scholarly journals Integrated Analysis of mRNA and MicroRNA Co-expressed Network for the Differentiation of Bovine Skeletal Muscle Cells After Polyphenol Resveratrol Treatment

2021 ◽  
Vol 8 ◽  
Author(s):  
Dan Hao ◽  
Xiao Wang ◽  
Yu Yang ◽  
Bo Thomsen ◽  
Lars-Erik Holm ◽  
...  
Keyword(s):  
Actin Cytoskeleton ◽  
Enrichment Analysis ◽  
Myoblast Differentiation ◽  
Integrated Analysis ◽  
Messenger Rnas ◽  
Cytoskeleton Organization ◽  
Kegg Pathways ◽  
Highly Correlated ◽  
Bovine Skeletal Muscle ◽  
Go Terms

Resveratrol (RSV) has been confirmed to benefit human health. Resveratrol supplemented in the feeds of animals improved pork, chicken, and duck meat qualities. In this study, we identified differentially expressed (DE) messenger RNAs (mRNAs) (n = 3,856) and microRNAs (miRNAs) (n = 93) for the weighted gene co-expression network analysis (WGCNA) to investigate the co-expressed DE mRNAs and DE miRNAs in the primary bovine myoblasts after RSV treatment. The mRNA results indicated that RSV treatments had high correlations with turquoise module (0.91, P-value = 0.01) and blue module (0.93, P-value < 0.01), while only the turquoise module (0.96, P-value < 0.01) was highly correlated with the treatment status using miRNA data. After biological enrichment analysis, the 2,579 DE genes in the turquoise module were significantly enriched in the Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The top two GO terms were actin filament-based process (GO:0030029) and actin cytoskeleton organization (GO:0030036). The top two KEGG pathways were regulation of actin cytoskeleton (bta04810) and tight junction (bta04530). Then, we constructed the DE mRNA co-expression and DE miRNA co-expression networks in the turquoise module and the mRNA–miRNA targeting networks based on their co-expressions in the key module. In summary, the RSV-induced miRNAs participated in the co-expression networks that could affect mRNA expressions to regulate the primary myoblast differentiation. Our study provided a better understanding of the roles of RSV in inducing miRNA and of the characteristics of DE miRNAs in the key co-expressed module in regulation of mRNAs and revealed new candidate regulatory miRNAs and genes for the beef quality traits.

scholarly journals Resveratrol stimulates microRNA expression during differentiation of bovine primary myoblasts

2021 ◽  
Author(s):  
Dan Hao ◽  
Xiao Wang ◽  
Xiaogang Wang ◽  
Bo Thomsen ◽  
Kaixing Qu ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Insulin Signaling ◽  
Target Genes ◽  
Group Versus ◽  
Enrichment Analysis ◽  
Treated Group ◽  
Insulin Signaling Pathway ◽  
Myoblast Differentiation ◽  
P Value ◽  
Go Terms

Background: Resveratrol (RSV), a phenolic compound, is present in many human dietary sources, such as peanuts, peanut butter, grapes skin, and grape wine. RSV has been widely known for its benefits on human health. Beef from cattle skeletal muscle is one of the main sources of protein for human consumption. Previous studies have also found that pork and chicken qualities are influenced by the feed supplementation with RSV. In addition, our previous study demonstrated the RSV effects on bovine myoblast differentiation using messenger RNA (mRNA) data. In this study, we mainly focused on the influences of RSV on microRNA (miRNA) expression. Method: We used 20 μM RSV to treat primary bovine myoblasts and extracted RNA for miRNA sequencing. After quality control and alignment for clean reads, we conducted quantification and analysis of differentially expressed (DE) miRNAs in the case (RSV-treated) group versus control (non-RSV treated) group. Next, we predicted the target genes for the DE miRNAs and analyzed them for the enrichments of Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Results: Finally, we identified 93 DE miRNAs (adjusted P-value < 0.05), of them 44 were upregulated and 49 were downregulated. Bta-miR-34c was the most significantly upregulated miRNA. In silico, prediction results indicated 1,869 target genes for the 93 DE miRNAs. GO enrichment analysis for the genes targeted by DE miRNAs revealed two significant GO terms (adjusted P-value < 0.05), in which the most significant one was stereocilium (GO:0032420). KEGG enrichment analysis showed five significant pathways, and the top significant KEGG pathway was the insulin signaling pathway (bta04910) (adjusted P-value < 0.05). Conclusions: This study provided an improved understanding of effects of RSV on primary bovine myoblast differentiation through the miRNA modulations. The results suggested that RSV could promote differentiation of primary bovine myoblast by stimulating the miRNA expressions. The target genes of DE miRNAs were significantly enriched in the insulin signaling pathway, thus potentially contributing to improving muscle leanness by increasing the energy metabolism.

