ≤ 0.05). Enrichment analysis showed that target genes of the differentially expressed miRNAs were enriched on many muscle development-related gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, especially mitogen-activated protein kinase (MAPK) signaling pathways. An interaction network was constructed using the target genes of the differentially expressed miRNAs. These results complement the current duck miRNA database and offer several miRNA candidates for future studies of skeletal muscle development in the duck.

scholarly journals Transcriptome analysis reveals potential mechanisms and pathways underlying embryonic development with respect to muscle growth and egg production in slow and fast growing chickens

2021 ◽  
Author(s):  
M. Kanakachari ◽  
R. Ashwini ◽  
R. N. Chatterjee ◽  
T. K Bhattacharya
Keyword(s):  
Fatty Acid ◽  
Signaling Pathways ◽  
Fatty Acid Metabolism ◽  
Egg Production ◽  
Muscle Development ◽  
Acid Metabolism ◽  
Muscle Growth ◽  
Differentially Expressed ◽  
Thigh Muscle ◽  
And Control

Abstract Background: Chicken is one of the important meat sources throughout the globe. Muscle development and egg production are important genetic traits in commercially raising chickens. However, not much information is available in the fast and slow growth of chicken to determine the expression of genes involved in muscle development and egg production in embryo initiation and developmental stages. This study was designed to investigate why improved Aseel (PD4) growing slowly compared with the control broiler (CB), microarray was conducted with the 7th-day embryo and 18th-day thigh muscle of improved Aseel (PD4) and control broiler (CL), respectively.Results: In the differential transcripts screening, all the transcripts obtained by microarray of slow and fast growth groups were screened by fold change ≥1 and false discovery rate (FDR) <0.05. In total, 19022 transcripts were differentially expressed between the 7th-day embryo and 18th-day thigh muscle of improved Aseel compared to the control broiler. Further analysis showed that a high number of transcripts are differentially regulated in the 7th-day improved Aseel embryo (15382) and fewer transcripts were differentially regulated (3640) in the 18th-day thigh muscle of improved Aseel compared to control broiler. In the 7th and 18th-day improved Aseel embryo, 10127, 2102, 5255, and 1538 transcripts were up and down-regulated, respectively. The commonly up and down-regulated transcripts are 545 and 381 between the 7th and 18th-day of embryos. In this study, we have selected 18 Gallus gallus candidate reference genes from NCBI and total RNA was isolated from control broiler, improved Aseel embryo tissues, and studied their expression profiles by real-time quantitative PCR (qPCR). The best housekeeping gene was identified by using geNorm, NormFinder, BestKeeper, Delta CT, and RefFinder analytical software. The result showed that the TFRC gene is the most stable and further it is used for qPCR data normalization. Further, to validate the differentially expressed genes (DEGs) related to muscle growth, myostatin signaling and development, fatty acid metabolism genes in improved Aseel (PD4) and control broiler embryo tissues by qPCR. Conclusion: Our study identified DEGs that regulate myostatin signaling and differentiation pathway, glycolysis and gluconeogenesis, fatty acid metabolism, Jak-STAT, mTOR, and TGF-β signaling pathways, tryptophan metabolism, PI3K-Akt signaling pathways in improved Aseel. The results revealed that the gene expression architecture is present in the improved Aseel exhibiting embryo growth that will help to improve muscle development, differentiation, egg production, as well as protein synthesis in improved Aseel native chicken. Our findings may be used as a model for improving the growth in improved Aseel as well as optimizing the growth in the control broiler.

scholarly journals IDH2 Deficiency Is Critical in Myogenesis and Fatty Acid Metabolism in Mice Skeletal Muscle

2020 ◽  
Vol 21 (16) ◽  
pp. 5596
Author(s):  
Jeong Hoon Pan ◽  
Jingsi Tang ◽  
Young Jun Kim ◽  
Jin Hyup Lee ◽  
Eui-Cheol Shin ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Fatty Acid ◽  
Fatty Acid Metabolism ◽  
Energy Homeostasis ◽  
Muscle Development ◽  
Acid Metabolism ◽  
Uncoupling Protein ◽  
Acid Oxidation ◽  
Oxidative Decarboxylation ◽  
Muscle Weight

