scholarly journals Identification of Cassava MicroRNAs under Abiotic Stress

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Carolina Ballén-Taborda ◽  
Germán Plata ◽  
Sarah Ayling ◽  
Fausto Rodríguez-Zapata ◽  
Luis Augusto Becerra Lopez-Lavalle ◽  
...  
Keyword(s):  
Posttranscriptional Regulation ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Biotic And Abiotic Stresses ◽  
Specific Expression ◽  
Adverse Conditions ◽  
Stress Control ◽  
Significant Attention ◽  
Lower Expression

The study of microRNAs (miRNAs) in plants has gained significant attention in recent years due to their regulatory role during development and in response to biotic and abiotic stresses. Although cassava (Manihot esculentaCrantz) is tolerant to drought and other adverse conditions, most cassava miRNAs have been predicted using bioinformatics alone or through sequencing of plants challenged by biotic stress. Here, we use high-throughput sequencing and different bioinformatics methods to identify potential cassava miRNAs expressed in different tissues subject to heat and drought conditions. We identified 60 miRNAs conserved in other plant species and 821 potential cassava-specific miRNAs. We also predicted 134 and 1002 potential target genes for these two sets of sequences. Using real time PCR, we verified the condition-specific expression of 5 cassava small RNAs relative to a non-stress control. We also found, using publicly available expression data, a significantly lower expression of the predicted target genes of conserved and nonconserved miRNAs under drought stress compared to other cassava genes. Gene Ontology enrichment analysis along with condition specific expression of predicted miRNA targets, allowed us to identify several interesting miRNAs which may play a role in stress-induced posttranscriptional regulation in cassava and other plants.

Bioinformatics Analysis and Validation of Differentially Expressed MicroRNAs with Their Target Genes Involved in GLP-1RA Facilitated Osteogenesis

2020 ◽  
Vol 15 ◽  
Author(s):  
Na Wang ◽  
Yukun Li ◽  
Sijing Liu ◽  
Liu Gao ◽  
Chang Liu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Bioinformatics Analysis ◽  
Differentially Expressed ◽  
Functional Study ◽  
Regulation Network ◽  
Glucagon Like Peptide 1 ◽  
G Protein Coupled ◽  
Lower Expression

Background: Recent studies revealed that the hypoglycemic hormone, glucagon-like peptide-1 (GLP-1), acted as an important modulator in osteogenesis of bone marrow derived mesenchymal stem cells (BMSCs). Objectives: The aim of this study was to identify the specific microRNA (miRNA) using bioinformatics analysis and validate the presence of differentially expressed microRNAs with their target genes after GLP-1 receptor agonist (GLP-1RA) administration involved in ostogenesis of BMSCs. Methods: MiRNAs were extracted from BMSCs after 5 days’ treatment and sent for high-throughput sequencing for differentially expressed (DE) miRNAs analyses. Then the expression of the DE miRNAs verified by the real-time RT-PCR analyses. Target genes were predicted, and highly enriched GOs and KEGG pathway analysis were conducted using bioinformatics analysis. For the functional study, two of the target genes, SRY (sex determining region Y)-box 5 (SOX5) and G protein-coupled receptor 84 (GPR84), were identified. Results: A total of 5 miRNAs (miRNA-509-5p, miRNA-547-3p, miRNA-201-3p, miRNA-201-5p, and miRNA-novel-272-mature) were identified differentially expressed among groups. The expression of miRNA-novel-272-mature were decreased during the osteogenic differentiation of BMSCs, and GLP-1RA further decreased its expression. MiRNA-novel-272-mature might interact with its target mRNAs to enhance osteogenesis. The lower expression of miRNA-novel-272-mature led to an increase in SOX5 and a decrease in GPR84 mRNA expression, respectively. Conclusions: Taken together, these results provide further insights to the pharmacological properties of GLP-1RA and expand our knowledge on the role of miRNAs-mRNAs regulation network in BMSCs’ differentiation.

