Common Gene Modules Identified for Chicken Adiposity by Network Construction and Comparison

Gao, Zhuoran; Ding, Ran; Zhai, Xiangyun; Wang, Yuhao; Chen, Yaofeng; Ch, Yang; Du, Zhiqiang

doi:10.3389/fgene.2020.00537

Cited by 10 publications

(9 citation statements)

References 62 publications

(83 reference statements)

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“…For module grouping, the partition threshold used is 0.25. Finally, a color is assigned to each gene module, and genes that are not assembled into any module are grouped into gray modules ( 14 ).…”

Section: Methodsmentioning

confidence: 99%

Weighted Gene Co-Expression Network Analysis Identifies Key Modules and Central Genes Associated With Bovine Subcutaneous Adipose Tissue

et al. 2022

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BackgroundFat deposition is an important economic trait in livestock and poultry production. However, the relationship between various genes and signal pathways of fat deposition is still unclear to a large extent. The purpose of this study is to analyze the potential molecular targets and related molecular pathways in bovine subcutaneous adipose tissue.ResultsWe downloaded the GSE116775 microarray dataset from Gene Expression Omnibus (GEO). The weighted gene co-expression network (WGCNA) was used to analyze the gene expression profile, and the key gene modules with the highest correlation with subcutaneous adipose tissue were identified, and the functional enrichment of the key modules was analyzed. Then, the “real” Hub gene was screened by in-module analysis and protein–protein interaction network (PPI), and its expression level in tissue samples and adipocytes was verified. The study showed that a total of nine co-expression modules were identified, and the number of genes in these modules ranged from 101 to 1,509. Among them, the blue module is most closely related to subcutaneous adipose tissue, containing 1,387 genes. These genes were significantly enriched in 10 gene ontologies including extracellular matrix organization, biological adhesion, and collagen metabolic process, and were mainly involved in pathways including ECM-receptor interaction, focal adhesion, cAMP signaling pathway, PI3K-AKT signaling pathway, and regulation of lipolysis in adipocytes. In the PPI network and coexpression network, five genes (CAV1, ITGA5, COL5A1, ABL1, and HSPG2) were identified as “real” Hub genes. Analysis of Hub gene expression by dataset revealed that the expression of these Hub genes was significantly higher in subcutaneous adipose tissue than in other tissues. In addition, real-time fluorescence quantitative PCR (qRT-PCR) analysis based on tissue samples and adipocytes also confirmed the above results.ConclusionIn this study, five key genes related to subcutaneous adipose tissue were discovered, which laid a foundation for further study of the molecular regulation mechanism of subcutaneous adipose tissue development and adipose deposition.

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Section: Methodsmentioning

confidence: 99%

Weighted Gene Co-Expression Network Analysis Identifies Key Modules and Central Genes Associated With Bovine Subcutaneous Adipose Tissue

et al. 2022

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“…The cAMP and calcium signaling pathways act as the second messengers in eukaryotic cells [ 80 ] and regulate the intracellular lipolysis in adipocytes through calcium ions and cAMP levels [ 81 ]. There is substantial evidence that MAPK signaling pathway [ 82 , 83 ], lipid metabolism, insulin signaling [ 84 ], AMPK signaling pathway, Wnt signaling pathway [ 85 , 86 , 87 , 88 ], and TGF-beta signaling pathway [ 89 , 90 ] perform crucial roles in adipogenesis. The results of the present study support the interactive roles of the signaling pathways in the regulation of adipogenesis.…”

Section: Discussionmentioning

confidence: 99%

RNA-Seq Reveals Function of Bta-miR-149-5p in the Regulation of Bovine Adipocyte Differentiation

