The Prepropalustrin-2CE2 and Preprobrevinin-2CE3　Gene from Rana　Chensinensis: Gene Expression, Genomic Organization, and Functional Analysis of the Promoter Activity

2021 ◽  
Vol 28 ◽  
Author(s):  
Ruifen Zhang ◽  
Jing Gao ◽  
Hui Xie ◽  
Yan Sun ◽  
Yuan Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Antimicrobial Peptides ◽  
Antimicrobial Peptide ◽  
Luciferase Reporter ◽  
Expression Levels ◽  
Environmental Stimuli ◽  
Rana Chensinensis ◽  
Peptide Gene ◽  
Gene Expression Levels

Background: Palustrin-2CE2 and brevinin-2CE3 are antimicrobial peptides from Rana chensinensis. In R. chensinensis tadpoles, the expression of prepropalustrin-2CE2 and preprobrevinin-2CE3 increased with the developmental stage. In addition, the expression of the two genes was dramatically upregulated with stimulation by Escherichia coli, Staphylococcus aureus, and the chemical lipopolysaccharide (LPS). The genomic organization of the two antimicrobial peptide genes was confirmed. Both prepropalustrin-2CE2 and preprobrevinin-2CE3 contain three exons separated by two large introns. Additionally, several presumed transcription factor binding sites were identified in the promoter sequence. Functional analysis of the promoter was performed using a luciferase reporter system, and further confirmed by yeast one-hybrid experiment and EMSA assay. The results indicated that the transcription factors NF-κB and RelA are involved in regulating the expression of prepropalustrin-2CE2 and preprobrevinin-2CE3. As amphibian populations decline globally, this study provides new data demonstrating how frogs defend against pathogens from the environment by regulating AMP expression. For amphibians, antimicrobial peptides are innate immune molecules that resist adverse external environmental stimuli. However, the regulation mechanism of antimicrobial peptide gene expression in frogs is still unclear. Objective: The two antimicrobial peptides, palustrin-2CE2 and brevinin-2CE3, are produced under external stimulation in Rana chensinensis. Using this model, we analyzed the gene structure and regulatory elements of the two antimicrobial peptide genes and explored the regulatory effects of related transcription factors on the two genes. Method: Different stimuli such as E. coli, S. aureus, and chemical substance lipopolysaccharide (LPS) were applied to Rana chensinensis tadpoles at different developmental stages, and antimicrobial peptide expression levels were detected by RT-PCR. Bioinformatics analysis and 5'-RACE and genome walking technologies were employed to analyze the genome structure and promoter region of the antimicrobial peptide genes. With dual-luciferase reporter gene assays, yeast one-hybrid experiment and EMSA assays, we assessed the regulatory effect of the endogenous regulators of the cell on the antimicrobial peptide promoter. Results: The transcription levels of prepropalustrin-2CE2 and preprobrevinin-2CE3 were significantly upregulated after different stimulations. Genomic structure analysis showed that both genes contained three exons and two introns. Promoter analysis indicated that there are binding sites for regulatory factors of the NF-κB family in the promoter region, and experiments showed that endogenous NF-κB family regulatory factors in frog cells activate the promoters of the antimicrobial peptide genes. Yeast one-hybrid experiment and EMSA assay demonstrated that RelA and NF-κB1 might interact with specific motifs in the prepropalustrin-2CE2 promoter. Conclusion: In this paper, we found that the gene expression levels of the antimicrobial peptides, palustrin-2CE2 and brevinin-2CE3, in R. chensinensis will increase under environmental stimuli, and we verified that the changes in gene expression levels are affected by the transcription factors RelA and NF-κB1. The yeast one-hybrid experiment and EMSA assay confirmed that RelA and NF-κB1 could directly interact with the frog antimicrobial peptide gene promoter, providing new data for the regulatory mechanism of antimicrobial peptides in response to environmental stimuli.

scholarly journals Transcription factors gene expression in chronic rhinosinusitis with and without nasal polyps

2019 ◽  
Vol 53 (3) ◽  
pp. 323-330 ◽  
Author(s):  
Tanja Kosak Soklic ◽  
Matija Rijavec ◽  
Mira Silar ◽  
Ana Koren ◽  
Izidor Kern ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Chronic Rhinosinusitis ◽  
Nasal Polyps ◽  
Quantitative Polymerase Chain Reaction ◽  
Orphan Receptor ◽  
Expression Levels ◽  
Cd8 Cells ◽  
Persistent Symptoms ◽  
Gene Expression Levels