scholarly journals Identification of Infertility-Associated Topologically Important Genes Using Weighted Co-expression Network Analysis

2021 ◽  
Vol 12 ◽  
Author(s):  
Jingni Wu ◽  
Xiaomeng Xia ◽  
Ye Hu ◽  
Xiaoling Fang ◽  
Sandra Orsulic
Keyword(s):  
Network Analysis ◽  
Topological Analysis ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Gene Expression Omnibus ◽  
Gene Set Enrichment Analysis ◽  
Messenger Rnas ◽  
Hub Genes ◽  
Protein Protein Interaction ◽  
Highly Correlated

Endometriosis has been associated with a high risk of infertility. However, the underlying molecular mechanism of infertility in endometriosis remains poorly understood. In our study, we aimed to discover topologically important genes related to infertility in endometriosis, based on the structure network mining. We used microarray data from the Gene Expression Omnibus (GEO) database to construct a weighted gene co-expression network for fertile and infertile women with endometriosis and to identify gene modules highly correlated with clinical features of infertility in endometriosis. Additionally, the protein–protein interaction network analysis was used to identify the potential 20 hub messenger RNAs (mRNAs) while the network topological analysis was used to identify nine candidate long non-coding RNAs (lncRNAs). Functional annotations of clinically significant modules and lncRNAs revealed that hub genes might be involved in infertility in endometriosis by regulating G protein-coupled receptor signaling (GPCR) activity. Gene Set Enrichment Analysis showed that the phospholipase C-activating GPCR signaling pathway is correlated with infertility in patients with endometriosis. Taken together, our analysis has identified 29 hub genes which might lead to infertility in endometriosis through the regulation of the GPCR network.

scholarly journals Genome-wide identification and characterization of perirenal adipose tissue microRNAs in rabbits fed a high-fat diet

2021 ◽  
Author(s):  
Jie Wang ◽  
Jiahao Shao ◽  
Yanhong Li ◽  
Mauricio A Elzo ◽  
Xianbo Jia ◽  
...  
Keyword(s):  
Intermediate Filament ◽  
High Fat Diet ◽  
Metabolic Regulation ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Normal Diet ◽  
Pathway Enrichment Analysis ◽  
High Fat ◽  
Cytoskeleton Organization ◽  
Kegg Pathways

MicroRNAs (miRNAs) are a class of endogenous single-stranded RNA molecules that play an important role in gene regulation in animals by pairing with target gene mRNA. Extensive evidence shows that miRNAs are key players in metabolic regulation and the development of obesity. However, the systemic understanding of miRNAs in the adipogenesis of obese rabbit need further investigate. Here, seven small RNA libraries from rabbits fed either a standard normal diet (SND; n = 3) or high-fat diet (HFD; n = 4) were constructed and sequenced. Differentially expressed (DE) miRNAs were identified using the edgeR data analysis package from R. Software miRanda and RNAhybrid were used to predict the target genes of miRNAs. To further explore the functions of DE miRNAs, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed. A total of 81,449,996 clean reads were obtained from the seven libraries, of which, 52 known DE miRNAs (24 up-regulated, 28 down-regulated) and 31 novel DE miRNAs (14 up-regulated, 17 down-regulated) were identified. GO enrichment analysis revealed that the DE miRNAs target genes were involved in intermediate filament cytoskeleton organization, intermediate filament-based process, and alpha-tubulin binding. DE miRNAs were involved in p53 signaling, linoleic acid metabolism, and other adipogenesis-related KEGG pathways. Our study further elucidates the possible functions of DE miRNAs in rabbit adipogenesis, contributing to the understanding of rabbit obesity.