Mitochondrial NADP+-dependent isocitrate dehydrogenase (IDH2) catalyzes the oxidative decarboxylation of isocitrate into α-ketoglutarate with concurrent reduction of NADP+ to NADPH. However, it is not fully understood how IDH2 is intertwined with muscle development and fatty acid metabolism. Here, we examined the effects of IDH2 knockout (KO) on skeletal muscle energy homeostasis. Calf skeletal muscle samples from 10-week-old male IDH2 KO and wild-type (WT; C57BL/6N) mice were harvested, and the ratio of skeletal muscle weight to body and the ratio of mitochondrial to nucleic DNA were measured. In addition, genes involved in myogenesis, mitochondria biogenesis, adipogenesis, and thermogenesis were compared. Results showed that the ratio of skeletal muscle weight to body weight was lower in IDH2 KO mice than those in WT mice. Of note, a noticeable shift in fiber size distribution was found in IDH2 KO mice. Additionally, there was a trend of a decrease in mitochondrial content in IDH2 KO mice than in WT mice (p = 0.09). Further, mRNA expressions for myogenesis and mitochondrial biogenesis were either decreased or showed a trend of decrease in IDH2 KO mice. Moreover, genes for adipogenesis pathway (Pparg, Znf423, and Fat1) were downregulated in IDH2 KO mice. Interestingly, mRNA and protein expression of uncoupling protein 1 (UCP1), a hallmark of thermogenesis, were remarkably increased in IDH2 KO mice. In line with the UCP1 expression, IDH2 KO mice showed higher rectal temperature than WT mice under cold stress. Taken together, IDH2 deficiency may affect myogenesis, possibly due to impairments of muscle generation and abnormal fatty acid oxidation as well as thermogenesis in muscle via upregulation of UCP1.

scholarly journals Effects of Plant Sterols Intake on Systematic and Tissue Specific Lipid Metabolism in C57BL/6J Mice

2021 ◽  
Vol 5 (Supplement_2) ◽  
pp. 388-388
Author(s):  
Qian Zhu ◽  
Jingjing Wu ◽  
Daxue He ◽  
Xuemei Lian
Keyword(s):  
Fatty Acid ◽  
Lipid Metabolism ◽  
Fatty Acid Metabolism ◽  
Acid Metabolism ◽  
Plant Sterols ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Tissue Specific ◽  
Free Sterols ◽  
Specific Lipid

Abstract Objectives To investigate the effects of plant sterols intake on systematic and tissue specific lipid metabolism in C57BL/6J mice. Methods Male C57BL/6J mice were randomly divided into control diet group (CS) and plant sterol group (PS, 2% plant sterols). After 28 weeks of continuous feeding, the serum of the mice were collected for biochemical and mass spectrometry tests. Serum levels of total cholesterol (TC), triglyceride (TG) and free sterols were determined. The livers and lungs were collected for free sterol quantification and RNA-seq analysis. Results Compared with the CS group, 2% plant sterols intake significantly reduced the levels of TC in the serum of mice (P &lt; 0.05), with the TG level unchanged. The quantitative results of free sterols showed that the concentration of campesterol were increased, and the cholestanol levels were decreased significantly in the serum and liver of the PS group mice. The results of RNA-seq analysis were used to further evaluate its impact on the lipid metabolism related gene expression profile in the livers and lungs. The results showed that HMGCR, SQLE, HMGCS1, SREBF1, and other genes related to cholesterol synthesis in the PS group were significantly up-regulated in the liver, but not in the lung; Among the first 20 targeting pathways related to the action of plant sterols, the liver differentially expressed genes were enriched in lipid metabolism (steroid biosynthesis, terpenoid skeleton biosynthesis, peroxisome, bile acid secretion, PPAR, MAPK, fatty acid metabolism.), inflammation related (Cell adhesion molecules, leukocyte trans-endothelial migration) and amino acid metabolism (glutathione, valine, leucine and isoleucine metabolism). The differential genes in lung tissue are enriched in lipid metabolism (acetone metabolism, fatty acid metabolism, insulin resistance, terpenoid skeleton biosynthesis, iron death, PPAR), cell function (internal Swallowing, aging) and vascular smooth muscle contraction etc. Conclusions Differentially expressed gene networks reflect the multi-dimensional regulation of plant sterols on tissue specific lipid metabolism, which lays a good foundation for further revealing its mechanism. Funding Sources Yihaikerry Nutrition and Food Safety Foundation, Chinese Nutrition Society; Project of Technology Innovation and Application, Chongqing, China

scholarly journals Morphological changes and functional circRNAs screening of rabbit skeletal muscle development

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Qi Zheng ◽  
Cuiyun Zhu ◽  
Jing Jing ◽  
Yinghui Ling ◽  
Shuaiqi Qin ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Muscle Development ◽  
Expression Profiles ◽  
Paraffin Section ◽  
Rabbit Skeletal Muscle ◽  
Differentially Expressed ◽  
Adult Rabbit ◽  
Rna Seq ◽  
Skeletal Muscle Development ◽  
Host Genes