Abstract Background Chronic rhinosinusitis (CRS) current therapeutic approaches still fail in some patients with severe persistent symptoms and recurrences after surgery. We aimed to evaluate the master transcription factors gene expression levels of T cell subtypes in chronic rhinosinusitis with nasal polyps (CRSwNP) and chronic rhinosinusitis without nasal polyps (CRSsNP) that could represent new, up-stream targets for topical DNAzyme treatment. Patients and methods Twenty-two newly diagnosed CRS patients (14 CRSwNP and 8 CRSsNP) were prospectively biopsied and examined histopathologically. Gene expression levels of T-box transcription factor (T-bet, TBX21), GATA binding protein 3 (GATA3), Retinoic acid-related orphan receptor C (RORC) and Forkhead box P3 (FOXP3) were analyzed by real-time quantitative polymerase chain reaction (RT-qPCR). Results Eosinophilic CRSwNP was characterized by higher level of GATA3 gene expression compared to noneosinophilic CRSwNP, whereas there was no difference in T-bet, RORC and FOXP3 between eosinophilic and noneosinophilic CRSwNP. In CRSsNP, we found simultaneous upregulation of T-bet, GATA3 and RORC gene expression levels in comparison to CRSwNP; meanwhile, there was no difference in FOXP3 gene expression between CRSwNP and CRSsNP. Conclusions In eosinophilic CRSwNP, we confirmed the type 2 inflammation by elevated GATA3 gene expression level. In CRSsNP, we unexpectedly found simultaneous upregulation of T-bet and GATA3 that is currently unexplained; however, it might originate from activated CD8+ cells, abundant in nasal mucosa of CRSsNP patients. The elevated RORC in CRSsNP could be part of homeostatic nasal immune response that might be better preserved in CRSsNP patients compared to CRSwNP patients. Further data on transcription factors expression rates in CRS phenotypes are needed.

scholarly journals Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors

2020 ◽  
Author(s):  
Johanna Hörberg ◽  
Kevin Moreau ◽  
Anna Reymer
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Binding Sites ◽  
Regulation Of Gene Expression ◽  
Dna Complexes ◽  
Response Element ◽  
Response Elements ◽  
Expression Levels ◽  
The Stability ◽  
Gene Expression Levels

AbstractActivator proteins 1 (AP-1) comprise one of the largest families of eukaryotic basic leucine zipper transcription factors. Despite advances in the characterization of AP-1 DNA-binding sites, our ability to predict new binding sites and explain how the proteins achieve different gene expression levels remains limited. Here we address the role of sequence-specific DNA dynamics for stability and specific binding of AP-1 factors, using microseconds long molecular dynamics simulations. As a model system, we employ yeast AP-1 factor Yap1 binding to three different response elements from two genetic environments. Our data show that Yap1 actively exploits the sequence-specific plasticity of DNA within the response element to form stable protein-DNA complexes. The stability also depends on the four to six flanking nucleotides, adjacent to the response elements. The flanking sequences modulate the conformational adaptability of the response element, making it more shape-efficient to form specific contacts with the protein. Bioinformatics analysis of differential expression of the studied genes supports our conclusions: the stability of Yap1-DNA complexes, modulated by the flanking environment, influences the gene expression levels. Our results provide new insights into mechanisms of protein-DNA recognition and the biological regulation of gene expression levels in eukaryotes.

scholarly journals Differential Expression of MicroRNAs in Silent and Functioning Corticotroph Tumors

2020 ◽  
Vol 9 (6) ◽  
pp. 1838
Author(s):  
Araceli García-Martínez ◽  
Antonio C. Fuentes-Fayos ◽  
Carmen Fajardo ◽  
Cristina Lamas ◽  
Rosa Cámara ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Potential Role ◽  
Therapeutic Option ◽  
Pharmacological Treatments ◽  
Expression Levels ◽  
Qrt Pcr ◽  
Gene Expression Levels

