scholarly journals Construction of potential periodontitis-related miRNA-mRNA regulatory network

2020 ◽  
Author(s):  
Zheng Zhang ◽  
Youli Zheng ◽  
Xiaowei Bian ◽  
Mingguang Jin
Keyword(s):  
Candidate Genes ◽  
Regulatory Network ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Expression Profiles ◽  
Multivariate Logistic Regression Analysis ◽  
Gene Expression Profiles ◽  
Mirna Expression Profile ◽  
Differentially Expressed ◽  
B Cell Differentiation

Abstract Background MicroRNAs (miRNAs) are found to be involved in the pathogenesis of periodontitis, a major cause of tooth loss in adults. However, a comprehensive miRNA-mRNA regulatory network has still not been established. Methods One miRNA expression profile and 2 gene expression profiles were downloaded from the GEO database and analyzed using GEO2R. Candidate genes commonly appeared in differentially expressed mRNAs (DE-mRNAs) and target genes of differentially expressed miRNAs (DE-miRNAs) were selected for functional and pathway enrichment analyses using Enrichr database. Multivariate Logistic regression analysis was used to screen independent variables among candidate genes. The diagnostic values of screened genes were determined by the area under the receiver operating characteristic (ROC) curve (AUC). Results A total of 5 DE-miRNAs (4 upregulated and 1 downregulated) and 11 candidate genes (3 upregulated and 8 downregulated) were screened. After the construction of miRNA-mRNA regulatory network, 12 miRNA-mRNA pairs were identified. In the network, the upregulated genes were significantly enriched in cellular triglyceride homeostasis and positive regulation of B cell differentiation, whereas the downregulated genes were enriched in vesicle organization, negative regulation of lymphocyte and leukocyte migration. EPCAM and RAB30 were screened as risk factors of periodontitis. The combined AUC of these 2 genes was 0.896 (GSE10334) and 0.916 (GSE16134). Conclusion In this study, we established a potential periodontitis-related miRNA-mRNA regulatory network, which brings new insights into the molecular mechanisms and provides key clues in seeking novel therapeutic targets for periodontitis. In the future, more experiments need to be carried out to validate our current findings.

scholarly journals Identification and characterization of mRNAs and lncRNAs in the uterus of polytocous and monotocous Small Tail Han sheep (Ovis aries)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6938 ◽  
Author(s):  
Yongfu La ◽  
Jishun Tang ◽  
Xiaoyun He ◽  
Ran Di ◽  
Xiangyu Wang ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
Ovis Aries ◽  
Differentially Expressed ◽  
Retinol Metabolism ◽  
Two Phases

Background Long non-coding RNAs (lncRNAs) regulate endometrial secretion and uterine volume. However, there is little research on the role of lncRNAs in the uterus of Small Tail Han sheep (FecB++). Herein, RNA-seq was used to comparatively analyze gene expression profiles of uterine tissue between polytocous and monotocous sheep (FecB++) in follicular and luteal phases. Methods To identify lncRNA and mRNA expressed in the uterus, the expression of lncRNA and mRNA in the uterus of Small Tail Han sheep (FecB++) from the polytocous group (n = 6) and the monotocous group (n = 6) using RNA-sequencing and real-time polymerase chain reaction (RT-PCR). Identification of differentially expressed lncRNAs and mRNAs were performed between the two groups and two phases . Gene ontology (GO) and pathway enrichment analyses were performed to analyze the biological functions and pathways for the differentially expressed mRNAs. LncRNA-mRNA co-expression network was constructed to further analyses the function of related genes. Results In the follicular phase, 473 lncRNAs and 166 mRNAs were differentially expressed in polytocous and monotocous sheep; in the luteal phase, 967 lncRNAs and 505 mRNAs were differentially expressed in polytocous and monotocous sheep. GO and KEGG enrichment analysis showed that the differentially expressed lncRNAs and their target genes are mainly involved in ovarian steroidogenesis, retinol metabolism, the oxytocin signaling pathway, steroid hormone biosynthesis, and the Foxo signaling pathway. Key lncRNAs may regulate reproduction by regulating genes involved in these signaling pathways and biological processes. Specifically, UGT1A1, LHB, TGFB1, TAB1, and RHOA, which are targeted by MSTRG.134747, MSTRG.82376, MSTRG.134749, MSTRG.134751, and MSTRG.134746, may play key regulatory roles. These results offer insight into molecular mechanisms underlying sheep prolificacy.

