scholarly journals Transcriptomic analysis of nonylphenol effect on Saccharomyces cerevisiae

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10794
Author(s):  
Ceyhun Bereketoglu ◽  
Gozde Nacar ◽  
Tugba Sari ◽  
Bulent Mertoglu ◽  
Ajay Pradhan
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Adaptive Response ◽  
Cell Cycle Progression ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Yeast Cells ◽  
Genome Wide ◽  
Go Enrichment ◽  
Go Enrichment Analysis

Nonylphenol (NP) is a bioaccumulative environmental estrogen that is widely used as a nonionic surfactant. We have previously examined short-term effects of NP on yeast cells using microarray technology. In the present study, we investigated the adaptive response of Saccharomyces cerevisiae BY4742 cells to NP exposure by analyzing genome-wide transcriptional profiles using RNA-sequencing. We used 2 mg/L NP concentration for 40 days of exposure. Gene expression analysis showed that a total of 948 genes were differentially expressed. Of these, 834 genes were downregulated, while 114 genes were significantly upregulated. GO enrichment analysis revealed that 369 GO terms were significantly affected by NP exposure. Further analysis showed that many of the differentially expressed genes were associated with oxidative phosphorylation, iron and copper acquisition, autophagy, pleiotropic drug resistance and cell cycle progression related processes such as DNA and mismatch repair, chromosome segregation, spindle checkpoint activity, and kinetochore organization. Overall, these results provide considerable information and a comprehensive understanding of the adaptive response to NP exposure at the gene expression level.

scholarly journals Integrative analysis of transcriptome-wide association study and gene expression profiling identifies candidate genes associated with stroke

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7435
Author(s):  
Jian Yang ◽  
Bin Yan ◽  
Yajuan Fan ◽  
Lihong Yang ◽  
Binbin Zhao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Candidate Genes ◽  
Expression Profiling ◽  
Enrichment Analysis ◽  
Integrative Analysis ◽  
Functional Gene ◽  
Gene Sets ◽  
Go Enrichment ◽  
Go Enrichment Analysis

Background Stroke is a major public health burden worldwide. Although genetic variation is known to play a role in the pathogenesis of stroke, the specific pathogenic mechanisms are still unclear. Transcriptome-wide association studies (TWAS) is a powerful approach to prioritize candidate risk genes underlying complex traits. However, this approach has not been applied in stroke. Methods We conducted an integrative analysis of TWAS using data from the MEGASTROKE Consortium and gene expression profiling to identify candidate genes for the pathogenesis of stroke. Gene ontology (GO) enrichment analysis was also conducted to detect functional gene sets. Results The TWAS identified 515 transcriptome-wide significant tissue-specific genes, among which SLC25A44 (P = 5.46E−10) and LRCH1 (P = 1.54E−6) were significant by Bonferroni test for stroke. After validation with gene expression profiling, 19 unique genes were recognized. GO enrichment analysis identified eight significant GO functional gene sets, including regulation of cell shape (P = 0.0059), face morphogenesis (P = 0.0247), and positive regulation of ATPase activity (P = 0.0256). Conclusions Our study identified multiple stroke-associated genes and gene sets, and this analysis provided novel insights into the genetic mechanisms underlying stroke.

scholarly journals Effects of Fibronectin 1 on Cell Proliferation, Senescence and Apoptosis of Human Glioma Cells Through the PI3K/AKT Signaling Pathway

2018 ◽  
Vol 48 (3) ◽  
pp. 1382-1396 ◽  
Author(s):  
Yu-Xiang Liao ◽  
Zhi-Ping Zhang ◽  
Jie Zhao ◽  
Jing-Ping Liu
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Cell Proliferation ◽  
Signaling Pathway ◽  
Enrichment Analysis ◽  
Akt Signaling ◽  
Pathway Enrichment Analysis ◽  
Akt Signaling Pathway ◽  
Go Enrichment ◽  
Go Enrichment Analysis