Guo

Khan

Raza

et al. 2021

Animals

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Intramuscular fat is a real challenge for the experts of animal science to improve meat quality traits. Research on the mechanism of adipogenesis provides invaluable information for the improvement of meat quality traits. This study investigated the effect of bta-miR-149-5p and its underlying mechanism on lipid metabolism in bovine adipocytes. Bovine adipocytes were differentiated and transfected with bta-miR-149-5p mimics or its negative control (NC). A total of 115 DEGs including 72 upregulated and 43 downregulated genes were identified in bovine adipocytes. The unigenes and GO term biological processes were the most annotated unigene contributor parts at 80.08%, followed by cellular component at 13.4% and molecular function at 6.7%. The KEGG pathways regulated by the DEGs were PI3K-Akt signaling pathway, calcium signaling pathway, pathways in cancer, MAPK signaling pathway, lipid metabolism/metabolic pathway, PPAR signaling pathway, AMPK signaling pathway, TGF-beta signaling pathway, cAMP signaling pathway, cholesterol metabolism, Wnt signaling pathway, and FoxO signaling pathway. In addition to this, the most important reactome enrichment pathways were R−BTA−373813 receptor CXCR2 binding ligands CXCL1 to 7, R−BTA−373791 receptor CXCR1 binding CXCL6 and CXCL8 ligands, R−BTA−210991 basigin interactions, R−BTA−380108 chemokine receptors binding chemokines, R−BTA−445704 calcium binding caldesmon, and R−BTA−5669034 TNFs binding their physiological receptors. Furthermore, the expression trend of the DEGs in these pathways were also exploited. Moreover, the bta-miR-149-5p significantly (p < 0.01) downregulated the mRNA levels of adipogenic marker genes such as CCND2, KLF6, ACSL1, Cdk2, SCD, SIK2, and ZEB1 in bovine adipocytes. In conclusion, our results suggest that bta-miR-149-5p regulates lipid metabolism in bovine adipocytes. The results of this study provide a basis for studying the function and molecular mechanism of the bta-miR-149-5p in regulating bovine adipogenesis.

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“…The weighted gene co‐expression network analysis (WGCNA) was conducted based on the expression profile, using the R statistical package (Gao et al., 2020; Langfelder & Horvath, 2008). Briefly, the raw gene expression data were first pre‐processed, and then soft threshold powers (β) were screened to fulfil the scale‐free network assumption.…”

Section: Methodsmentioning

confidence: 99%

Single‐cell RNA‐seq reveals mRNAs and lncRNAs important for oocytes in vitro matured in pigs

Yang

Liu

et al. 2021

Reprod Domestic Animals

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The faithful execution of molecular programme underlying oocyte maturation and meiosis is vital to generate competent haploid gametes for efficient mammalian reproduction. However, the organization and principle of molecular circuits and modules for oocyte meiosis remain obscure. Here, we employed the recently developed single‐cell RNA‐seq technique to profile the transcriptomes of germinal vesicle (GV) and metaphase II (MII) oocytes, aiming to discover the dynamic changes of mRNAs and long non‐coding RNAs (lncRNAs) during oocyte in vitro meiotic maturation. During the transition from GV to MII, total number of detected RNAs (mRNAs and lncRNAs) in oocytes decreased. Moreover, 1,807 (602 up‐ and 1,205 down‐regulated) mRNAs and 313 (177 up‐ and 136 down‐regulated) lncRNAs were significantly differentially expressed (DE), i.e., more mRNAs down‐regulated, but more lncRNAs up‐regulated. During maturation of pig oocytes, mitochondrial mRNAs were actively transcribed, eight of which (ND6, ND5, CYTB, ND1, ND2, COX1, COX2 and COX3) were significantly up‐regulated. Both DE mRNAs and targets of DE lncRNAs were enriched in multiple biological and signal pathways potentially associated with oocyte meiosis. Highly abundantly expressed mRNAs (including DNMT1, UHRF2, PCNA, ARMC1, BTG4, ASNS and SEP11) and lncRNAs were also discovered. Weighted gene co‐expression network analysis (WGCNA) revealed 20 hub mRNAs in three modules to be important for oocyte meiosis and maturation. Taken together, our findings provide insights and resources for further functional investigation of mRNAs/lncRNAs in in vitro meiotic maturation of pig oocytes.

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Common Gene Modules Identified for Chicken Adiposity by Network Construction and Comparison

Cited by 10 publications

References 62 publications

Weighted Gene Co-Expression Network Analysis Identifies Key Modules and Central Genes Associated With Bovine Subcutaneous Adipose Tissue

Weighted Gene Co-Expression Network Analysis Identifies Key Modules and Central Genes Associated With Bovine Subcutaneous Adipose Tissue

RNA-Seq Reveals Function of Bta-miR-149-5p in the Regulation of Bovine Adipocyte Differentiation

Single‐cell RNA‐seq reveals mRNAs and lncRNAs important for oocytes in vitro matured in pigs

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