scholarly journals PSXIII-30 Analysis of gene expression profiles in liver and muscle tissue of pigs divergent in feed efficiency

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 475-475
Author(s):  
Stafford Vigors ◽  
Torres Sweeney
Keyword(s):  
Energy Metabolism ◽  
Immune Function ◽  
Feed Efficiency ◽  
Molecular Mechanisms ◽  
Protein Targeting ◽  
Expression Profiles ◽  
Cell Signalling ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Joint Analysis

Abstract The improvement of feed efficiency is a key economic goal within the pig production industry. The objective of this study was to examine transcriptomic differences in both the liver and muscle in pigs divergent for feed efficiency, thus improving our understanding of the molecular mechanisms influencing feed efficiency and enabling the identification of candidate biomarkers. Residual feed intake (RFI) was calculated in two populations of pigs from two different farms of origin. The 6 most efficient (LRFI) and 6 least efficient (HRFI) animals in each population were selected for further analysis of Longissimus Dorsi muscle and liver. Three different analysis were performed: 1) Identification of differentially expressed genes (DE) in liver, 2) Identification of DE genes in muscle and 3) Identification of genes commonly DE in both tissues. Hierarchical clustering revealed that transcriptomic data segregated based on the RFI value of the pig rather than farm of origin. A total of 6464 genes were identified as being differentially expressed (DE) in muscle, while 964 genes were identified as being DE in liver. In the muscle-only analysis, genes associated with RNA, protein synthesis and energy metabolism were downregulated in the LRFI animals while in the liver-only analysis, genes associated with cell signalling and lipid homeostasis were upregulated in the LRFI animals. Genes that were commonly DE between muscle and liver (n = 526) were used for the joint analysis. These 526 genes were associated with protein targeting to membrane, extracellular matrix organization and immune function. There are pathways common to both muscle and liver in particular genes associated with immune function. In contrast, tissue-specific pathways contributing to differences in feed efficiency were also identified with genes associated with energy metabolism identified in muscle and lipid metabolism in liver. This study identifies key mechanisms driving changes in feed efficiency in pigs.

scholarly journals Transcriptome profiling of peanut (Arachis hypogaea) gynophores in gravitropic response

2013 ◽  
Vol 40 (12) ◽  
pp. 1249 ◽  
Author(s):  
Hai-fen Li ◽  
Xiao-Ping Chen ◽  
Fang-he Zhu ◽  
Hai-Yan Liu ◽  
Yan-Bin Hong ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Arachis Hypogaea ◽  
Molecular Mechanisms ◽  
Carbon Fixation ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Pentose Phosphate ◽  
Differentially Expressed ◽  
Pcr Analysis

Peanut (Arachis hypogaea L.) produces flowers aerially, but the fruit develops underground. This process is mediated by the gynophore, which always grows vertically downwards. The genetic basis underlying gravitropic bending of gynophores is not well understood. To identify genes related to gynophore gravitropism, gene expression profiles of gynophores cultured in vitro with tip pointing upward (gravitropic stimulation sample) and downward (control) at both 6 and 12 h were compared through a high-density peanut microarray. After gravitropic stimulation, there were 174 differentially expressed genes, including 91 upregulated and 83 downregulated genes at 6 h, and 491 differentially expressed genes including 129 upregulated and 362 downregulated genes at 12 h. The differentially expressed genes identified were assigned to 24 functional categories. Twenty pathways including carbon fixation, aminoacyl-tRNA biosynthesis, pentose phosphate pathway, starch and sucrose metabolism were identified. The quantitative real-time PCR analysis was performed for validation of microarray results. Our study paves the way to better understand the molecular mechanisms underlying the peanut gynophore gravitropism.

scholarly journals Integrated analysis of miRNA and mRNA expression profiles in testes of Duroc and Meishan boars

2019 ◽  
Author(s):  
Haisheng Ding ◽  
Min Liu ◽  
Changfan Zhou ◽  
Xiangbin You ◽  
Tao Su ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Male Gamete ◽  
Mirna Expression Profile ◽  
Mapk Signaling ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Testis Development ◽  
Differentially Expressed Mirnas

