scholarly journals Insights into the Mechanism of Bovine Spermiogenesis Based on Comparative Transcriptomic Studies

2020 ◽  
Author(s):  
Xin Li ◽  
Chenying Duan ◽  
Ruyi Li ◽  
Dong Wang
Keyword(s):  
Gene Expression ◽  
Semen Quality ◽  
Regulation Of Gene Expression ◽  
Physiological Mechanism ◽  
Interaction Network ◽  
Differential Analysis ◽  
Epididymal Sperm ◽  
Protein Protein Interaction ◽  
Acrosome Formation ◽  
And Function

Abstract To reduce the reproductive loss caused by semen quality and provide theoretical guidance for the eradication of human male infertility, differential analysis of the bovine transcriptome among round spermatids, elongated spermatids, and epididymal sperm was carried out with the reference of the mouse transcriptome, and the homology trends of gene expression to the mouse were also analysed. First, to explore the physiological mechanism of spermiogenesis that profoundly affects semen quality, homological trends of differential genes were compared during spermiogenesis in dairy cattle and mice. Next, the Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, protein-protein interaction network (PPI network), and bioinformatics analysis uncovered the regulation network of acrosome formation during the transition from round to elongated spermatids. In addition, processes that regulate gene expression during spermiogenesis from elongated spermatid to epididymal sperm, such as ubiquitination, acetylation, deacetylation, glycosylation, and the functional gene ART3 may play an important role during spermiogenesis. Therefore, its localisation in the seminiferous tubule was investigated by immunofluorescent analysis, and its structure and function were also predicted. This study provides important data for revealing the mystery of life during spermiogenesis resulting from acrosome formation, histone replacement, and the fine regulation of gene expression.

scholarly journals Insights into the mechanism of bovine spermiogenesis based on comparative transcriptomic studies

2020 ◽  
Author(s):  
Xin Li ◽  
Chenying Duan ◽  
Ruyi Li ◽  
Dong Wang
Keyword(s):  
Gene Expression ◽  
Semen Quality ◽  
Regulation Of Gene Expression ◽  
Physiological Mechanism ◽  
Interaction Network ◽  
Differential Analysis ◽  
Epididymal Sperm ◽  
Protein Protein Interaction ◽  
Acrosome Formation ◽  
And Function

AbstractTo reduce the reproductive loss caused by semen quality and provide theoretical guidance for the eradication of human male infertility, differential analysis of the bovine transcriptome among round spermatids, elongated spermatids, and epididymal sperm was carried out with the reference of the mouse transcriptome, and the homology trends of gene expression to the mouse were also analysed. First, to explore the physiological mechanism of spermiogenesis that profoundly affects semen quality, homological trends of differential genes were compared during spermiogenesis in dairy cattle and mice. Next, the Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, protein-protein interaction network (PPI network), and bioinformatics analysis uncovered the regulation network of acrosome formation during the transition from round to elongated spermatids. In addition, processes that regulate gene expression during spermiogenesis from elongated spermatid to epididymal sperm, such as ubiquitination, acetylation, deacetylation, glycosylation, and the functional gene ART3 may play an important role during spermiogenesis. Therefore, its localisation in the seminiferous tubule was investigated by immunofluorescent analysis, and its structure and function were also predicted. This study provides important data for revealing the mystery of life during spermiogenesis resulting from acrosome formation, histone replacement, and the fine regulation of gene expression.

scholarly journals Insights into the Mechanism of Bovine Spermiogenesis Based on Comparative Transcriptomic Studies

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 80
Author(s):  
Xin Li ◽  
Chenying Duan ◽  
Ruyi Li ◽  
Dong Wang
Keyword(s):  
Gene Expression ◽  
Semen Quality ◽  
Regulation Of Gene Expression ◽  
Physiological Mechanism ◽  
Interaction Network ◽  
Seminiferous Tubules ◽  
Differential Analysis ◽  
Epididymal Sperm ◽  
Bioinformatics Analyses ◽  
Acrosome Formation