Background/Aims: The current study aimed to investigate the role by which fibronectin 1 (FN1) influences the cell cycle, senescence and apoptosis in human glioma cells through the PI3K/ AKT signaling pathway. Methods: Differentially expressed genes (DEGs) were identified based on gene expression data (GSE12657, GSE15824 and GSE45921 datasets) and probe annotation files from Gene Expression Omnibus. The DEGs were identified in connection with gene ontology (GO) enrichment analysis and with the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. The positive expression of the FN1 protein was detected by immunohistochemistry. The glioma cell lines U251 and T98G were selected and assigned into blank, negative control (NC) and siRNA-FN1 groups. A dual luciferase reporter gene assay was used to investigate the effects of FN1 on transcriptional activity through the PI3K/AKT signaling pathway. An MTT assay was applied for the detection of cell proliferation, while flow cytometry was employed for cell cycle stage and cellular apoptosis detection. β-galactosidase staining was utilized to detect cellular senescence, a scratch test was applied to evaluate cell migration, and a transwell assay was used to analyze cell invasion. Western blotting and qRT-PCR methods were used to detect the protein and mRNA expression levels, respectively, of the FN1 gene and the related genes in the PI3K/AKT pathway (PI3K, AKT and PTEN), the cell cycle (pRb, CDK4 and Cyclin D1) and cell senescence (p16 and p21) among the collected tissues and cells. Results: GSE12657 profiling revealed FN1 to be the most upregulated gene in glioma. Regarding the GSE12657 and GSE15824 datasets, FN1 gene expression was higher in glioma tissues than in normal tissues. GO enrichment analysis and KEGG pathway enrichment analysis indicated that FN1 is involved in the synthesis of extracellular matrix (ECM) components and the PI3K/AKT signaling pathway. Verification was provided, indicating the role played by the FN1 gene in the regulation of the PI3K/AKT signaling pathway, as silencing the FN1 gene was found to inhibit cell proliferation, promote cell apoptosis and senescence, and reduce migration and invasion through the down-regulation of FN1 gene expression and disruption of the PI3K-AKT signaling pathway. Conclusion: The findings of this study provide evidence highlighting the prominent role played by FN1 in stimulating glioma growth, invasion, and survival through the activation of the PI3K/AKT signaling pathway.

scholarly journals Identification of Hub Genes Associated With Progression and Prognosis of Bladder Cancer by Integrated Bioinformatics Analysis.

2021 ◽  
Author(s):  
Daoquan Liu ◽  
Jianhong Ma ◽  
Sheng Wei ◽  
Jianmin Liu ◽  
Mingzhou Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bladder Cancer ◽  
Muscle Contraction ◽  
Focal Adhesion ◽  
Enrichment Analysis ◽  
Hub Genes ◽  
Expression Levels ◽  
Qrt Pcr ◽  
Go Enrichment ◽  
Go Enrichment Analysis

Abstract Background: Bladder cancer (BLCA) is the most popular malignant carcinomas in genitourinary system which has a high incidence and is prone to relapse. However, the molecular mechanism of BLCA remains to be unclear. Moreover, there is still a shortage of effective biomarkers that can predict progression and prognosis of BLCA. The objective of current study is to screen significant genes as biomarkers to forecast the progression and prognosis of BLCA patients.Methods: Gene expression profile downloaded from TCGA database and GEO database was used. Differential gene expression analysis and WGCNA were conducted to identify differential co-expression genes. In addition, GO enrichment analysis and KEGG pathway analysis were used to explore the functions of these genes. Moreover, PPI network, OS and DFS were used to identify survival-related hub genes. Finally, the expression levels of these genes were validated by qRT-PCR and HPA database.Results: About 124 differential co-expression genes were identified. And these genes were mainly enriched in muscle system process and muscle contraction (BP), contractile fiber, myofibril, sarcomere, focal adhesion and cell-substrate junction (CC) and actin binding (MF) in GO enrichment analysis, while enriched in vascular smooth muscle contraction, focal adhesion, cardiac muscle contraction, hypertrophic cardiomyopathy, dilated cardiomyopathy and regulation of actin cytoskeleton in KEGG analysis. Furthermore, five survival-related hub genes (MYH11, ACTA2, CALD1, TPM1, MYLK) were identified via overall OS and DFS. In addition, the expression levels of the five survival-related genes were upregulated with the procession of BLCA, such as grade, stage and TNM stage. Finally, all survival-related hub genes were found to be down-regulated in BLCA via qRT-PCR and HPA database.Conclusions: Our current study verified five new key genes in BLCA, which could help us better understand the pathogenesis of BLCA. And these five hub genes may be involved in the development and progression of BLCA and served as potential biomarkers.

scholarly journals Selection of Cashmere Fineness Functional Genes by Translatomics