Abstract Background: MicroRNAs (miRNAs) are small non-coding RNAs playing vital roles in regulating posttranscriptional gene expression. Elucidating the expression regulation of miRNAs underlying pig testis development will contribute to a better understanding of boar fertility and spermatogenesis. Results: In this study, miRNA expression profile was investigated in testes of Duroc and Meishan boars at 20, 75, and 270 days of age by high-throughput sequencing. Forty-five differentially expressed miRNAs were identified from testes of Duroc and Meishan boars before and after puberty. Integrated analysis of miRNA and mRNA profiles predicted many miRNA-mRNA pairs. Gene ontology and biological pathway analyses revealed that predicted target genes of ssc-mir-423-5p, ssc-mir-34c, ssc-mir-107, ssc-165 mir-196b-5p, ssc-mir-92a, ssc-mir-320, ssc-mir-10a-5p, and ssc-mir-181b were involved in sexual reproduction, male gamete generation, and spermatogenesis, and GnRH, Wnt, and MAPK signaling pathway. Four significantly differentially expressed miRNAs and their predicted target genes were validated by quantitative real-time polymerase chain reaction, and phospholipase C beta 1 ( PLCβ1) gene was verified to be a target of ssc-mir-423-5p . Conclusions: This study provides an insight into the functional roles of miRNAs in testis development and spermatogenesis and offers useful resources for understanding differences in sexual function development caused by the change in miRNAs expression between Duroc and Meishan boars.

scholarly journals Integrated analysis of sex-biased mRNA and miRNA expression profiles in the gonad of the discus fish (Symphysodon aequifasciatus)

2018 ◽  
Author(s):  
yuanshuai Fu ◽  
Zhe Xu ◽  
Zaizhong Chen ◽  
Bin Wen ◽  
Jianzhong Gao
Keyword(s):  
Molecular Mechanisms ◽  
Target Genes ◽  
High Efficiency ◽  
Expression Profiles ◽  
Gonad Development ◽  
Differentially Expressed ◽  
Cdna Libraries ◽  
Integrated Analysis ◽  
Illumina Hiseq ◽  
Differentially Expressed Mirnas

The discus fish (Symphysodon aequifasciatus) is an ornamental fish that is well-known around the world. Phenotype investigation indicated that there are no significant differences in appearance between males and females of the discus fish. To better understand the sexual development mechanisms and obtain a high efficiency sex identification method in the artificial reproduction process of the discus fish, we constructed six cDNA libraries from three adult testes and three adult ovaries, and perform RNA-sequencing for identifying sex-biased candidate genes, microRNA (miRNA), and metabolic pathway using the Illumina Hiseq 4000. A total of 50,082 non-redundant genes (unigenes) were identified, of which 18,570 unigenes were significantly overexpressed in testes, and 11,182 unigenes were significantly overexpressed in ovaries, and 8 differentially expressed unigenes were validated by quantitative Real-Time PCR (qPCR). A total of 551 miRNAs were identified, of which 47 miRNAs were differentially expressed between testes and ovaries, and 7 differentially expressed miRNAs and one non-differential miRNA were validated by qPCR. Twenty-four of these differentially expressed miRNAs and their 15 predicted target genes constituted 41 important miRNA-mRNA interaction pairs, which may be important candidates for sex-related miRNAs and sex-related genes in the discus fish. Some of vital sex-related metabolic pathways were also identified that may play key roles in regulating gonad development of the discus fish. These results can provide important insights to better understand molecular mechanisms for sexual dimorphism in gonads development.

scholarly journals Transcriptome Profiling Provides Insights into Molecular Mechanism in Peanut Semi-dwarf Mutant

2020 ◽  
Author(s):  
Fengdan Guo ◽  
Junjie Ma ◽  
Lei Hou ◽  
Suhua Shi ◽  
Jinbo Sun ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Plant Height ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Main Stem ◽  
Differentially Expressed ◽  
Dwarf Mutant ◽  
Mature Stage ◽  
Stem Height