To reduce subfertility caused by low semen quality and provide theoretical guidance for the eradication of human male infertility, we sequenced the bovine transcriptomes of round, elongated spermatids and epididymal sperms. The differential analysis was carried out with the reference of the mouse transcriptome, and the homology trends of gene expression to the mouse were also analysed. First, to explore the physiological mechanism of spermiogenesis that profoundly affects semen quality, homological trends of differential genes were compared during spermiogenesis in dairy cattle and mice. Next, Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment, protein–protein interaction network (PPI network), and bioinformatics analyses were performed to uncover the regulation network of acrosome formation during the transition from round to elongated spermatids. In addition, processes that regulate gene expression during spermiogenesis from elongated spermatid to epididymal sperm, such as ubiquitination, acetylation, deacetylation, and glycosylation, and the functional ART3 gene may play important roles during spermiogenesis. Therefore, its localisation in the seminiferous tubules and epididymal sperm were investigated using immunofluorescent analysis, and its structure and function were also predicted. Our findings provide a deeper understanding of the process of spermiogenesis, which involves acrosome formation, histone replacement, and the fine regulation of gene expression.

scholarly journals Data mining of immune-related prognostic genes in metastatic melanoma microenvironment

2020 ◽  
Vol 40 (11) ◽  
Author(s):  
Wei Han ◽  
Biao Huang ◽  
Xiao-Yu Zhao ◽  
Guo-Liang Shen
Keyword(s):  
Gene Expression ◽  
Tumor Microenvironment ◽  
Metastatic Melanoma ◽  
Interaction Network ◽  
Gene Expression Omnibus ◽  
The Cancer Genome Atlas ◽  
Protein Protein Interaction ◽  
Subtype Identification ◽  
Cancer Genome Atlas ◽  
Immune Related Genes

Abstract Skin cutaneous melanoma (SKCM) is one of the most deadly malignancies. Although immunotherapies showed the potential to improve the prognosis for metastatic melanoma patients, only a small group of patients can benefit from it. Therefore, it is urgent to investigate the tumor microenvironment in melanoma as well as to identify efficient biomarkers in the diagnosis and treatments of SKCM patients. A comprehensive analysis was performed based on metastatic melanoma samples from the Cancer Genome Atlas (TCGA) database and ESTIMATE algorithm, including gene expression, immune and stromal scores, prognostic immune-related genes, infiltrating immune cells analysis and immune subtype identification. Then, the differentially expressed genes (DEGs) were obtained based on the immune and stromal scores, and a list of prognostic immune-related genes was identified. Functional analysis and the protein–protein interaction network revealed that these genes enriched in multiple immune-related biological processes. Furthermore, prognostic genes were verified in the Gene Expression Omnibus (GEO) databases and used to predict immune infiltrating cells component. Our study revealed seven immune subtypes with different risk values and identified T cells as the most abundant cells in the immune microenvironment and closely associated with prognostic outcomes. In conclusion, the present study thoroughly analyzed the tumor microenvironment and identified prognostic immune-related biomarkers for metastatic melanoma.

Uncovering potential lncRNAs and nearby mRNAs in systemic lupus erythematosus from the Gene Expression Omnibus dataset

Epigenomics ◽  
2019 ◽  
Vol 11 (16) ◽  
pp. 1795-1809 ◽  
Author(s):  
Haiyu Cao ◽  
Dong Li ◽  
Huixiu Lu ◽  
Jing Sun ◽  
Haibin Li
Keyword(s):  
Gene Expression ◽  
Systemic Lupus Erythematosus ◽  
Lupus Erythematosus ◽  
Noncoding Rnas ◽  
Interaction Network ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
Systemic Lupus ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Network

Aim: The aim of this study was to find potential differentially expressed long noncoding RNAs (lncRNAs) and mRNAs in systemic lupus erythematosus. Materials & methods: Differentially expressed lncRNAs and mRNAs were obtained in the Gene Expression Omnibus dataset. Functional annotation of differentially expressed mRNAs was performed, followed by protein–protein interaction network analysis. Then, the interaction network of lncRNA-nearby targeted mRNA was built. Results: Several interaction pairs of lncRNA-nearby targeted mRNA including NRIR-RSAD2, RP11-153M7.5-TLR2, RP4-758J18.2-CCNL2, RP11-69E11.4-PABPC4 and RP11-496I9.1-IRF7/ HRAS/ PHRF1 were identified. Measles and MAPK were significantly enriched signaling pathways of differentially expressed mRNAs. Conclusion: Our study identified several differentially expressed lncRNAs and mRNAs. And their interactions may play a crucial role in the process of systemic lupus erythematosus.