scholarly journals Identification of pivotal lncRNAs in papillary thyroid cancer using lncRNA–mRNA–miRNA ceRNA network analysis

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7441 ◽  
Author(s):  
Weiwei Liang ◽  
Fangfang Sun
Keyword(s):  
Gene Expression ◽  
Thyroid Cancer ◽  
Network Analysis ◽  
Papillary Thyroid Cancer ◽  
Enrichment Analysis ◽  
Integrated Analysis ◽  
Pathway Enrichment Analysis ◽  
Papillary Thyroid ◽  
Cerna Network ◽  
Go Terms

Background To identify pivotal lncRNAs in papillary thyroid cancer (PTC) using lncRNA–mRNA–miRNA ceRNA network analysis. Methods We obtained gene expression profiles from the gene expression omnibus database. Cancer specific lncRNA, cancer specific miRNA and cancer specific mRNA were identified. An integrated analysis was conducted to detect potential lncRNA–miRNA–mRNA ceRNA in regulating disease transformation. The lncRNA regulated gene ontology (GO) terms and regulated pathways were performed by function analysis. Survival analysis was performed for the pivotal lncRNAs. Results A total of four lncRNAs, 15 miRNAs and 375 mRNAs are identified as the key mediators in the pathophysiological processes of PTC. GO annotation enrichment analysis showed the most relevant GO terms are signal transduction, integral component of membrane and calcium ion binding. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed different changed genes mainly enriched in pathways in cancer, PI3K-Akt signaling pathway and focal adhesion. Among four lncRNAs, only SLC26A4-AS1 was significantly associated with PTC patient disease free survival. Conclusion This study has constructed lncRNA–mRNA–miRNA ceRNA networks in PTC. The study provides a set of pivotal lncRNAs for future investigation into the molecular mechanisms.

scholarly journals Genome-wide Identification and Characterization of Perirenal Adipose Tissue MiRNAs in Rabbits Fed With a High-fat Diet

2020 ◽  
Author(s):  
Jie Wang ◽  
Jiahao Shao ◽  
Yanhong Li ◽  
Mauricio A. Elzo ◽  
Xianbo Jia ◽  
...  
Keyword(s):  
Intermediate Filament ◽  
High Fat Diet ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Normal Diet ◽  
Pathway Enrichment Analysis ◽  
High Fat ◽  
Alpha Tubulin ◽  
Cytoskeleton Organization ◽  
Kegg Pathways

Abstract Background MicroRNAs (miRNAs) are a class of endogenous single-stranded RNA molecules that play an important role in gene regulation in animals by pairing with target gene mRNAs. However, the functions of miRNAs in the adipogenesis of obese rabbits are poorly understood. Methods Six small RNA libraries from rabbits under a standard normal diet (SND; n = 3) and a high-fat diet (HFD; n = 3) were constructed and sequenced. Differentially expressed (DE) miRNAs were identified using the edgeR data analysis package from R. Software miRanda and RNAhybrid were used to predict the target genes of miRNAs. To further explore the functions of DE miRNAs, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed. Results A total of 69577441 clean reads were obtained from the six libraries, of which, 52 known DE miRNAs (24 up-regulated, 28 down-regulated) and 31 novel DE miRNAs (14 up-regulated, 17 down-regulated) were identified. GO enrichment analysis revealed that the DE miRNAs target genes were involved in intermediate filament cytoskeleton organization, intermediate filament-based process, and alpha-tubulin binding. DE miRNAs were involved in p53 signaling, linoleic acid metabolism, and other adipogenesis-related KEGG pathways. Conclusions Our study further elucidates the possible functions of DE miRNAs in rabbit adipogenesis, contributing to the understanding of rabbit obesity.