The potential role of miRNAs in the silencing mechanisms of pituitary neuroendocrine tumors (PitNETs) has not been addressed. The aim of the present study was to evaluate the expression levels and the potential associated role of some miRNAs, pathways, and transcription factors in the silencing mechanisms of corticotroph tumors (CTs). Accordingly, the expression of miR-375, miR-383, miR-488, miR-200a and miR-103; of PKA, MAP3K8, MEK, MAPK3, NGFIB, NURR1, PITX1, and STAT3 were analyzed via qRT-PCR in 23 silent and 24 functioning CTs. miR-200a and miR-103 showed significantly higher expression in silent than in functioning CTs, even after eliminating the bias of tumor size, therefore enabling the differentiation between the two variants. Additionally, miR-383 correlated negatively with TBX19 in silent CTs, a transcription factor related with the processing of POMC that can participate in the silencing mechanisms of CTs. Finally, the gene expression levels of miR-488, miR-200a, and miR-103 were significantly higher in macroadenomas (functioning and silent) than in microadenomas. The evidence from this study indicates that miRNAs could be involved in the pathophysiology of CTs. The translational implications of these findings suggest that pharmacological treatments specifically targeting these miRNAs could become a promising therapeutic option for these patients.

scholarly journals DE NOVO SEQUENCING AND ANALYSIS OF THE RANA CHENSINENSIS TRANSCRIPTOME TO DISCOVER PUTATIVE GENES ASSOCIATED WITH POLYUNSATURATED FATTY ACIDS

2020 ◽  
Author(s):  
Jingmeng Sun ◽  
Zhuoming Wang ◽  
Weiyu Zhang
Keyword(s):  
Gene Expression ◽  
Fatty Acids ◽  
Polyunsaturated Fatty Acids ◽  
Unsaturated Fatty Acids ◽  
De Novo ◽  
Differential Expression Analysis ◽  
Expression Levels ◽  
Rana Chensinensis ◽  
Oviductus Ranae ◽  
Gene Expression Levels

ABSTRACTRana chensinensis (R. chensinensis) is an important wild animal found in China, and a precious animal in Chinese herbal medicine. R. chensinensis is rich in polyunsaturated fatty acids (PUFAS). However, information regarding the genes of R. chensinensis related to the synthesis of PUFAs is limited. To identify these genes, we performed Illumina sequencing of R. chensinensis RNA from the skin and Oviductus Ranae. The Illumina Hiseq 2000 platform was used for sequencing, and the I-Sanger cloud platform was used for transcriptome de novo sequencing and information analysis to generate a database. Through the database generated by the transcriptome and the pathway map, we found the pathway for the biosynthesis of R. chensinensis PUFAs. The Pearson coefficient method was used to analyze the correlation of gene expression levels between samples, and the similarity of gene expression in different tissues and the characteristics in their respective tissues were found. Twelve differentially expressed genes of PUFA in skin and Oviductus Ranae were screened by gene differential expression analysis. The 12 unigenes expression levels of qRT-PCR were used to verify the results of gene expression levels consistent with transcriptome analysis. Based on the sequencing, key genes involved in biosynthesis of unsaturated fatty acids were isolated, which established a biotechnological platform for further research on R. chensinensis.

scholarly journals A Sparse and Low-Rank Regression Model for Identifying the Relationships Between DNA Methylation and Gene Expression Levels in Gastric Cancer and the Prediction of Prognosis

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 854
Author(s):  
Yishu Wang ◽  
Lingyun Xu ◽  
Dongmei Ai
Keyword(s):  
Gene Expression ◽  
Gastric Cancer ◽  
Dna Methylation ◽  
Regression Model ◽  
The Cancer Genome Atlas ◽  
Low Rank ◽  
Expression Levels ◽  
Rank Regression ◽  
Prediction Of Prognosis ◽  
Gene Expression Levels

DNA methylation is an important regulator of gene expression that can influence tumor heterogeneity and shows weak and varying expression levels among different genes. Gastric cancer (GC) is a highly heterogeneous cancer of the digestive system with a high mortality rate worldwide. The heterogeneous subtypes of GC lead to different prognoses. In this study, we explored the relationships between DNA methylation and gene expression levels by introducing a sparse low-rank regression model based on a GC dataset with 375 tumor samples and 32 normal samples from The Cancer Genome Atlas database. Differences in the DNA methylation levels and sites were found to be associated with differences in the expressed genes related to GC development. Overall, 29 methylation-driven genes were found to be related to the GC subtypes, and in the prognostic model, we explored five prognoses related to the methylation sites. Finally, based on a low-rank matrix, seven subgroups were identified with different methylation statuses. These specific classifications based on DNA methylation levels may help to account for heterogeneity and aid in personalized treatments.

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