scholarly journals Molecular mechanisms detected in yak lung tissue via transcriptome-wide analysis provide insights into adaptation to high altitudes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Qianyun Ge ◽  
Yongbo Guo ◽  
Wangshan Zheng ◽  
Shengguo Zhao ◽  
Yuan Cai ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Lung Tissue ◽  
Molecular Mechanisms ◽  
Differentially Expressed ◽  
P Value ◽  
High Altitudes ◽  
Transcriptional Changes ◽  
Nonlinear Regulation ◽  
Different Altitudes

AbstractDue to their long-term colonization of and widespread distribution in plateau environments, yaks can serve as an ideal natural animal model for the adaptive evolution of other plateau species, including humans. Some studies reported that the lung and heart are two key organs that show adaptive transcriptional changes in response to high altitudes, and most of the genes that show differential expression in lung tissue across different altitudes display nonlinear regulation. To explore the molecular mechanisms that are activated in yak lung tissue in response to hypoxia, the mRNAs, lncRNAs and miRNAs of lung tissue from 9 yaks living at three different altitudes (3400 m, 4200 m and 5000 m), with three repetitions per altitude, were sequenced. Two Zaosheng cattle from 1500 m were selected as low-altitude control. A total of 21,764 mRNAs, 14,168 lncRNAs and 1209 miRNAs (305 known and 904 novel miRNAs) were identified. In a comparison of yaks and cattle, 4975 mRNAs, 3326 lncRNAs and 75 miRNAs were differentially expressed. A total of 756 mRNAs, 346 lncRNAs and 83 miRNAs were found to be differentially expressed among yaks living at three different altitudes (fold change ≥ 2 and P-value < 0.05). The differentially expressed genes between yaks and cattle were functionally enriched in long-chain fatty acid metabolic process and protein processing, while the differentially expressed genes among yaks living at three different altitudes were enriched in immune response and the cell cycle. Furthermore, competing endogenous RNA (ceRNA) networks were investigated to illustrate the roles of ceRNAs in this process, the result was also support the GO and KEGG analysis. The present research provides important genomic insights for discovering the mechanisms that are activated in response to hypoxia in yak lung tissue.

scholarly journals Transcriptomic Analysis Provides Novel Insights into Heat Stress Responses in Sheep

Animals ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 387 ◽  
Author(s):  
Zengkui Lu ◽  
Mingxing Chu ◽  
Qing Li ◽  
Meilin Jin ◽  
Xiaojuan Fei ◽  
...  
Keyword(s):  
Heat Stress ◽  
Differentially Expressed Genes ◽  
Stress Responses ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Transcriptomic Analysis ◽  
Differentially Expressed ◽  
P Value ◽  
Comprehensive Overview

With the intensified and large-scale development of sheep husbandry and global warming, sheep heat stress has become an increasingly important issue. However, little is known about the molecular mechanisms related to sheep responses to heat stress. In this study, transcriptomic analysis of liver tissues of sheep in the presence and absence of heat stress was conducted, with the goal of identifying genes and pathways related to regulation when under such stress. After a comparison with the sheep reference genome, 440,226,436 clean reads were obtained from eight libraries. A p-value ≤ 0.05 and fold change ≥ 2 were taken as thresholds for categorizing differentially expressed genes, of which 1137 were identified. The accuracy and reliability of the RNA-Seq results were confirmed by qRT-PCR. The identified differentially expressed genes were significantly associated with 419 GO terms and 51 KEGG pathways, which suggested their participation in biological processes such as response to stress, immunoreaction, and fat metabolism. This study’s results provide a comprehensive overview of sheep heat stress-induced transcriptional expression patterns, laying a foundation for further analysis of the molecular mechanisms of sheep heat stress.

scholarly journals Transcriptomics Analysis of Primordium Formation in Pleurotus eryngii

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1863
Author(s):  
Dou Ye ◽  
Fang Du ◽  
Yajie Zou ◽  
Qingxiu Hu
Keyword(s):  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Pleurotus Eryngii ◽  
Differentially Expressed ◽  
Light Perception ◽  
Cell Wall Degradation ◽  
Molecular Processes ◽  
Carbohydrate Hydrolysis ◽  
Transcriptional Changes ◽  
Upregulated Genes

