Transcriptomics analysis of proliferation and differentiation of Guangxi cattle muscle stem cells
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PROVIDER: PRJNA639164 | ENA |
REPOSITORIES: ENA
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Project description:More and more studies have shown that mRNAs and non-coding RNAs are involved in human diseases and various biological processes of animals, and play an important functional role in animal muscle growth and development. In this study, the expression levels of myogenic marker molecules MYOD1, MYOG, and MyHC increased after cattle muscle stem cells transition from proliferation to differentiation, which promoted the differentiation and maturation of cells. Then, we used RNA sequencing and bioinformatics to analyze the RNA expression of muscle stem cell proliferation phase (GM) and differentiation phase (DM). The results showed that 19,341 protein-coding RNAs (mRNAs) and 12,920 non-coding RNAs participated in the proliferation and differentiation of cattle muscle stem cells. And there were 2,148 differential mRNAs and 888 non-coding RNAs, including 113 miRNAs, 662 lncRNAs, and 113 circRNAs. These differentially expressed mRNAs are enriched in ECM receptor function, cell cycle, TGF-beta, PI3K-Akt and other signaling pathways, covering biological processes such as cell proliferation, invasion, differentiation, and autophagy. At the same time, we verified the expression levels of 7 mRNAs, 3 miRNAs, 2 lncRNAs, and 12 circRNAs by real-time quantitative PCR analysis, and selected circUBE2Q2 for functional verification. The expression profiling analysis showed that circUBE2Q2 was expressed in multiple tissues, and its expression in muscle stem cell differentiation phase was significantly higher than that in proliferation phase. In vitro cell experiments, circUBE2Q2 significantly promoted the differentiation and apoptosis of MuSCs and had no effect on proliferation. It indicates that circRNA plays a role in the muscle development of Guangxi cattle. Our research revealed the role of RNA expression in the proliferation and differentiation of Guangxi cattle muscle stem cells. These results provide new clues for the analysis of the mechanism by which mRNAs and non-coding RNAs regulate the proliferation and differentiation of Guangxi cattle muscle stem cells.
2021-06-12 | GSE152398 | GEO
Project description:Sex condition has been demonstrated to alter meat quality and sex is a major factor that affects the fatty acid composition of lipids of carcass dissectible or intramuscular depot fats. But the possible genetic molecular mechanism of gender causing meat quality differences is not well defined. Qinchuan cattle, Qinghai yak and Guangxi buffalo are three typical indigenous species of cattle in China. Obivious differences of meat quality exist among the three species of cattle. Few studies have been conducted to elucidate the muscle tissue expression of genes involved in pathways and mechanisms leading to meat quality differences beyond the phenotype properties of beef. Bovine Genome Arrays were used to construct muscle expression profiles of the longuissimus dorsi from Qinchuan cattle at 36 months and screen differentially expressed genes in the longuissimus dorsi muscle tissues among different genders of Qinchuan cattle, between Qinchuan cattle and Qinghai yak, and between Qinchuan cattle and Guangxi buffalo.
2009-12-23 | GSE19586 | GEO
Project description:Long non-coding RNAs (lncRNAs) have been identified in various tissues and cell types from human, monkey, porcine and mouse. However, expression profile of lncRNAs across Guangxi native cattle and swamp buffalo muscle development has never been investigated. Here, we examine the expression of lncRNA in cattle and buffalo muscle at adult stage(12 months), exhibiting the first report of lncRNA in the Guangxi native cattle and swamp buffalo muscle development of a large animal. 16,236 lncRNA candidates were obtained from buffalo skeletal muscle samples, of which a number of lncRNAs were highly abundant, and 2,161 lncRNAs were differentially expressed between buffalo and cattle. Real-time quantitative PCR (qPCR) analysis confirmed the expression profile of these lncRNAs, including several highly abundant lncRNAs, and a subset of differently expressed lncRNAs according to the high-throughput RNA sequencing (RNA-seq) data. These results indicate that abundant lncRNA is differentially expressed in bovine muscle, indicating important and diverse functions in mammalian muscle development.