2022 ◽  
Vol 12 ◽  
Author(s):  
Yu Zhang ◽  
Dongyun Zhang ◽  
Yanan Xu ◽  
Yuting Qin ◽  
Ming Gu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Enrichment Analysis ◽  
Phenotypic Traits ◽  
Functional Region ◽  
Papillomavirus Infection ◽  
Extracellular Region ◽  
Genome Wide ◽  
Go Enrichment ◽  
Go Enrichment Analysis ◽  
Differential Genes

Cashmere fineness is an important index to evaluate cashmere quality. Liaoning Cashmere Goat (LCG) has a large cashmere production and long cashmere fiber, but its fineness is not ideal. Therefore, it is important to find genes involved in cashmere fineness that can be used in future endeavors aiming to improve this phenotype. With the continuous advancement of research, the regulation of cashmere fineness has made new developments through high-throughput sequencing and genome-wide association analysis. It has been found that translatomics can identify genes associated with phenotypic traits. Through translatomic analysis, the skin tissue of LCG sample groups differing in cashmere fineness was sequenced by Ribo-seq. With these data, we identified 529 differentially expressed genes between the sample groups among the 27197 expressed genes. From these, 343 genes were upregulated in the fine LCG group in relation to the coarse LCG group, and 186 were downregulated in the same relationship. Through GO enrichment analysis and KEGG enrichment analysis of differential genes, the biological functions and pathways of differential genes can be found. In the GO enrichment analysis, 491 genes were significantly enriched, and the functional region was mainly in the extracellular region. In the KEGG enrichment analysis, the enrichment of the human papillomavirus infection pathway was seen the most. We found that the COL6A5 gene may affect cashmere fineness.

scholarly journals Short-Term Effects on Gene-Expression and on DNA-Methylation at the Genome-Wide Level of the Iberian Ham Intake and Compared With Orange Intake: A Crossover Randomized Trial

2021 ◽  
Vol 5 (Supplement_2) ◽  
pp. 937-937
Author(s):  
Dolores Corella ◽  
José Sorlí ◽  
Eva Asensio ◽  
Rocío Barragán ◽  
Olga Portolés ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Randomized Trial ◽  
Intervention Group ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
European Ancestry ◽  
Pathway Enrichment Analysis ◽  
Short Term ◽  
Genome Wide

Abstract Objectives Diet regulates gene expression and methylation profiles by several mechanisms. However, studies analyzing the simultaneous effect of specific foods on gene-expression and DNA methylation at the genome-wide level are very scarce. Therefore our aims were: To study the short-term transcriptomics and epigenomcis effects at the genome-wide level of the Iberian ham intake compared with orange intake in the same subjects. Methods We carried out a cross-over randomized trial (registered at ISRCTN17906849) in 33 healhty volunteers (aged 18–50 years and 50% females) of European ancestry. After 12h fasting, participants were randomly allocated to eat 67.5 g of Iberian ham (100% pure iberian breed and 100% acorn fed) or 500 g of peeled oranges (Citrus reticulata) depening on the intervention group. After a washout period, subjects were crossed over to the alternate treatment arm. Blood samples were taken at 0-h and at 4-h to isolate DNA and RNA from leukocytes. A random sample of 16 participants was selected for omics analyses (gene expression with the. GeneChip Human Gene 2.0 ST Array, and the EPIC-Illumina array (850K) for methylation). Eight arrays (2 times and 2 treatments per 2 omics) were obtained for each participant. Differences in gene expression and methylation (4 h vs baseline) were analyzed for Iberian ham, oranges and combined. Kyoto Encyclopedia of Genes and Genomes (KEGG) was used for pathway enrichment analysis. Results The top-ranked genes differentially expressed P < 1 × 10–5) after Iberian ham intake (4 h vs baseline) were PKBP5 and PICALM. Pantothenate and CoA biosyntesis and the JAK-STAT singaling pathways were the most significantly enriched (P < 5 × 10–7). After orange intake, the top-ranked differentially expressed genes (P < 5 × 10–6) were: SMAP2 and RHEB, the pathways being (P < 5 × 10–9): Cellular senescence and ABC transporters. We detected top-ranked methylated CpGs both for ham and oranges, resulting the Chemokine signaling pathway differentially methylated for oranges and in the Neurothrophine singaling pathway for Iberian ham intake. Comparative combined analysis revealed additional differences. Conclusions A short-term intake of Iberian ham or oranges results in differences in gene expression as well as in DNA-methylation. Funding Sources CIBEROBN-06/03/035, PROMETEO-17/2017 APOSTD/2019/136), P1–1B2013–54 and COGRUP/2016/06

scholarly journals Transcriptome Profiling of Mouse Brain and Lung under Dip2A Regulation Using RNA-Sequencing

