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

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.

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

10.1101/2020.09.25.313908 ◽

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.

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

10.21203/rs.3.rs-93395/v1 ◽

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.

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Neural lineage induction reveals multi-scale dynamics of 3D chromatin organization

10.1101/004168 ◽

2014 ◽

Author(s):

Aleksandra Pekowska ◽

Bernd Klaus ◽

Felix Alexander Klein ◽

Simon Anders ◽

Malgorzata Oles ◽

...

Keyword(s):

Gene Expression ◽

Regulation Of Gene Expression ◽

Embryonic Stem ◽

Neural Induction ◽

Interaction Network ◽

Regulatory Elements ◽

Chromatin Organization ◽

Spatial Proximity ◽

Enhancer Element ◽

Neural Lineage

Regulation of gene expression underlies cell identity. Chromatin structure and gene activity are linked at multiple levels, via positioning of genomic loci to transcriptionally permissive or repressive environments and by connecting cis-regulatory elements such as promoters and enhancers. However, the genome-wide dynamics of these processes during cell differentiation has not been characterized. Using tethered chromatin conformation capture (TCC) sequencing we determined global three-dimensional chromatin structures in mouse embryonic stem (ES) and neural stem (NS) cell derivatives. We found that changes in the propensity of genomic regions to form inter-chromosomal contacts are pervasive in neural induction and are associated with the regulation of gene expression. Moreover, we found a pronounced contribution of euchromatic domains to the intra-chromosomal interaction network of pluripotent cells, indicating the existence of an ES cell-specific mode of chromatin organization. Mapping of promoter-enhancer interactions in pluripotent and differentiated cells revealed that spatial proximity without enhancer element activity is a common architectural feature in cells undergoing early developmental changes. Activity-independent formation of higher-order contacts between cis-regulatory elements, predominant at complex loci, may thus provide an additional layer of transcriptional control.

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System Review about Function Role of ESCC Driver Gene KDM6A by Network Biology Approach

The Scientific World JOURNAL ◽

10.1155/2016/1970904 ◽

2016 ◽

Vol 2016 ◽

pp. 1-6 ◽

Cited By ~ 1

Author(s):

Jihua Ran ◽

Hui Li ◽

Huiwu Li

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Regulation Of Gene Expression ◽

Chromatin Modification ◽

Interaction Network ◽

Driver Gene ◽

Cell Cycle Gene ◽

Ppi Network ◽

System Review

Background.KDM6A (Lysine (K)-Specific Demethylase 6A) is the driver gene related to esophageal squamous cell carcinoma (ESCC). In order to provide more biological insights into KDM6A, in this paper, we treat PPI (protein-protein interaction) network derived from KDM6A as a conceptual framework and follow it to review its biological function.Method.We constructed a PPI network with Cytoscape software and performed clustering of network with Clust&See. Then, we evaluate the pathways, which are statistically involved in the network derived from KDM6A. Lastly, gene ontology analysis of clusters of genes in the network was conducted.Result.The network includes three clusters that consist of 74 nodes connected via 453 edges. Fifty-five pathways are statistically involved in the network and most of them are functionally related to the processes of cell cycle, gene expression, and carcinogenesis. The biology themes of clusters 1, 2, and 3 are chromatin modification, regulation of gene expression by transcription factor complex, and control of cell cycle, respectively.Conclusion.The PPI network presents a panoramic view which can facilitate for us to understand the function role of KDM6A. It is a helpful way by network approach to perform system review on a certain gene.

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Identification of key microRNAs of plasma extracellular vesicles and their diagnostic and prognostic significance in melanoma

Open Medicine ◽

10.1515/med-2020-0111 ◽

2020 ◽

Vol 15 (1) ◽

pp. 464-482

Author(s):

Jiachao Xiong ◽

Yan Xue ◽

Yu Xia ◽

Jiayi Zhao ◽

Yuchong Wang

Keyword(s):

Gene Expression ◽

Extracellular Vesicles ◽

Target Genes ◽

Malignant Tumors ◽

Prognostic Significance ◽

Interaction Network ◽

Microarray Dataset ◽

Differential Analysis ◽

Expression Levels ◽

Prognostic Analysis

AbstractMelanoma is one of the most highly metastatic, aggressive and fatal malignant tumors in skin cancer. This study employs bioinformatics to identify key microRNAs and target genes (TGs) of plasma extracellular vesicles (pEVs) and their diagnostic and prognostic significance in melanoma. The gene expression microarray dataset (GSE100508) was downloaded from the Gene Expression Omnibus database. Differential analysis of miRNAs in pEVs was performed to compare melanoma samples and healthy samples. Then, TGs of the differential miRNAs (DE-miRNAs) in melanoma were selected, and differential genes were analyzed by bioinformatics (including Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment, protein–protein interaction network and prognostic analysis). A total of 55 DE-miRNAs were found, and 3,083 and 1,351 candidate TGs were diagnostically correlated with the top ten upregulated DE-miRNAs and all downregulated DE-miRNAs, respectively. Prognostic analysis results showed that high expression levels of hsa-miR-550a-3p, CDK2 and POLR2A and low expression levels of hsa-miR-150-5p in melanoma patients were associated with significantly reduced overall survival. In conclusion, bioinformatics analysis identified key miRNAs and TGs in pEVs of melanoma, which may represent potential biomarkers for the early diagnosis and treatment of this cancer.

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Linking transcription, RNA polymerase II elongation and alternative splicing

Biochemical Journal ◽

10.1042/bcj20200475 ◽

2020 ◽

Vol 477 (16) ◽

pp. 3091-3104 ◽

Cited By ~ 1

Author(s):

Luciana E. Giono ◽

Alberto R. Kornblihtt

Keyword(s):

Gene Expression ◽

Alternative Splicing ◽

Rna Polymerase Ii ◽

Environmental Changes ◽

Transcription Elongation ◽

Single Gene ◽

Regulation Of Gene Expression ◽

Regulation Of Transcription ◽

Stepping Stones ◽

Eukaryotic Transcription

Gene expression is an intricately regulated process that is at the basis of cell differentiation, the maintenance of cell identity and the cellular responses to environmental changes. Alternative splicing, the process by which multiple functionally distinct transcripts are generated from a single gene, is one of the main mechanisms that contribute to expand the coding capacity of genomes and help explain the level of complexity achieved by higher organisms. Eukaryotic transcription is subject to multiple layers of regulation both intrinsic — such as promoter structure — and dynamic, allowing the cell to respond to internal and external signals. Similarly, alternative splicing choices are affected by all of these aspects, mainly through the regulation of transcription elongation, making it a regulatory knob on a par with the regulation of gene expression levels. This review aims to recapitulate some of the history and stepping-stones that led to the paradigms held today about transcription and splicing regulation, with major focus on transcription elongation and its effect on alternative splicing.

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