scholarly journals Network Pharmacology Reveals That Resveratrol Can Alleviate COVID-19-Related Hyperinflammation

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Zijian Xiao ◽  
Qing Ye ◽  
Xiaomei Duan ◽  
Tao Xiang
Keyword(s):  
Signaling Pathway ◽  
Antiviral Agent ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Bioinformatic Analysis ◽  
Gene Expression Omnibus ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Kegg Pathways ◽  
Go Terms

Hyperinflammation is related to the development of COVID-19. Resveratrol is considered an anti-inflammatory and antiviral agent. Herein, we used a network pharmacological approach and bioinformatic gene analysis to explore the pharmacological mechanism of Resveratrol in COVID-19 therapy. Potential targets of Resveratrol were obtained from public databases. SARS-CoV-2 differentially expressed genes (DEGs) were screened out via bioinformatic analysis Gene Expression Omnibus (GEO) datasets GSE147507, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis; then, protein-protein interaction network was constructed. The common targets, GO terms, and KEGG pathways of Resveratrol targets and SARS-CoV-2 DEGs were confirmed. KEGG Mapper queried the location of common targets in the key pathways. A notable overlap of the GO terms and KEGG pathways between Resveratrol targets and SARS-CoV-2 DEGs was revealed. The shared targets between Resveratrol targets and SARS-CoV-2 mainly involved the IL-17 signaling pathway, NF-kappa B signaling pathway, and TNF signaling pathway. Our study uncovered that Resveratrol is a promising therapeutic candidate for COVID-19 and we also revealed the probable key targets and pathways involved. Ultimately, we bring forward new insights and encourage more studies on Resveratol to benefit COVID-19 patients.

Identification of key mRNAs, miRNAs, and mRNA-miRNA network involved in papillary thyroid carcinoma

2020 ◽  
Vol 15 ◽  
Author(s):  
Wei Han ◽  
Dongchen Lu ◽  
Chonggao Wang ◽  
Mengdi Cui ◽  
Kai Lu
Keyword(s):  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Differential Expression Analysis ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Integrated Analysis ◽  
Papillary Thyroid ◽  
Gene Set Enrichment ◽  
Mirna Expression Data

Background: In the past decades, the incidence of thyroid cancer (TC) has been gradually increasing, owing to the widespread use of ultrasound scanning devices. However, the key mRNAs, miRNAs, and mRNA-miRNA network in papillary thyroid carcinoma (PTC) has not been fully understood. Material and Methods: In this study, multiple bioinformatics methods were employed, including differential expression analysis, gene set enrichment analysis, and miRNA-mRNA interaction network construction. Results: First, we investigated the key miRNAs that regulated significantly more differentially expressed genes based on GSEA method. Second, we searched for the key miRNAs based on the mRNA-miRNA interaction subnetwork involved in PTC. We identified hsa-mir-1275, hsa-mir-1291, hsa-mir-206 and hsa-mir-375 as the key miRNAs involved in PTC pathogenesis. Conclusion: The integrated analysis of the gene and miRNA expression data not only identified key mRNAs, miRNAs, and mRNA-miRNA network involved in papillary thyroid carcinoma, but also improved our understanding of the pathogenesis of PTC.

scholarly journals Differential Morpho-Physiological and Transcriptomic Responses to Heat Stress in Two Blueberry Species

2021 ◽  
Vol 22 (5) ◽  
pp. 2481
Author(s):  
Jodi Callwood ◽  
Kalpalatha Melmaiee ◽  
Krishnanand P. Kulkarni ◽  
Amaranatha R. Vennapusa ◽  
Diarra Aicha ◽  
...  
Keyword(s):  
Heat Stress ◽  
Molecular Mechanisms ◽  
Stomatal Closure ◽  
Enrichment Analysis ◽  
Leaf Size ◽  
Vaccinium Corymbosum ◽  
Climatic Conditions ◽  
Differentially Expressed ◽  
Transcriptomic Changes ◽  
Go Terms