Primordium formation is an important stage preceding the growth and development of the Pleurotus eryngii fruiting body. However, the molecular mechanisms underlying primordium formation remain unclear. In the present study, comparative transcriptomics was performed between mature mycelia and primordium to analyze the transcriptional properties during primordium formation in P. eryngii. A total of 19,655 differentially expressed genes (10,718 upregulated genes and 8937 downregulated genes) were identified. These differentially expressed genes were involved in cell wall degradation, carbohydrate hydrolysis, light perception, and cAMP signal transduction. These results aid further understanding of the transcriptional changes and the molecular processes underlying primordium formation and differentiation, which may lay the foundation for improving the cultivation and quality control of P. eryngii.

scholarly journals Meta-analysis based gene expression profiling reveals functional genes in ovarian cancer

2020 ◽  
Vol 40 (11) ◽  
Author(s):  
Lin Zhao ◽  
Yuhui Li ◽  
Zhen Zhang ◽  
Jing Zou ◽  
Jianfu Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Ovarian Cancer ◽  
Gene Expression Profiling ◽  
Differentially Expressed Genes ◽  
Expression Profiling ◽  
Molecular Mechanisms ◽  
Meta Analysis ◽  
Differentially Expressed ◽  
Functional Genes ◽  
P Value

Abstract Background: Ovarian cancer causes high mortality rate worldwide, and despite numerous attempts, the outcome for patients with ovarian cancer are still not well improved. Microarray-based gene expressional analysis provides with valuable information for discriminating functional genes in ovarian cancer development and progression. However, due to the differences in experimental design, the results varied significantly across individual datasets. Methods: In the present study, the data of gene expression in ovarian cancer were downloaded from Gene Expression Omnibus (GEO) and 16 studies were included. A meta-analysis based gene expression analysis was performed to identify differentially expressed genes (DEGs). The most differentially expressed genes in our meta-analysis were selected for gene expression and gene function validation. Results: A total of 972 DEGs with P-value &lt; 0.001 were identified in ovarian cancer, including 541 up-regulated genes and 431 down-regulated genes, among which 92 additional DEGs were found as gained DEGs. Top five up- and down-regulated genes were selected for the validation of gene expression profiling. Among these genes, up-regulated CD24 molecule (CD24), SRY (sex determining region Y)-box transcription factor 17 (SOX17), WFDC2, epithelial cell adhesion molecule (EPCAM), innate immunity activator (INAVA), and down-regulated aldehyde oxidase 1 (AOX1) were revealed to be with consistent expressional patterns in clinical patient samples of ovarian cancer. Gene functional analysis demonstrated that up-regulated WFDC2 and INAVA promoted ovarian cancer cell migration, WFDC2 enhanced cell proliferation, while down-regulated AOX1 was functional in inducing cell apoptosis of ovarian cancer. Conclusion: Our study shed light on the molecular mechanisms underlying the development of ovarian cancer, and facilitated the understanding of novel diagnostic and therapeutic targets in ovarian cancer.

scholarly journals Meta-analysis based gene expressional profiling reveals functional genes in ovarian cancer

2020 ◽  
Author(s):  
Lin Zhao ◽  
Yuhui Li ◽  
Zhen Zhang ◽  
Hong Guo ◽  
Jianfu Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Ovarian Cancer ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Meta Analysis ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
Functional Genes ◽  
P Value ◽  
Clinical Patient

Abstract Background Ovarian cancer causes high mortality rate worldwide, and despite numerous attempts, the outcome for patients with ovarian cancer are still not well improved. Microarray based gene expressional analysis provides with valuable information for discriminating functional genes in ovarian cancer development and progression. However, due to the differences in experimental design, the results varied significantly across individual datasets. Methods In the present study, the data of gene expression in ovarian cancer was downloaded from Gene Expression Omnibus and 16 studies were included. A meta-analysis based gene expression analysis was performed to identify differentially expressed genes (DEGs). The most differentially expressed genes in our meta-analysis were selected for gene expression and gene function validation. Results A total of 972 DEGs with P -value<0.001 were identified in ovarian cancer, including 541 up-regulated genes and 431 down-regulated genes, among which 92 additional DEGs were found as gained DEGs. Top five up-and down-regulated genes were selected for the validation of gene expressional profiling. Among these genes, up-regulated CD24 , SOX17 , WFDC2 , EPCAM , INAVA , and down-regulated AOX1 were revealed to be with consistent expressional patterns in clinical patient samples of ovarian cancer. Gene functional analysis demonstrated that up-regulated WFCD2 and INAVA promoted ovarian cancer cell migration, WFDC2 enhanced cell proliferation, while down-regulated AOX1 was functional in inducing cell apoptosis of ovarian cancer. Interestingly. Conclusion Our study shed light on the molecular mechanisms underlying the development of ovarian cancer, and facilitated the understanding of novel diagnostic and therapeutic targets in ovarian cancer.

