Differential expression of miRNAs in response to dsRNA of various target genes in Noctuidae

2016 ◽  
Author(s):  
R. Asokan
Keyword(s):  
Differential Expression ◽  
Target Genes

Screening candidate microR-15a- IRAK2 regulatory pairs for predicting the response to Staphylococcus aureus-induced mastitis in dairy cows

2019 ◽  
Vol 86 (4) ◽  
pp. 425-431 ◽  
Author(s):  
Zhi Chen ◽  
Jingpeng Zhou ◽  
Xiaolong Wang ◽  
Yang Zhang ◽  
Xubin Lu ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Differential Expression ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Interleukin 1 ◽  
Differentially Expressed ◽  
Luciferase Reporter ◽  
Expression Of Genes ◽  
Chinese Holstein Cows ◽  
Reporter Assays

AbstractWe established a mastitis model using exogenous infection of the mammary gland of Chinese Holstein cows with Staphylococcus aureus and extracted total RNA from S. aureus-infected and healthy mammary quarters. Differential expression of genes due to mastitis was evaluated using Affymetrix technology and results revealed a total of 1230 differentially expressed mRNAs. A subset of affected genes was verified via Q-PCR and pathway analysis. In addition, Solexa high-throughput sequencing technology was used to analyze profiles of miRNA in infected and healthy quarters. These analyses revealed a total of 52 differentially expressed miRNAs. A subset of those results was verified via Q-PCR. Bioinformatics techniques were used to predict and analyze the correlations among differentially expressed miRNA and mRNA. Results revealed a total of 329 pairs of negatively associated miRNA/mRNA, with 31 upregulated pairs of mRNA and 298 downregulated pairs of mRNA. Differential expression of miR-15a and interleukin-1 receptor-associated kinase-like 2 (IRAK2), were evaluated by western blot and luciferase reporter assays. We conclude that miR-15a and miR-15a target genes (IRAK2) constitute potential miRNA–mRNA regulatory pairs for use as biomarkers to predict a mastitis response.

scholarly journals Identifying Key MicroRNAs Targeted by Narenmandula in a Rodent Nephropathy Model

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Xiulan Wang ◽  
Chun Chang ◽  
Wenjie Jin ◽  
Arun Arun ◽  
Sudunabuqi Sudunabuqi ◽  
...  
Keyword(s):  
Renal Function ◽  
Differential Expression ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Control Group ◽  
Doxorubicin Hydrochloride ◽  
Treatment Control ◽  
Number Of Genes ◽  
Version 2.0 ◽  
Treatment Control Group

Background. Untreated nephropathy can progress to renal failure. The traditional Mongolian remedy Narenmandula regulates the kidney “yang.” This study aimed to identify key microRNAs (miRNAs) targeted by Narenmandula in a rat model of nephropathy. Methods. Fifteen rats exhibiting normal renal function were randomized to three study arms. Nephropathy was induced in n = 10 rats using doxorubicin hydrochloride, followed by either Narenmandula treatment (treatment group) or no treatment (control group). In n = 5 rats, no doxorubicin was given and renal function remained unchanged (healthy group). Microarray analysis identified miRNAs which were differentially expressed (DE-miRNAs) between groups. Target genes of DE-miRNAs were predicted using miRWalk version 2.0, followed by enrichment analysis using DAVID, and construction of the miRNA coregulatory network using Cytoscape. Results. Nephropathy was successfully induced, with doxorubicin resulting in differential expression of 3645 miRNAs (1324 upregulated and 2321 downregulated). Narenmandula treatment induced differential expression of a total of 159 miRNAs (102 upregulated and 57 downregulated). Upregulated DE-miRNAs (e.g., miR-497-5p, miR-195-5p, miR-181a-5p, miR-181c-5p, and miR-30e-5p) and downregulated DE-miRNAs (e.g., miR-330-3p and miR-214-3p) regulated a high number of target genes. Moreover, the miRNA pairs (e.g., miR-195-5p—miR-497-5p, miR-181a-5p—miR-181c-5p, and miR-30e-5p—miR-30a-5p) coregulated a high number of genes. Enrichment analysis indicated functional synergy between miR-30e-5p—miR-30a-3p, miR-34a-5p—miR-30e-5p, miR-30e-5p—miR-195-3p, and miR-30a-3p—miR-195-3p pairs. Conclusion. Narenmandula may modulate doxorubicin-induced nephropathy via targeting miR-497-5p, miR-195-5p, miR-181a-5p, miR-181c-5p, miR-30e-5p, miR-330-3p, miR-214-3p, miR-34a-5p, miR-30a-3p, and miR-30a-5p.