2019 ◽  
Author(s):  
Rajiv kumar sah ◽  
Anlan Yang ◽  
Fatoumata Binta Bah ◽  
Salah Adlat ◽  
Ameer Ali Bohio ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Neuronal Cell ◽  
Enrichment Analysis ◽  
Transcriptome Profiling ◽  
Transcriptional Analysis ◽  
Reference Sequence ◽  
Wild Type ◽  
Genome Wide ◽  
Go Enrichment ◽  
Go Enrichment Analysis

AbstractDisconnected interacting 2 homolog A (DIP2A) gene is highly expressed in nervous system and respiratory system of developing embryos. However, genes regulated by Dip2a in developing brain and lung have not been systemically studied. Transcriptome of brain and lung in embryonic 19.5 day (E19.5) were compared between wild type and Dip2a-/- mice. Total RNAs were extracted from brain and lung of E19.5 embryos for RNA-Seq. Clean reads were mapped to mouse reference sequence (mm9) using Tophat and assembled into transcripts by Cufflinks. Edge R and DESeq were applied to identify differentially expressed genes (DEGs) and annotated under GO, COG, KEGG and TF. An average of 50 million reads per sample was mapped to the reference sequence. A total of 214 DEGs were detected in brain (82 up and 132 down) and 1900 DEGs in lung (1259 up and 641 down). GO enrichment analysis indicated that DEGs in both Brain and Lung were mainly enriched in biological processes ‘DNA-templated transcription and Transcription from RNA polymerase II promoter’, ‘multicellular organism development’, ‘cell differentiation’ and ‘apoptotic process’. In addition, COG classification showed that both were mostly involved in ‘Replication, Recombination and Repair’, ‘Signal transduction and mechanism’, ‘Translation, Ribosomal structure and Biogenesis’ and ‘Transcription’. KEGG enrichment analysis showed that brain was mainly enriched in ‘Thryoid cancer’ pathway whereas lung in ‘Complement and Coagulation Cascades’ pathway. Transcription factor (TF) annotation analysis identified Zinc finger domain containing (ZF) proteins were mostly regulated in lung and brain. Interestingly, study identified genes Skor2, Gpr3711, Runx1, Erbb3, Frmd7, Fut10, Sox11, Hapln1, Tfap2c and Plxnb3 from brain that play important roles in neuronal cell maturation, differentiation and survival; genes Hoxa5, Eya1, Ctsh, Erff1, Lama1, Lama2, Rspo2, Sox11, Spry4, Shh, Igf1 and Wnt7a from lung are important in lung development and morphogenesis. Expression levels of the candidate genes were validated by qRT-PCR. Genome wide transcriptional analysis using wild type and Dip2a knockout mice in brain and lung at embryonic day 19.5 (E19.5) provided a genetic basis of molecular function of these genes.

scholarly journals Transcriptome in Combination Proteome Unveils the Phenylpropane Pathway Involved in Garlic (Allium sativum) Greening

2021 ◽  
Vol 8 ◽  
Author(s):  
Jinxiang Wu ◽  
Zhonglu Niu ◽  
Xiaoming Lu ◽  
Xiaozhen Tang ◽  
Xuguang Qiao ◽  
...  
Keyword(s):  
Metabolic Pathway ◽  
Allium Sativum ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Go Enrichment ◽  
Phenylpropanoid Biosynthesis ◽  
Full Length Transcript ◽  
Go Enrichment Analysis ◽  
Garlic Greening