Identification of Differentially Expressed Genes Associated with Papillary Thyroid Carcinoma

2020 ◽  
Vol 23 (6) ◽  
pp. 546-553
Author(s):  
Hongyuan Cui ◽  
Mingwei Zhu ◽  
Junhua Zhang ◽  
Wenqin Li ◽  
Lihui Zou ◽  
...  
Keyword(s):  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Cellular Proliferation ◽  
Mrna Level ◽  
Thyroid Tissue ◽  
Differentially Expressed ◽  
Thyroid Tumors ◽  
Papillary Thyroid

Objective: Next-generation sequencing (NGS) was performed to identify genes that were differentially expressed between normal thyroid tissue and papillary thyroid carcinoma (PTC). Materials & Methods: Six candidate genes were selected and further confirmed with quantitative real-time polymerase chain reaction (qRT-PCR), and immunohistochemistry in samples from 24 fresh thyroid tumors and adjacent normal tissues. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was used to investigate signal transduction pathways of the differentially expressed genes. Results: In total, 1690 genes were differentially expressed between samples from patients with PTC and the adjacent normal tissue. Among these, SFRP4, ZNF90, and DCN were the top three upregulated genes, whereas KIRREL3, TRIM36, and GABBR2 were downregulated with the smallest p values. Several pathways were associated with the differentially expressed genes and involved in cellular proliferation, cell migration, and endocrine system tumor progression, which may contribute to the pathogenesis of PTC. Upregulation of SFRP4, ZNF90, and DCN at the mRNA level was further validated with RT-PCR, and DCN expression was further confirmed with immunostaining of PTC samples. Conclusion: These results provide new insights into the molecular mechanisms of PTC. Identification of differentially expressed genes should not only improve the tumor signature for thyroid tumors as a diagnostic biomarker but also reveal potential targets for thyroid tumor treatment.

scholarly journals Expression Profile of New Marker Genes Involved in Differentiation of Canine Adipose-Derived Stem Cells into Osteoblasts

2021 ◽  
Vol 22 (13) ◽  
pp. 6663
Author(s):  
Maurycy Jankowski ◽  
Mariusz Kaczmarek ◽  
Grzegorz Wąsiatycz ◽  
Claudia Dompe ◽  
Paul Mozdziak ◽  
...  
Keyword(s):  
Stem Cells ◽  
In Vitro Culture ◽  
Osteogenic Differentiation ◽  
Molecular Mechanisms ◽  
Marker Genes ◽  
P Value ◽  
Illumina Platform

Next-generation sequencing (RNAseq) analysis of gene expression changes during the long-term in vitro culture and osteogenic differentiation of ASCs remains to be important, as the analysis provides important clues toward employing stem cells as a therapeutic intervention. In this study, the cells were isolated from adipose tissue obtained during routine surgical procedures and subjected to 14-day in vitro culture and differentiation. The mRNA transcript levels were evaluated using the Illumina platform, resulting in the detection of 19,856 gene transcripts. The most differentially expressed genes (fold change >|2|, adjusted p value < 0.05), between day 1, day 14 and differentiated cell cultures were extracted and subjected to bioinformatical analysis based on the R programming language. The results of this study provide molecular insight into the processes that occur during long-term in vitro culture and osteogenic differentiation of ASCs, allowing the re-evaluation of the roles of some genes in MSC progression towards a range of lineages. The results improve the knowledge of the molecular mechanisms associated with long-term in vitro culture and differentiation of ASCs, as well as providing a point of reference for potential in vivo and clinical studies regarding these cells’ application in regenerative medicine.

scholarly journals Analysis of Transcriptional Changes in Different Brassica napus Synthetic Allopolyploids

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 82
Author(s):  
Yunxiao Wei ◽  
Guoliang Li ◽  
Shujiang Zhang ◽  
Shifan Zhang ◽  
Hui Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Napus ◽  
Differentially Expressed Genes ◽  
Expression Patterns ◽  
Female Parent ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Transcriptional Changes ◽  
Aa Genome ◽  
High Degree