scholarly journals Analysis of small RNA changes in different Brassica napus synthetic allopolyploids

2019 ◽  
Author(s):  
Yunxiao Wei ◽  
Fei Li ◽  
Shujiang Zhang ◽  
Shifan Zhang ◽  
Hui Zhang ◽  
...  
Keyword(s):  
Differential Expression ◽  
Small Rna ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Small Rna Sequencing ◽  
Go Enrichment ◽  
Polyploid Formation ◽  
Differentially Expressed Mirnas ◽  
New Perspective ◽  
Go Enrichment Analysis

Allopolyploidy is an evolutionary and mechanisticaly 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 small RNA changes of eight F2 synthetic B. napus using small RNA sequencing. We found that a part of miRNAs and siRNAs were non-additively expressed in the synthesized B. napus allotetraploid. Differentially expressed miRNAs and siRNAs differed among eight F2 individuals, and the differential expression of miR159 and miR172 was consistent with that of flowering time trait. The GO enrichment analysis of differential expression miRNA target genes found that most of them were concentrated in ATP-related pathways, which might be a potential regulatory process contributing to heterosis. In addition, the number of siRNAs present in the offspring was significantly higher than that of the parent, and the number of high parents was significantly higher than the number of low parents. The results have shown that the differential expression of miRNA lays the foundation for solving the trait separation phenomenon, and the significant increase of siRNA alleviates the shock of the newly synthesized allopolyploidy. It provides a new perspective of small RNA changes and trait separation in the early stages of allopolyploid polyploid formation.

scholarly journals Bile acids and bilirubin effects on osteoblastic gene profile. Implications in the pathogenesis of osteoporosis in liver diseases

2019 ◽  
Author(s):  
Silvia Ruiz-Gaspà ◽  
Nuria Guañabens ◽  
Susana Jurado González ◽  
Marta Dubreuil ◽  
Andres Combalia ◽  
...  
Keyword(s):  
Differential Expression ◽  
Liver Diseases ◽  
Target Genes ◽  
Lithocholic Acid ◽  
Culture Conditions ◽  
Matrix Gla Protein ◽  
Osteoblastic Cells ◽  
Human Osteosarcoma Cells ◽  
Apoptotic Genes ◽  
End Stage

AbstractOsteoporosis in advanced cholestatic and end-stage liver disease is related to low bone formation. Previous studies have demonstrated the deleterious consequences of lithocholic acid (LCA) and bilirubin on osteoblastic cells. These effects are partially or completely neutralized by ursodeoxycholic acid (UDCA). We have assessed the differential gene expression of osteoblastic cells under different culture conditions. The experiments were performed in human osteosarcoma cells (Saos-2) cultured with LCA 10 μM), bilirubin (50 μM) or UDCA (10 and 100 μM) at 2 and 24 hours. Expression of 87 genes related to bone metabolism and other signalling pathways were assessed by TaqMan micro fluidic cards. Several genes were up-regulated by LCA, most of them pro-apoptotic (BAX, BCL10, BCL2L13, BCL2L14), but also MGP (matrix Gla protein), BGLAP (osteocalcin), SPP1 (osteopontin) and CYP24A1, and down-regulated bone morphogenic protein genes (BMP3 and BMP4) and DKK1 (Dickkopf-related protein 1). Parallel effects were observed with bilirubin, which up-regulated apoptotic genes and CSF2 (colony-stimulating factor 2) and down-regulated antiapoptotic genes (BCL2 and BCL2L1), BMP3, BMP4 and RUNX2. UDCA 100 μM had specific consequences since differential expression was observed, up-regulating BMP2, BMP4, BMP7, CALCR (calcitonin receptor), SPOCK3 (osteonectin), BGLAP (osteocalcin) and SPP1 (osteopontin), and down-regulating pro-apoptotic genes. Furthermore, most of the differential expression changes induced by both LCA and bilirubin were partially or completely neutralized by UDCA. Conclusion: Our observations reveal novel target genes, whose regulation by retained substances of cholestasis may provide additional insights into the pathogenesis of osteoporosis in cholestatic and end-stage liver diseases.

scholarly journals Profiling of Exosomal MicroRNAs Expression in Umbilical Cord Blood from Normal and Preeclampsia Patients