Abstract Background: Plant height, mainly decided by main stem height, is the major agronomic trait and closely correlated to crop yield. A number of studies had been conducted on model plants and crops to understand the molecular and genetic basis of plant height. However, little is known on the molecular mechanisms of peanut main stem height. Results: In this study, a semi-dwarf peanut mutant was identified from 60 Co γ-ray induced mutant population and designated as semi-dwarf mutant 2 ( sdm2 ). The height of sdm2 was only 59.3% of its wild line Fenghua 1 (FH1) at the mature stage. The sdm2 has less internode number and short internode length to compare with FH1. Gene expression profiles of stem and leaf from both sdm2 and FH1 were analyzed using high throughput RNA sequencing. The differentially expressed genes (DEGs) were involved in hormone biosynthesis and signaling pathways, cell wall synthetic and metabolic pathways. BR, GA and IAA biosynthesis and signal transduction pathways were significantly enriched. The expression of several genes in BR biosynthesis and signaling were found to be significantly down-regulated in sdm2 as compared to FH1. Many transcription factors encoding genes were identified as DEGs. Conclusions: A large number of genes were found differentially expressed between sdm2 and FH1. These results provide useful information for uncovering the molecular mechanism regulating peanut stem height. It could facilitate identification of causal genes for breeding peanut varieties with semi-dwarf phenotype.

scholarly journals Integrated analysis of miRNA and mRNA expression profiles in testes of Duroc and Meishan boars

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Haisheng Ding ◽  
Min Liu ◽  
Changfan Zhou ◽  
Xiangbin You ◽  
Tao Su ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Male Gamete ◽  
Mirna Expression Profile ◽  
Mapk Signaling ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Testis Development ◽  
Differentially Expressed Mirnas

Abstract Background MicroRNAs (miRNAs) are small non-coding RNAs playing vital roles in regulating posttranscriptional gene expression. Elucidating the expression regulation of miRNAs underlying pig testis development will contribute to a better understanding of boar fertility and spermatogenesis. Results In this study, miRNA expression profile was investigated in testes of Duroc and Meishan boars at 20, 75, and 270 days of age by high-throughput sequencing. Forty-five differentially expressed miRNAs were identified from testes of Duroc and Meishan boars before and after puberty. Integrated analysis of miRNA and mRNA profiles predicted many miRNA-mRNA pairs. Gene ontology and biological pathway analyses revealed that predicted target genes of ssc-mir-423-5p, ssc-mir-34c, ssc-mir-107, ssc-mir-196b-5p, ssc-mir-92a, ssc-mir-320, ssc-mir-10a-5p, and ssc-mir-181b were involved in sexual reproduction, male gamete generation, and spermatogenesis, and GnRH, Wnt, and MAPK signaling pathway. Four significantly differentially expressed miRNAs and their predicted target genes were validated by quantitative real-time polymerase chain reaction, and phospholipase C beta 1 (PLCβ1) gene was verified to be a target of ssc-mir-423-5p. Conclusions This study provides an insight into the functional roles of miRNAs in testis development and spermatogenesis and offers useful resources for understanding differences in sexual function development caused by the change in miRNAs expression between Duroc and Meishan boars.

scholarly journals A systemic study of indoxacarb resistance in Spodoptera litura revealed complex expression profiles and regulatory mechanism

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Li Shi ◽  
Yao Shi ◽  
Ya Zhang ◽  
Xiaolan Liao
Keyword(s):  
Spodoptera Litura ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Expression Profiles ◽  
Resistance Mechanisms ◽  
Differentially Expressed ◽  
Glutathione S Transferase ◽  
Differentially Expressed Mirnas ◽  
Important Pest ◽  
Resistant Strains

Abstract The tobacco cutworm, Spodoptera litura, is an important pest of crop and vegetable plants worldwide, and its resistance to insecticides have quickly developed. However, the resistance mechanisms of this pest are still unclear. In this study, the change in mRNA and miRNA profiles in the susceptible, indoxacarb-resistant and field indoxacarb-resistant strains of S. litura were characterized. Nine hundred and ten co-up-regulated and 737 co-down-regulated genes were identified in the resistant strains. Further analysis showed that 126 co-differentially expressed genes (co-DEGs) (cytochrome P450, carboxy/cholinesterase, glutathione S-transferase, ATP-binding cassette transporter, UDP-glucuronosyl transferase, aminopeptidase N, sialin, serine protease and cuticle protein) may play important roles in indoxacarb resistance in S. litura. In addition, a total of 91 known and 52 novel miRNAs were identified, and 10 miRNAs were co-differentially expressed in the resistant strains of S. litura. Furthermore, 10 co-differentially expressed miRNAs (co-DEmiRNAs) had predicted co-DEGs according to the expected miRNA-mRNA negative regulation pattern and 37 indoxacarb resistance-related co-DEGs were predicted to be the target genes. These results not only broadened our understanding of molecular mechanisms of insecticide resistance by revealing complicated profiles, but also provide important clues for further study on the mechanisms of miRNAs involved in indoxacarb resistance in S. litura.