Abstract Background The temporal expression pattern of circular RNAs (circRNAs) across developmental stages is essential for skeletal muscle growth and functional analysis. However, there are few analyses on the potential functions of circRNAs in rabbit skeletal muscle development. Results Initially, the paraffin sections showed extremely significant differences in the diameter, number, area and density of skeletal muscle fibers of the fetus, child, adult rabbit hind legs (P < 0.01). Then, RNA-seq libraries of these three stages were constructed. A total of 481 differentially expressed circRNAs (DE-circRNAs) and 5,658 differentially expressed genes (DEGs) were identified. Subsequently, DE-circRNAs, whose host genes were DEGs or non-DEGs, were analyzed by GO respectively. In the fetus vs. child group, up-regulated DE-circRNAs (whose host genes were DEGs) were related to muscle fiber structure, and down-regulated ones were related to mitosis. The up-regulated DE-circRNAs (whose host genes were non-DEGs) were involved in enzyme activity, methylation and glycosylation, and the down-regulated ones were involved in mitosis and catabolism. In the fetus vs. adult group, the up-regulated DE-circRNAs (whose host genes were DEGs) were related to skeletal muscle basic structure, and the down-regulated ones were also associated with cell proliferation. But the up-regulated DE-circRNAs (whose host genes were non-DEGs) were connected with regulation of histone ubiquitination, chromatin and organelles. The down-regulated DE-circRNAs were connected with the catabolism processes. In addition, novel_circ_0022663 and novel_circ_0005489, which might have coding potential, and novel_circ_0004210 and novel_circ_0001669, which might have miRNA sponge capability, were screened out. Conclusions In this study, hind leg muscles of fetus, child and adult rabbits were collected for paraffin section and RNA-seq to observe the structural changes of skeletal muscle and obtain circRNA expression profiles at different stages. These data provided a catalog of circRNAs related to muscle development in New Zealand rabbits, allowing us to better understand the functional transitions in mammalian muscle development.

scholarly journals Identification of differentially expressed genes in the longissimus dorsi muscle of Luchuan and Duroc pigs by transcriptome sequencing

2020 ◽  
Author(s):  
Pengcheng Pan ◽  
Zhaoxian Qin ◽  
Wan Xie ◽  
Di Jiao ◽  
Baojian Chen ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Fatty Acid ◽  
Meat Quality ◽  
Fatty Acid Metabolism ◽  
Transcriptome Sequencing ◽  
Acid Metabolism ◽  
Differentially Expressed ◽  
Longissimus Dorsi ◽  
Longissimus Dorsi Muscle ◽  
Dorsi Muscle

AbstractThe Duroc pig originated in the United States and is a typical lean meat pig. The breed grows fast and the body size is large, but the meat quality is poor. The Luchuan pig is one of the eight local excellent breeds in China; it has tender meat but a small size. To study the factors that determine growth, we selected the longissimus dorsi muscle of Luchuan and Duroc pigs for transcriptome sequencing. The results of transcriptome showed that 3682 genes were differentially expressed (DEGs) in the longissimus dorsi muscle of Duroc and Luchuan pigs. We screened out forty genes related to muscle development and selected the Myosin light chain-2 (MYL2) gene to perform preliminary research. Gene Ontology (GO) enrichment of biological functions and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that most of the forty gene were mainly involved in the Akt/FoxO signaling pathway, Fatty acid metabolism, Arachidonic acid metabolism and Glycine, serine and threonine metabolism. Such pathways contributed to skeletal muscle growth, fatty acid metabolism and intramuscular fat deposition. These results provide insight into the mechanisms underlying the formation of skeletal muscle and provide candidate genes to improve growth traits and meat quality traits, as well as contribute to improving the growth and development traits of pigs through molecular breeding.

Role of the AMP-activated protein kinase in regulating fatty acid metabolism during exerciseThis paper is one of a selection of papers published in this Special Issue, entitled 14th International Biochemistry of Exercise Conference – Muscles as Molecular and Metabolic Machines, and has undergone the Journal’s usual peer review process.

2009 ◽  
Vol 34 (3) ◽  
pp. 315-322 ◽  
Author(s):  
Gregory R. Steinberg
Keyword(s):  
Skeletal Muscle ◽  
Fatty Acids ◽  
Adipose Tissue ◽  
Fatty Acid ◽  
Protein Kinase ◽  
Fatty Acid Metabolism ◽  
Acid Metabolism ◽  
Moderate Intensity ◽  
Amp Activated Protein Kinase

During moderate-intensity exercise, fatty acids are the predominant substrate for working skeletal muscle. The release of fatty acids from adipose tissue stores, combined with the ability of skeletal muscle to actively fine tune the gradient between fatty acid and carbohydrate metabolism, depending on substrate availability and energetic demands, requires a coordinated system of metabolic control. Over the past decade, since the discovery that AMP-activated protein kinase (AMPK) was increased in accordance with exercise intensity, there has been significant interest in the proposed role of this ancient stress-sensing kinase as a critical integrative switch controlling metabolic responses during exercise. In this review, studies examining the role of AMPK as a regulator of fatty acid metabolism in both adipose tissue and skeletal muscle during exercise will be discussed. Exercise induces activation of AMPK in adipocytes and regulates triglyceride hydrolysis and esterfication through phosphorylation of hormone sensitive lipase (HSL) and glycerol-3-phosphate acyl-transferase, respectively. In skeletal muscle, exercise-induced activation of AMPK is associated with increases in fatty acid uptake, phosphorylation of HSL, and increased fatty acid oxidation, which is thought to occur via the acetyl-CoA carboxylase-malony-CoA-CPT-1 signalling axis. Despite the importance of AMPK in regulating fatty acid metabolism under resting conditions, recent evidence from transgenic models of AMPK deficiency suggest that alternative signalling pathways may also be important for the control of fatty acid metabolism during exercise.

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