Blueberries (Vaccinium spp.) are highly vulnerable to changing climatic conditions, especially increasing temperatures. To gain insight into mechanisms underpinning the response to heat stress, two blueberry species were subjected to heat stress for 6 and 9 h at 45 °C, and leaf samples were used to study the morpho-physiological and transcriptomic changes. As compared with Vaccinium corymbosum, Vaccinium darrowii exhibited thermal stress adaptation features such as small leaf size, parallel leaf orientation, waxy leaf coating, increased stomatal surface area, and stomatal closure. RNAseq analysis yielded ~135 million reads and identified 8305 differentially expressed genes (DEGs) during heat stress against the control samples. In V. corymbosum, 2861 and 4565 genes were differentially expressed at 6 and 9 h of heat stress, whereas in V. darrowii, 2516 and 3072 DEGs were differentially expressed at 6 and 9 h, respectively. Among the pathways, the protein processing in the endoplasmic reticulum (ER) was the highly enriched pathway in both the species: however, certain metabolic, fatty acid, photosynthesis-related, peroxisomal, and circadian rhythm pathways were enriched differently among the species. KEGG enrichment analysis of the DEGs revealed important biosynthesis and metabolic pathways crucial in response to heat stress. The GO terms enriched in both the species under heat stress were similar, but more DEGs were enriched for GO terms in V. darrowii than the V. corymbosum. Together, these results elucidate the differential response of morpho-physiological and molecular mechanisms used by both the blueberry species under heat stress, and help in understanding the complex mechanisms involved in heat stress tolerance.

scholarly journals Preferential Ribosome Loading on the Stress-Upregulated mRNA Pool Shapes the Selective Translation under Stress Conditions

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 304
Author(s):  
Yan Chen ◽  
Min Liu ◽  
Zhicheng Dong
Keyword(s):  
Enrichment Analysis ◽  
Close Correlation ◽  
Stress Conditions ◽  
Functional Categories ◽  
Molecular Pattern ◽  
Mrna Pool ◽  
Selective Translation ◽  
Stress Responsive Genes ◽  
Highly Correlated ◽  
Response To Water

The reprogramming of gene expression is one of the key responses to environmental stimuli, whereas changes in mRNA do not necessarily bring forth corresponding changes of the protein, which seems partially due to the stress-induced selective translation. To address this issue, we systematically compared the transcriptome and translatome using self-produced and publicly available datasets to decipher how and to what extent the coordination and discordance between transcription and translation came to be in response to wounding (self-produced), dark to light transition, heat, hypoxia, Pi starvation and the pathogen-associated molecular pattern (elf18) in Arabidopsis. We found that changes in total mRNAs (transcriptome) and ribosome-protected fragments (translatome) are highly correlated upon dark to light transition or heat stress. However, this close correlation was generally lost under other four stresses analyzed in this study, especially during immune response, which suggests that transcription and translation are differentially coordinated under distinct stress conditions. Moreover, Gene Ontology (GO) enrichment analysis showed that typical stress responsive genes were upregulated at both transcriptional and translational levels, while non-stress-specific responsive genes were changed solely at either level or downregulated at both levels. Taking wounding responsive genes for example, typical stress responsive genes are generally involved in functional categories related to dealing with the deleterious effects caused by the imposed wounding stress, such as response to wounding, response to water deprivation and response to jasmonic acid, whereas non-stress-specific responsive genes are often enriched in functional categories like S-glycoside biosynthetic process, photosynthesis and DNA-templated transcription. Collectively, our results revealed the differential as well as targeted coordination between transcriptome and translatome in response to diverse stresses, thus suggesting a potential model wherein preferential ribosome loading onto the stress-upregulated mRNA pool could be a pacing factor for selective translation.

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