scholarly journals Potential Regulatory Effects of miR-182-3p in Osteosarcoma via Targeting EBF2

2019 ◽  
Vol 2019 ◽  
pp. 1-9 ◽  
Author(s):  
Gaoyang Chen ◽  
Wenqing Yu ◽  
Zhaoyan Li ◽  
Qingyu Wang ◽  
Qiwei Yang ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Profiles ◽  
Differential Expression Analysis ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Luciferase Reporter ◽  
Luciferase Reporter Gene ◽  
Potential Target ◽  
Proliferation Activity ◽  
Regulatory Effects

Osteosarcoma (OS) is one of the most common primary malignant bone tumors in adolescents with a high mortality rate. MicroRNA (miRNA) is a kind of noncoding RNAs and has been proved to participate in many physiological processes. Many miRNAs have been reported to act as function regulators in OS. In our study, the miRNA and gene expression profiles of OS were downloaded from GEO Datasets and the differential expression analysis was performed using GEO2R. 58 up- and 126 downregulated miRNAs were found. In the three OS gene profiles, 125 up- and 27 downregulated genes were found to be differentially expressed in at least two profiles. The miRNA-mRNA networks were constructed to predict the potential target genes of 10 most up- and downregulated miRNA. Venn analysis was used to detect the coexpressed differentially expressed genes (DEGs). EBF2, one of the upregulated DEGs, was also a potential target gene of miR-182-3p. Knockdown and overexpression of miR-182-3p resulted in overexpression and downexpression of EBF2 separately. Luciferase reporter gene experiment further verified the binding site of miR-182-3p and EBF2. CCK8 assay showed that miR-182-3p knockdown can further enhance the proliferation activity of OS cells, while overexpressing miR-182-3p can inhibit the proliferation activity of OS cells. Our research indicated that downexpression of miR-182-3p in OS cells results in overexpression of EBF2 and promotes the progression of OS.

scholarly journals Genetic and pharmacological inactivation of adenosine A2A receptor reveals an Egr-2-mediated transcriptional regulatory network in the mouse striatum

2005 ◽  
Vol 23 (1) ◽  
pp. 89-102 ◽  
Author(s):  
Liqun Yu ◽  
Peter M. Haverty ◽  
Juliana Mariani ◽  
Yumei Wang ◽  
Hai-Ying Shen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Regulatory Network ◽  
Molecular Mechanisms ◽  
Transcriptional Regulatory Network ◽  
Expression Profiles ◽  
Mrna Level ◽  
Gene Expression Profiles ◽  
Bioinformatics Analyses ◽  
Mouse Striatum ◽  
Transcriptional Regulatory

The adenosine A2A receptor (A2AR) is highly expressed in the striatum, where it modulates motor and emotional behaviors. We used both microarray and bioinformatics analyses to compare gene expression profiles by genetic and pharmacological inactivation of A2AR and inferred an A2AR-controlled transcription network in the mouse striatum. A comparison between vehicle (VEH)-treated A2AR knockout (KO) mice (A2AR KO-VEH) and wild-type (WT) mice (WT-VEH) revealed 36 upregulated genes that were partially mimicked by treatment with SCH-58261 (SCH; an A2AR antagonist) and 54 downregulated genes that were not mimicked by SCH treatment. We validated the A2AR as a specific drug target for SCH by comparing A2AR KO-SCH and A2AR KO-VEH groups. The unique downregulation effect of A2AR KO was confirmed by comparing A2AR KO-SCH with WT-SCH gene groups. The distinct striatal gene expression profiles induced by A2AR KO and SCH should provide clues to the molecular mechanisms underlying the different phenotypes observed after genetic and pharmacological inactivation of A2AR. Furthermore, bioinformatics analysis discovered that Egr-2 binding sites were statistically overrepresented in the proximal promoters of A2AR KO-affected genes relative to the unaffected genes. This finding was further substantiated by the demonstration that the Egr-2 mRNA level increased in the striatum of both A2AR KO and SCH-treated mice and that striatal Egr-2 binding activity in the promoters of two A2AR KO-affected genes was enhanced in A2AR KO mice as assayed by chromatin immunoprecipitation. Taken together, these results strongly support the existence of an Egr-2-directed transcriptional regulatory network controlled by striatal A2ARs.

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