Biological role of miRNA-146a at virus infections. Modern strategy of search of new safe pharmacological agents for treatment

2021 ◽  
Vol 19 (2) ◽  
pp. 145-174
Author(s):  
Petr D. Shabanov ◽  
Vladimir I. Vashchenko
Keyword(s):  
Virus Infection ◽  
Posttranscriptional Regulation ◽  
Target Genes ◽  
Viral Infections ◽  
Current Knowledge ◽  
Recipient Cell ◽  
Viral Disease ◽  
Cellular Mirnas ◽  
Specific Expression ◽  
Regulatory Pathways

Cellular microRNAs (miRNAs) were identified as a key player in the posttranscriptional regulation of cellular-genes regulatory pathways. Here, we review the current knowledge on the interaction between RNA viruses and cellular miRNAs. We also discuss how cell and tissue-specific expression of miRNAs can directly affect viral pathogenesis. They also emerged as a significant regulator of the immune response. In particular, miR-146a acts as an importance modulator of function and differentiation cells of the innate and adaptive immunity. It has been associated with disorder including cancer and viral infections. Given its significance in the regulation of key cellular processes, it is not surprising which virus infection have found ways to dysregulation of miRNAs. miR-146a has been identified in exosomes (exosomal miR-146a). After the exosomes release from donor cells, they are taken up by the recipient cell and probably the exosomal miR-146a is able to modulate the antiviral response in the recipient cell and result in making them more susceptible to virus infection. In this review, we discuss recent reports regarding miR-146a expression levels, target genes, function, and contributing role in the pathogenesis of the viral infection and provide a clue to develop the new preventive and therapeutic strategies for medical treatment viral disease, and СOVID-19.

scholarly journals Identification of MicroRNAs and Their Targets Involved in Paeonia rockii Petal Variegation Using High-throughput Sequencing

2019 ◽  
Vol 144 (2) ◽  
pp. 118-129 ◽  
Author(s):  
Qianqian Shi ◽  
Xiaoxiao Zhang ◽  
Xiang Li ◽  
Lijuan Zhai ◽  
Xiaoning Luo ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Posttranscriptional Regulation ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Tree Peony ◽  
Flower Opening ◽  
Paeonia Rockii ◽  
Flower Pigmentation

Tree peony (Paeonia sp.) is a popular traditional ornamental plant in China. Among the nine wild species, Paeonia rockii displays wide-ranging, deep purple variegation at the base of the petals, whereas Paeonia ostii exhibits purely white petals. Overall, the posttranscriptional regulation involved in tree peony flower opening and pigmentation remains unclear. To identify potential microRNAs (miRNAs) involved in flower variegation, six small RNA libraries of P. ostii and P. rockii petals at three different opening stages were constructed and sequenced. Using Illumina-based sequencing, 22 conserved miRNAs and 27 novel miRNAs were identified in P. rockii and P. ostii petals. Seventeen miRNAs were differentially expressed during flower development, and several putative target genes of these miRNAs belonged to transcription factor families, such as Myb domain (MYB), and basic helix-loop-helix (bHLH) transcription factors. Furthermore, an integrative analysis of the expression profiles of miRNAs and their corresponding target genes revealed that variegation formation might be regulated by miR159c, miR168, miR396a, and novel_miR_05, which target the MYB transcription factors, chalcone synthase (CHS), and ABC transporter. Our preliminary study is the first report of miRNAs involved in Paeonia flower pigmentation. It provides insight regarding the molecular mechanisms underlying the regulation of flower pigmentation in tree peony.

scholarly journals Aberrant Expressional Profiling of Known MicroRNAs in the Liver of Silver Carp (Hypophthalmichthys molitrix) Following Microcystin-LR Exposure Based on samllRNA Sequencing

Toxins ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 41 ◽  
Author(s):  
Yiyi Feng ◽  
Xi Chen ◽  
Junguo Ma ◽  
Bangjun Zhang ◽  
Xiaoyu Li
Keyword(s):  
Signaling Pathway ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Liver Toxicity ◽  
Silver Carp ◽  
Wnt Signaling Pathway ◽  
Enrichment Analysis ◽  
Control Group ◽  
Hypophthalmichthys Molitrix ◽  
Multiple Organs