scholarly journals The Crosstalk between Acetylation and Phosphorylation: Emerging New Roles for HDAC Inhibitors in the Heart

2018 ◽  
Vol 20 (1) ◽  
pp. 102 ◽  
Author(s):  
Justine Habibian ◽  
Bradley Ferguson
Keyword(s):  
Gene Expression ◽  
Protein Phosphorylation ◽  
Cross Talk ◽  
Electrostatic Interactions ◽  
Regulation Of Gene Expression ◽  
Hdac Inhibitors ◽  
Protein Activity ◽  
Histone Protein ◽  
Signal Transduction Protein ◽  
And Function

Approximately five million United States (U.S.) adults are diagnosed with heart failure (HF), with eight million U.S. adults projected to suffer from HF by 2030. With five-year mortality rates following HF diagnosis approximating 50%, novel therapeutic treatments are needed for HF patients. Pre-clinical animal models of HF have highlighted histone deacetylase (HDAC) inhibitors as efficacious therapeutics that can stop and potentially reverse cardiac remodeling and dysfunction linked with HF development. HDACs remove acetyl groups from nucleosomal histones, altering DNA-histone protein electrostatic interactions in the regulation of gene expression. However, HDACs also remove acetyl groups from non-histone proteins in various tissues. Changes in histone and non-histone protein acetylation plays a key role in protein structure and function that can alter other post translational modifications (PTMs), including protein phosphorylation. Protein phosphorylation is a well described PTM that is important for cardiac signal transduction, protein activity and gene expression, yet the functional role for acetylation-phosphorylation cross-talk in the myocardium remains less clear. This review will focus on the regulation and function for acetylation-phosphorylation cross-talk in the heart, with a focus on the role for HDACs and HDAC inhibitors as regulators of acetyl-phosphorylation cross-talk in the control of cardiac function.

scholarly journals Identification of differentially expressed genes in hepatocellular carcinoma by integrated bioinformatic analysis

2019 ◽  
Author(s):  
Guangxin Yan ◽  
Zhaoyu Liu
Keyword(s):  
Gene Expression ◽  
Hepatocellular Carcinoma ◽  
Cell Cycle ◽  
Dna Replication ◽  
Liver Cancer ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Interaction Network ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Network

AbstractHepatocellular carcinoma is one of the most common tumors in the world and has a high mortality rate. This study elucidates the mechanism of hepatocellular carcinoma- (HCC) related development. The HCC gene expression profile (GSE54238, GSE84004) was downloaded from Gene Expression Omnibus for comprehensive analysis. A total of 359 genes were identified, of which 195 were upregulated and 164 were downregulated. Analysis of the condensed results showed that “extracellular allotrope” is a substantially enriched term. “Cell cycle”, “metabolic pathway” and “DNA replication” are three significantly enriched Kyoto Encyclopedia of Genes and Genomespathways. Subsequently, a protein-protein interaction network was constructed. The most important module in the protein-protein interaction network was selected for path enrichment analysis. The results showed thatCCNA2, PLK1, CDC20, UBE2CandAURKAwere identified as central genes, and the expression of these five hub genes in liver cancer was significantly increased in The Cancer Genome Atlas. Univariate regression analysis was also performed to show that the overall survival and disease-free survival of patients in the high expression group were longer than in the expression group. In addition, genes in important modules are mainly involved in “cell cycle”, “DNA replication” and “oocyte meiosis” signaling pathways. Finally, through upstream miRNA analysis, mir-300 and mir-381-3p were found to coregulateCCNA2,AURKAandUBE2C. These results provide a set of targets that can help researchers to further elucidate the underlying mechanism of liver cancer.

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