Garlic (Allium sativum) is an important vegetable crop that is widely used in cooking and medicine. The greening phenomenon of garlic severely decreases the quality of garlic and hinders garlic processing. To study the mechanism of garlic greening, comprehensive full-length transcript sets were constructed. We detected the differences in greening between Pizhou (PZ) garlic and Laiwu (LW) garlic that were both stored at −2.5°C and protected from light at the same time. The results showed that 60,087 unigenes were respectively annotated to the NR, KEGG, GO, Pfam, eggNOG and Swiss Prot databases, and a total of 30,082 unigenes were annotated. The analysis of differential genes and differential proteins showed that PZ garlic and LW garlic had 923 differentially expressed genes (DEGs), of which 529 genes were up regulated and 394 genes were downregulated. Through KEGG and GO enrichment analysis, it was found that the most significant way of enriching DEGs was the phenylpropane metabolic pathway. Proteomics analysis found that there were 188 differentially expressed proteins (DAPs), 162 up-regulated proteins, and 26 down-regulated proteins between PZ garlic and LW garlic. The content of 10 proteins related to phenylpropanoid biosynthesis in PZ garlic was significantly higher than that of LW garlic. This study explored the mechanisms of garlic greening at a molecular level and further discovered that the formation of garlic green pigment was affected significantly by the phenylpropanoid metabolic pathway. This work provided a theoretical basis for the maintenance of garlic quality during garlic processing and the future development of the garlic processing industries.

scholarly journals Zebrafish Danio rerio trunk muscle structure and growth from a spatial transcriptomics perspective

2021 ◽  
Author(s):  
Guanting Liu ◽  
Takumi Ito ◽  
Yusuke Kijima ◽  
Kazutoshi Yoshitake ◽  
Shuichi Asakawa ◽  
...  
Keyword(s):  
Gene Expression ◽  
Muscle Development ◽  
Enrichment Analysis ◽  
Muscle Structure ◽  
Go Enrichment ◽  
Muscle Hyperplasia ◽  
Muscle Formation ◽  
Myosin Binding ◽  
Teleost Muscle ◽  
Go Enrichment Analysis

Compared to mammals, some fish exhibit indeterminate growth characteristics, meaning they can continue growing throughout their lives. Zebrafish trunk skeletal muscle can in general be classified into slow, intermediate, and fast based on morphological and physiological characteristics. After hatching, hyperplasia can be observed in the muscles of juvenile zebrafish, and with growth, hyperplasia in the fast muscles gradually decreases until it stagnates, after which fast muscle development relies on hypertrophy. In slow muscle, hyperplasia continues throughout life. Teleost muscle structure and growth has been described mainly by morphological and physiological features based on the expression of a limited number of proteins, transcripts, and metabolites. The details of mechanism remain unclear. Visium Spatial Gene Expression solution was used in this study. On the adult slide, 10 clusters were obtained based on whole gene expression similarities. The spatial expression of myosin heave chains, myosin light chains and myosin-binding proteins was investigated. GO enrichment analysis was also performed on different muscle regions of aged zebrafish. Dorsal and ventral slow muscles share the same processes such as myofibril assembly and muscle tissue development. On the larvae slide, 3 clusters were obtained, GO enrichment analysis suggest active muscle formation in zebrafish larvae.

scholarly journals Selenium Treatment Enhanced Clearance of Salmonella in Chicken Macrophages (HD11)

Antioxidants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 532 ◽  
Author(s):  
Zhexi Liu ◽  
Jianwei Huang ◽  
Yijuan Nie ◽  
Izhar Qazi ◽  
Yutao Cao ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Glutathione Metabolism ◽  
Rna Seq ◽  
Apoptotic Signaling ◽  
Go Enrichment ◽  
Selenium Treatment ◽  
Underlying Mechanisms ◽  
Go Enrichment Analysis

As an important micronutrient, selenium (Se) plays many essential roles in immune response and protection against pathogens in humans and animals, but underlying mechanisms of Se-based control of salmonella growth within macrophages remain poorly elucidated. In this study, using RNA-seq analyses, we demonstrate that Se treatment (at an appropriate concentration) can modulate the global transcriptome of chicken macrophages HD11. The bioinformatic analyses (KEGG pathway analysis) revealed that the differentially expressed genes (DEGs) were mainly enriched in retinol and glutathione metabolism, revealing that Se may be associated with retinol and glutathione metabolism. Meanwhile, Se treatment increased the number of salmonella invading the HD11 cells, but reduced the number of salmonella within HD11 cells, suggesting that enhanced clearance of salmonella within HD11 cells was potentially modulated by Se treatment. Furthermore, RNA-seq analyses also revealed that nine genes including SIVA1, FAS, and HMOX1 were differentially expressed in HD11 cells infected with salmonella following Se treatment, and GO enrichment analysis showed that these DEGs were mainly enriched in an extrinsic apoptotic signaling pathway. In summary, these results indicate that Se treatment may not only affect retinol and glutathione metabolism in macrophages, but could also inhibit salmonella-induced macrophage apoptosis via an extrinsic apoptotic signaling pathway involving SIVA1.

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