2019-12-20 | GSE123869 | GEO
Project description:Buffalo breeding has become an important branch of beef cattle industry. It is of great significance to study buffalo meat production and meat quality. However, the important role of mRNA and lncRNA molecules in muscle stem cells (MuSCs) development in buffalo has not been explored. Then, we performed mRNA and lncRNA expression profiling analysis on the proliferation and differentiation of MuSCs in buffalo. The results showed that there were 4,820 differentially genes, 12,227 mRNAs, and 1,352 lncRNAs. These differentially expressed mRNAs are enriched in biological processes such as cell cycle, p53 signaling pathway, RNA transport, and Calcium signaling pathway and others. We also identified a number of 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 role of mRNA and lncRNA expression in 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.
2021-07-28 | GSE164808 | GEO
Project description:Expression data from the longuissimus dorsi muscle of Qinchuan cattle, Qinghai yak and Guangxi buffalo at 36 months
| PRJNA122361 | ENA
Project description:Circular RNAs (circRNAs) have been identified in various tissues and cell types from human, monkey, porcine and mouse. However, expression profile of circRNAs across cattle muscle development has never been investigated. Here, we examine the expression of circRNA in cattle skeletal muscle at embryonic stage and adult stage, exhibiting the first report of circRNA in the cattle muscle development of a large animal. 12,981 circRNAs are identified and annotated in Qinchuan cattle muscle tissues, including 530 circular intronic RNAs (ciRNAs). We discovered that one parental gene could generate multiple circRNA isoforms with only one or two circRNA isoforms being expressed at higher levels, and several host genes produced different alternative circularization numbers between different muscle development stages. The most circRNA candidates contained two to seven exons, and the genomic distance of the back-splicing site was generally no more than 50 kb. The flanking intron length of most circRNAs was not more than 105 nt and the mean length of upstream or downstream flanking intron was about 11,000 nt. Real-time quantitative PCR (qPCR) analysis confirmed the expression profile of these circRNAs, including several highly abundant circRNAs, and a subset of differently expressed circRNAs according to the high-throughput RNA sequencing (RNA-seq) data. These results display that an abundant circRNAs are dynamically expressed in a spatio-temporal manner in cattle muscle, indicating important and diverse functions during mammalian muscle development.
2018-10-10 | GSE87908 | GEO
Project description:Transcriptomics analysis of proliferation and differentiation of buffalo muscle stem cells
| PRJNA692112 | ENA
Project description:Transcripome of longissimus dorsi muscle was compared between Korean cattle bulls and steers by using a customized bovine Combimatrix microarray containing 10,199 genes. A customized bovine Combimatrix microarray containing 10,199 genes were constructed, and transcripome of longissimus dorsi muscle was compared between Korean cattle bulls (3 bulls) and steers (3 high-marbled and 3 low-marbled steers) by using the microarray hybridzation.
2013-06-30 | E-GEOD-35085 | biostudies-arrayexpress
Project description:Transcripome of longissimus dorsi muscle was compared between Korean cattle bulls and steers by using a customized bovine Combimatrix microarray containing 10,199 genes.
2013-06-30 | GSE35085 | GEO
Project description:Compensatory growth is a naturally occurring accelerated growth phenomenon observed in cattle upon re-alimentation following a prior period of dietary restriction (Hornick et al., 2000). It is incorporated into man production systems as a method to reduce feed costs and consequently is economically important for animal production systems. The goal of our research project is to identify biomarkers for cattle with a superior ability to display compensatory growth. Transcriptional profiling studies of liver and muscle tissues in cattle have shown large numbers of differentially expressed genes in animals undergoing dietary restriction and subsequent compensatory growth when compared to a continuously-fed ad libitum control group of cattle (Connor et al., 2010; Keogh et al., 2016a,b). Given the identification of differential expression at the transcript level, the intended project aims to evaluate potential differences in protein abundance between animals that are diet restricted and subsequently undergo compensatory growth compared to a continuously-fed ad libitum control group of cattle. Differences in genes that are apparent at both the protein and the transcript level are more likely to be transferable across breed type (Snelling et al., 2013) and consequently have more utility for incorporation within genomic selection breeding programs for cattle evaluations.
2020-02-17 | PXD014374 | Pride