2021 ◽  
Author(s):  
Hai-Tao Pan ◽  
Xiao-Liang Shi ◽  
Min Fang ◽  
Xiang-Mei Sun ◽  
Pan-Pan Chen ◽  
...  
Keyword(s):  
Differential Expression ◽  
Target Genes ◽  
Negative Impact ◽  
Sequence Similarity ◽  
Experimental Studies ◽  
Microvascular Dysfunction ◽  
Differentially Expressed ◽  
Mirna Sequence ◽  
Illumina Platform ◽  
Serum Exosomes

Abstract Background: Epidemiological and experimental studies suggest that preeclampsia has a negative impact on maternity and offspring health. Previous studies report that dysregulation in utero-environment increases risk for elderly disease such as cardiovascular disease. However, the underlying mechanisms remain elusive. Specific microRNAs (miRNAs) are packaged in exosomes may regulate processes in offspring microvascular dysfunction.Methods: A comprehensive miRNA sequence-based approach to compare exosomes carry miRNAs (Exo-miRNAs) expression levels in umbilical serum between normal and preeclampsia patients was performed to explore mechanisms for development of cardiovascular dysfunction in offspring exposed to preeclampsia. by ExoQuick precipitations were used to isolate serum exosomes. Serum exosomes were then viewed under electron microscopy, and their characteristics determined by western blotting and nanoparticle-tracking analysis. Illumina platform was used to perform sequencing. Bioinformatics analysis was used to explore differentially expressed Exo-miRNAs in umbilical serum.Results: Based on sequence similarity, 1733 known miRNAs were retrieved. Furthermore, 157 mature miRNAs in serum exosomes were significantly differential expressed between PE and those control groups (P＜0.05, log2|FC|>1). Out, of the 157 miRNAs, 96 were upregulated miRNAs whereas 61 miRNAs were downregulated. The 157 differentially expressed miRNAs targeted 51424 differentially expressed genes. Functional analysis through KEGG pathway and Gene Ontology results uncovered that target genes of miRNAs with differential expression were significantly linked to several pathways and biological processes.Conclusion: The findings of this study showed differential expression of umbilical serum Exo-miRNAs in normal compared with PE patients, implying that these Exo-miRNAs play an important function in offspring microvascular dysfunction of preeclampsia.

scholarly journals Restored lncRNAs After ART Therapy Have Potential Key Roles in the Recovery From AIDS

2021 ◽  
Author(s):  
Yingying Zhou ◽  
Yuqing Huang ◽  
Tielong Chen ◽  
Wenjia Hu ◽  
Xiaoping Chen ◽  
...  
Keyword(s):  
Hiv Infection ◽  
Differential Expression ◽  
Art Therapy ◽  
Target Genes ◽  
Mononuclear Cells ◽  
Expression Profiles ◽  
Effective Control ◽  
Rna Seq ◽  
Peripheral Blood Mononuclear ◽  
Hiv Pathogenesis

Abstract Background: Many studies have shown that long noncoding RNAs (lncRNAs) derived from the host and human immunodeficiency virus (HIV) itself play important roles in virus-host interactions and viral pathogenesis. To identify potential key lncRNAs in the regulation of HIV pathogenesis, transcriptome analysis of peripheral blood mononuclear cells (PBMCs), which were derived from 6 HIV/acquired immunodeficiency syndrome (AIDS) subjects pre-HAART and post-HAART with effective control of plasma viremia (<20 HIV RNA copies/ml) and 6 healthy subjects, was performed by RNA sequencing (RNA-seq).Results: We identified a total of 974 lncRNAs whose expression levels were restored to normal after ART therapy. The results of the cis-acting analysis showed that only six lncRNAs have cis-regulated target genes, among which the target gene RP11-290F5.1, interferon regulatory factors 2 (IRF2), could promote HIV replication. We also identified lncRNA CTB-119C2.1, which regulates most mRNAs with differential expression between pre- and post-HAART, and the differences were significant. We selected lncRNA CTB-119C2.1 for qRT–PCR verification, and the results were consistent with those of RNA-seq. RAB3A and GADD45A, two of the lncRNA CTB-119C2.1-associated genes, have been shown to be associated with HIV infection. KEGG analysis of lncRNA CTB-119C2.1-associated genes revealed that most of the genes are involved in the p53 signaling pathway or pathways related to cell circulation and DNA replicationConclusion: In this study, we used RNA-seq to systematically compare the expression profiles of lncRNAs in HIV subjects between untreated and treated time points. We successfully identified some lncRNAs with differential expression during certain periods (no HIV infection, HIV infection before treatment, and after treatment). Their expression is associated with viral loads, and some of their regulating genes were found to be involved in HIV pathogenesis through bioinformatic analysis. These findings could help to reveal the underlying molecular mechanism of the progression of AIDS.

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