Allopolyploidy is an evolutionary and mechanistically intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the gene expression patterns of eight F2 synthetic Brassica napus using RNA sequencing. We found that B. napus allopolyploid formation was accompanied by extensive changes in gene expression. A comparison between F2 and the parent shows a certain proportion of differentially expressed genes (DEG) and activation\silent gene, and the two genomes (female parent (AA)\male parent (CC) genomes) showed significant differences in response to whole-genome duplication (WGD); non-additively expressed genes represented a small portion, while Gene Ontology (GO) enrichment analysis showed that it played an important role in responding to WGD. Besides, genome-wide expression level dominance (ELD) was biased toward the AA genome, and the parental expression pattern of most genes showed a high degree of conservation. Moreover, gene expression showed differences among eight individuals and was consistent with the results of a cluster analysis of traits. Furthermore, the differential expression of waxy synthetic pathways and flowering pathway genes could explain the performance of traits. Collectively, gene expression of the newly formed allopolyploid changed dramatically, and this was different among the selfing offspring, which could be a prominent cause of the trait separation. Our data provide novel insights into the relationship between the expression of differentially expressed genes and trait segregation and provide clues into the evolution of allopolyploids.

scholarly journals Identification of Differentially Expressed Genes in Porcine Ovaries at Proestrus and Estrus Stages Using RNA-Seq Technique

2018 ◽  
Vol 2018 ◽  
pp. 1-8 ◽  
Author(s):  
Songbai Yang ◽  
Xiaolong Zhou ◽  
Yue Pei ◽  
Han Wang ◽  
Ke He ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Hormone Secretion ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
The Novel ◽  
Kegg Pathways ◽  
Go Enrichment ◽  
Single Organism

Estrus is an important factor for the fecundity of sows, and it is involved in ovulation and hormone secretion in ovaries. To better understand the molecular mechanisms of porcine estrus, the expression patterns of ovarian mRNA at proestrus and estrus stages were analyzed using RNA sequencing technology. A total of 2,167 differentially expressed genes (DEGs) were identified (P≤0.05, log2  Ratio≥1), of which 784 were upregulated and 1,383 were downregulated in the estrus compared with the proestrus group. Gene Ontology (GO) enrichment indicated that these DEGs were mainly involved in the cellular process, single-organism process, cell and cell part, and binding and metabolic process. In addition, a pathway analysis showed that these DEGs were significantly enriched in 33 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including cell adhesion molecules, ECM-receptor interaction, and cytokine-cytokine receptor interaction. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) confirmed the differential expression of 10 selected DEGs. Many of the novel candidate genes identified in this study will be valuable for understanding the molecular mechanisms of the sow estrous cycle.

scholarly journals Comparative Transcriptomic Analysis of Embryo Implantation in Mice and Rats

2018 ◽  
Vol 50 (2) ◽  
pp. 668-678 ◽  
Author(s):  
Wen-Qian Zhang ◽  
Miao Zhao ◽  
Ming-Yu Huang ◽  
Ji-Long Liu
Keyword(s):  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Embryo Implantation ◽  
Differentially Expressed ◽  
Rat Uterus ◽  
Mouse Uterus ◽  
Pathway Network ◽  
Implantation Sites ◽  
High Selection ◽  
Transcriptomic Changes

Background/Aims: Embryo implantation is an essential process for eutherian pregnancy, but this process varies across eutherians. The genomic mechanisms that led to the emergence and diversification of embryo implantation are largely unknown. Methods: In this study, we analyzed transcriptomic changes during embryo implantation in mice and rats by using RNA-seq. Bioinformatics and evolutionary analyses were performed to characterize implantation-associated genes in these two species. Results: We identified a total of 518 differentially expressed genes in mouse uterus during implantation, of which 253 genes were up-regulated and 265 genes were down-regulated at the implantation sites compared with the inter-implantation sites. In rat uterus, there were 374 differentially expressed genes, of which 284 genes were up-regulated and 90 genes were down-regulated. A cross-species comparison revealed that 92 up-regulated genes and 20 down-regulated genes were shared. The differences and similarities between mice and rats were investigated further at the gene ontology, pathway, network, and causal transcription factor levels. Additionally, we found that embryo implantation might have evolved through the recruitment of ancient genes into uterine expression. The evolutionary rates of the differentially expressed genes in mouse and rat uterus were significantly lower than those of the non-changed genes, indicating that implantation-related genes are evolutionary conserved due to high selection pressure. Conclusion: Our study provides insights into the molecular mechanisms involved in the evolution of embryo implantation.

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