Microcystin-LR (MC-LR) poses a serious threat to human health due to its hepatotoxicity. However, the specific molecular mechanism of miRNAs in MC-LR-induced liver injury has not been determined. The aim of the present study was to determine whether miRNAs are regulated in MC-LR-induced liver toxicity by using high-throughput sequencing. Our research demonstrated that 53 miRNAs and 319 miRNAs were significantly changed after 24 h of treatment with MC-LR (50 and 200 μg/kg, respectively) compared with the control group. GO enrichment analysis revealed that these target genes were related to cellular, metabolic, and single-organism processes. Furthermore, KEGG pathway analysis demonstrated that the target genes of differentially expressed miRNAs in fish liver were primarily involved in the insulin signaling pathway, PPAR signaling pathway, Wnt signaling pathway, and transcriptional misregulation in cancer. Moreover, we hypothesized that 4 miRNAs (miR-16, miR-181a-3p, miR-451, and miR-223) might also participate in MC-LR-induced toxicity in multiple organs of the fish and play regulatory roles according to the qPCR analysis results. Taken together, our results may help to elucidate the biological function of miRNAs in MC-LR-induced toxicity.

scholarly journals Identification of Long Non-Coding RNAs Involved in Fat Deposition in Pigs Using Two High-Throughput Sequencing Methods

2020 ◽  
Author(s):  
Yibing Liu ◽  
Hong Ao ◽  
Fengxia Zhang ◽  
Xitong Zhao ◽  
Huatao Liu ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Gene Prediction ◽  
Enrichment Analysis ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Backfat Thickness ◽  
Acid Oxidation ◽  
Rna Seq

Abstract Background: Adipose is an important body tissue in pigs, and fatty traits are critical in pig production. The function of long non-coding RNA (lncRNA) in fat deposition and metabolism has been proven in previous studies. In this study, we focused on lncRNAs associated with fattening traits in pigs. The adipose tissue of six Landrace pigs with either extremely-high or -low backfat thickness ( n high = 3, n low = 3) was collected, after which we performed strand-specific RNA sequencing using biological replicates and pooling methods. Results: A total of 19,631 genes and 2,013 lncRNAs were identified using the coding potential calculator, coding-non-coding index, and Pfam database, including 334 known transcripts and 1,679 novel transcripts. Using edgeR, we determined that 220 lncRNAs and 1,512 genes were differentially expressed (|Fold Change| > 2 and false discovery rate < 0.05) between the two groups in biological replicate RNA sequencing (RNA-seq), and 127 lncRNAs and 2,240 genes were differently expressed in pooling RNA-seq. Further Kyoto Encyclopedia of Genes and Genomes and Gene Ontology enrichment analysis of the differentially expressed genes found that some of the genes were involved in several key pathways related to fat development. After targeting gene prediction, we determined that some cis-target genes of the differentially expressed lncRNAs play an important role in fat deposition. For example, ACSL3 is cis-targeted by lncRNA TCONS-00052400, and it can activate the conversion of long-chain fatty acids. In addition, lncRNA TCONS_00041740 was up-regulated in the high backfat thickness group, and its cis-target gene ACACB was also up-regulated in this group. It has been reported that ACACB is the rate-limiting enzyme in fatty acid oxidation. Conclusions: Since these genes have necessary functions in fat metabolism, the results imply that the lncRNAs detected in our study may affect fat deposition in pigs through regulation of their target genes. In summary, our study explored the regulation of lncRNA and their target genes on fat deposition in pigs and provided new insights for further investigation of the biological functions of lncRNA.

Contribution Value：A Indicator for Measuring the Contribution of ncRNAs to Transcriptome

2020 ◽  
Author(s):  
Xinyi Gu ◽  
Bo Jin ◽  
Zhidan Qi ◽  
Xiaofeng Yin
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Enrichment Analysis ◽  
P Value ◽  
Data Sets ◽  
Kegg Pathways ◽  
Multiple Data ◽  
C Value ◽  
Multiple Data Sets ◽  
Main Basis

Abstract Background：The expression difference multiple log2 FC and P value are often the main basis for screening ncRNA after high-throughput sequencing. However, the above two indicators can’t well reflect the regulatory effect of nonprotein coding RNA (ncRNA) on mRNA. Therefore, we propose a new indicator, Contribution value (C value), to characterize the contribution of ncRNAs to transcriptome transformation.Results：In this study, we analyzed multiple data sets from mice and humans. We take all differential expression mRNAs as a parent set and the GO and KEGG enrichment analysis were performed on it. C value can be simply regarded as the sum of the product of the richfactor of each ncRNA target genes participating in each term/pathway and the P value of that term/pathway obtained from the parent set. We found that C value was superior to log2 FC and P value in all operation results.Conclusions：We show that the C value, which takes into accounts the the KEGG pathways and GO terms involved in the development of the disease, provides a measure of another dimension compared with the log2FC and P value. These hidden interactions between ncRNAs and their target genes may provide more comprehensive analysis.

scholarly journals Identification and Characterization of Known and Novel MicroRNAs in Five Tissues of Wax Gourd (Benincasa hispida) Based on High-Throughput Sequencing

2021 ◽  
Vol 11 (21) ◽  
pp. 10068
Author(s):  
Jinqiang Yan ◽  
Min Wang ◽  
Wenrui Liu ◽  
Dasen Xie ◽  
Xiaoming He ◽  
...  
Keyword(s):  
High Throughput ◽  
Small Rna ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Patterns ◽  
Small Rna Sequencing ◽  
Specific Expression ◽  
Nac Transcription Factors ◽  
Benincasa Hispida ◽  
Wax Gourd

MicroRNAs (miRNAs) are endogenous single-stranded non-coding small RNAs of 20-24 nucleotides and play important roles in many plant biological and metabolic processes. Wax gourd is an important vegetable of Cucurbitacea family, with great economic and medicinal value. Although miRNAs have been extensively studied in model plant species, less is known in wax gourd (Benincasa hispida). In this study, in order to identify miRNAs in wax groud, five independent small RNA libraries were constructed using leaf, root, stem, flower, and fruit of B227. Based on high-throughput Illumina deep sequencing. In total, 422 known and 409 novel miRNAs were identified from five libraries. Comparative analysis revealed that many miRNAs were differentially expressed among different tissues, indicating tissue-specific expression of some miRNAs. qRT-PCR verified the reliability of small RNA sequencing results. Furthermore, miRNAs with similar expression patterns among five tissues were clustered into the same profile, among which many miRNAs were found with relatively high expression in the fruit of wax gourd. MiR164-x had the highest expression in fruit than in other tissues and many NAC transcription factors were predicted as its target genes. We propose that miR164 might regulate fruit development by forming miR164-NAC module in wax gourd. Taken together, this study provides the first global miRNAs profiling of wax gourd, and lays the foundation for understanding the regulatory roles of miRNAs in the growth and development processes of wax gourd.

Bioinformatics Analysis Reveals Functions of MicroRNAs in Rice Under the Drought Stress

2021 ◽  
Vol 15 (8) ◽  
pp. 927-936 ◽  
Author(s):  
Yan Peng ◽  
Yuewu Liu ◽  
Xinbo Chen
Keyword(s):  
Drought Stress ◽  
Target Genes ◽  
Hot Spot ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Protein Protein Interaction ◽  
Promising Tool ◽  
Differentially Expressed Mirnas ◽  
Aba Biosynthesis

Background: Drought is one of the most damaging and widespread abiotic stresses that can severely limit the rice production. MicroRNAs (miRNAs) act as a promising tool for improving the drought tolerance of rice and have become a hot spot in recent years. Objective: In order to further extend the understanding of miRNAs, the functions of miRNAs in rice under drought stress are analyzed by bioinformatics. Method: In this study, we integrated miRNAs and genes transcriptome data of rice under the drought stress. Some bioinformatics methods were used to reveal the functions of miRNAs in rice under drought stress. These methods included target genes identification, differentially expressed miRNAs screening, enrichment analysis of DEGs, network constructions for miRNA-target and target-target proteins interaction. Results: (1) A total of 229 miRNAs with differential expression in rice under the drought stress, corresponding to 73 rice miRNAs families, were identified. (2) 1035 differentially expressed genes (DEGs) were identified, which included 357 up-regulated genes, 542 down-regulated genes and 136 up/down-regulated genes. (3) The network of regulatory relationships between 73 rice miRNAs families and 1035 DEGs was constructed. (4) 25 UP_KEYWORDS terms of DEGs, 125 GO terms and 7 pathways were obtained. (5) The protein-protein interaction network of 1035 DEGs was constructed. Conclusion: (1) MiRNA-regulated targets in rice might mainly involve in a series of basic biological processes and pathways under drought conditions. (2) MiRNAs in rice might play critical roles in Lignin degradation and ABA biosynthesis. (3) MiRNAs in rice might play an important role in drought signal perceiving and transduction.

scholarly journals Improvement, identification, and target prediction for miRNAs in the porcine genome by using massive, public high-throughput sequencing data

2021 ◽  
Vol 99 (2) ◽  
Author(s):  
Yuhua Fu ◽  
Pengyu Fan ◽  
Lu Wang ◽  
Ziqiang Shu ◽  
Shilin Zhu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Target Prediction ◽  
Large Data ◽  
Sequencing Data ◽  
Regulate Gene Expression ◽  
High Throughput Sequencing Data ◽  
Annotation Information ◽  
Public Data ◽  
Broad Variety

Abstract Despite the broad variety of available microRNA (miRNA) research tools and methods, their application to the identification, annotation, and target prediction of miRNAs in nonmodel organisms is still limited. In this study, we collected nearly all public sRNA-seq data to improve the annotation for known miRNAs and identify novel miRNAs that have not been annotated in pigs (Sus scrofa). We newly annotated 210 mature sequences in known miRNAs and found that 43 of the known miRNA precursors were problematic due to redundant/missing annotations or incorrect sequences. We also predicted 811 novel miRNAs with high confidence, which was twice the current number of known miRNAs for pigs in miRBase. In addition, we proposed a correlation-based strategy to predict target genes for miRNAs by using a large amount of sRNA-seq and RNA-seq data. We found that the correlation-based strategy provided additional evidence of expression compared with traditional target prediction methods. The correlation-based strategy also identified the regulatory pairs that were controlled by nonbinding sites with a particular pattern, which provided abundant complementarity for studying the mechanism of miRNAs that regulate gene expression. In summary, our study improved the annotation of known miRNAs, identified a large number of novel miRNAs, and predicted target genes for all pig miRNAs by using massive public data. This large data-based strategy is also applicable for other nonmodel organisms with incomplete annotation information.

scholarly journals Integrated network analysis identifying potential novel drug candidates and targets for Parkinson's disease

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Pusheng Quan ◽  
Kai Wang ◽  
Shi Yan ◽  
Shirong Wen ◽  
Chengqun Wei ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Drug Target ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Functional Enrichment ◽  
Control Group ◽  
Drug Candidates ◽  
Novel Drug

AbstractThis study aimed to identify potential novel drug candidates and targets for Parkinson’s disease. First, 970 genes that have been reported to be related to PD were collected from five databases, and functional enrichment analysis of these genes was conducted to investigate their potential mechanisms. Then, we collected drugs and related targets from DrugBank, narrowed the list by proximity scores and Inverted Gene Set Enrichment analysis of drug targets, and identified potential drug candidates for PD treatment. Finally, we compared the expression distribution of the candidate drug-target genes between the PD group and the control group in the public dataset with the largest sample size (GSE99039) in Gene Expression Omnibus. Ten drugs with an FDR < 0.1 and their corresponding targets were identified. Some target genes of the ten drugs significantly overlapped with PD-related genes or already known therapeutic targets for PD. Nine differentially expressed drug-target genes with p < 0.05 were screened. This work will facilitate further research into the possible efficacy of new drugs for PD and will provide valuable clues for drug design.

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