scholarly journals Identification and Comparative Profiling of microRNAs at Different Diapause Stages of Galeruca Daurica Adults

2020 ◽  
Author(s):  
Tian-Feng Duan ◽  
Ling Li ◽  
Yao Tan ◽  
Yan-Yan Li ◽  
Bao-Ping Pang
Keyword(s):  
Small Rna ◽  
Target Genes ◽  
Expression Profiles ◽  
Mapk Signaling ◽  
Transcriptional Level ◽  
Regulate Gene Expression ◽  
Small Noncoding Rnas ◽  
Physiological Processes ◽  
Summer Diapause ◽  
G Protein Coupled

Abstract Background: MicroRNAs (miRNAs) are a class of small noncoding RNAs of approximately 22 nt in length, which regulate gene expression at the post-transcriptional level. Although the regulatory roles of miRNAs in various physiological processes throughout insect development have been investigated, it is almost unknown about the roles of miRNAs involved in the regulation of diapause in insects.Results: We constructed 12 small RNA libraries from Galeruca daurica adults at different diapause stages: pre-diapause (PD), diapause (D), post-diapause 1 (TD1), and post-diapause 2 (TD2). Using Illumina sequencing, a total of 95.06 million valid reads was obtained, and 230 miRNAs, including 143 conserved and 87 novel miRNAs, were identified from G. daurica. The expression profiles of these miRNAs were assessed across different diapause stages and miRNAs that were highly expressed at different diapause stages were identified. Comparative analysis of read counts indicated that both conserved and novel miRNAs were differently expressed among the four different diapause stages, and the differential expression was validated via qRT-PCR. The 25, 11, 15, 14, 26, and one miRNAs were differentially expressed in D/PD, D/TD1, D/TD2, TD1/PD, TD2/PD, and TD2/TD1, respectively. The KEGG and GO analysis of the predicted target genes suggested the essential roles of miRNAs in the regulation of summer diapause in G. daurica, especially via the juvenile hormone, ribosome, MAPK signaling, mTOR signaling, Ca2+ signaling, and G-protein coupled receptor signaling pathways.Conclusion: Our research results indicate that miRNAs may be involved in the regulation of summer diapause in G. daurica, and these results also provide an important new small RNA genomics resource for further studies on insect diapause.

scholarly journals miRNAs in the Odontogenesis Process

2018 ◽  
Vol 2 (2) ◽  
pp. 499-505
Author(s):  
Ignacio Roa
Keyword(s):  
Small Rna ◽  
Target Genes ◽  
The Body ◽  
Transcriptional Level ◽  
Regulate Gene Expression ◽  
Rna Molecules ◽  
Body Development ◽  
Proliferation And Differentiation ◽  
Specific Sequences ◽  
Regulate Gene

MicroRNAs (miRNAs) are a class of small RNA molecules noncoding to proteins, which regulate gene expression at post-transcriptional level by binding to specific sequences within target genes. miRNAs have been recognized as important regulatory factors in the body development and expression of certain diseases. Some miRNAs regulate the proliferation and differentiation of cells and tissues during odontogenesis.

scholarly journals Comparative Analysis of miRNA Expression Profiles between Heat-Tolerant and Heat-Sensitive Genotypes of Flowering Chinese Cabbage Under Heat Stress Using High-Throughput Sequencing

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 264 ◽  
Author(s):  
Waqas Ahmed ◽  
Ronghua Li ◽  
Yanshi Xia ◽  
Guihua Bai ◽  
Kadambot H. M. Siddique ◽  
...  
Keyword(s):  
Heat Stress ◽  
Heat Tolerance ◽  
Chinese Cabbage ◽  
Target Genes ◽  
Expression Profiles ◽  
Mapk Signaling ◽  
Differentially Expressed ◽  
Transcriptional Level ◽  
Flowering Chinese Cabbage ◽  
Heat Tolerant

Heat stress disturbs cellular homeostasis, thus usually impairs yield of flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee). MicroRNAs (miRNAs) play a significant role in plant responses to different stresses by modulating gene expression at the post-transcriptional level. However, the roles that miRNAs and their target genes may play in heat tolerance of flowering Chinese cabbage remain poorly characterized. The current study sequenced six small RNA libraries generated from leaf tissues of flowering Chinese cabbage collected at 0, 6, and 12 h after 38 °C heat treatment, and identified 49 putative novel miRNAs and 43 known miRNAs that differentially expressed between heat-tolerant and heat-sensitive flowering Chinese cabbage. Among them, 14 novel and nine known miRNAs differentially expressed only in the heat-tolerant genotype under heat-stress, therefore, their target genes including disease resistance protein TAO1-like, RPS6, reticuline oxidase-like protein, etc. might play important roles in enhancing heat-tolerance. Gene Ontology (GO) analysis revealed that targets of these differentially expressed miRNAs may play key roles in responses to temperature stimulus, cell part, cellular process, cell, membrane, biological regulation, binding, and catalytic activities. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified their important functions in signal transduction, environmental adaptation, global and overview maps, as well as in stress adaptation and in MAPK signaling pathways such as cell death. These findings provide insight into the functions of the miRNAs in heat stress tolerance of flowering Chinese cabbage.

scholarly journals Identification of MicroRNA as Sepsis Biomarker Based on miRNAs Regulatory Network Analysis

2014 ◽  
Vol 2014 ◽  
pp. 1-12 ◽  
Author(s):  
Jie Huang ◽  
Zhandong Sun ◽  
Wenying Yan ◽  
Yujie Zhu ◽  
Yuxin Lin ◽  
...  
Keyword(s):  
Regulatory Network ◽  
Expression Profiles ◽  
Delayed Diagnosis ◽  
Interaction Network ◽  
High Sensitivity ◽  
Regulate Gene Expression ◽  
Protein Protein Interaction ◽  
Small Noncoding Rnas ◽  
Mirna Expression Profiles ◽  
Pathways Analysis

Sepsis is regarded as arising from an unusual systemic response to infection but the physiopathology of sepsis remains elusive. At present, sepsis is still a fatal condition with delayed diagnosis and a poor outcome. Many biomarkers have been reported in clinical application for patients with sepsis, and claimed to improve the diagnosis and treatment. Because of the difficulty in the interpreting of clinical features of sepsis, some biomarkers do not show high sensitivity and specificity. MicroRNAs (miRNAs) are small noncoding RNAs which pair the sites in mRNAs to regulate gene expression in eukaryotes. They play a key role in inflammatory response, and have been validated to be potential sepsis biomarker recently. In the present work, we apply a miRNA regulatory network based method to identify novel microRNA biomarkers associated with the early diagnosis of sepsis. By analyzing the miRNA expression profiles and the miRNA regulatory network, we obtained novel miRNAs associated with sepsis. Pathways analysis, disease ontology analysis, and protein-protein interaction network (PIN) analysis, as well as ROC curve, were exploited to testify the reliability of the predicted miRNAs. We finally identified 8 novel miRNAs which have the potential to be sepsis biomarkers.

Dysregulation of tRNA-derived small RNAs and their potential roles in lupus nephritis

Lupus ◽  
2021 ◽  
pp. 096120332110614
Author(s):  
Yan Liang ◽  
Ji Zhang ◽  
Wenxian Qiu ◽  
Bo Chen ◽  
Ying Zhou ◽  
...  
Keyword(s):  
Lupus Nephritis ◽  
Signaling Pathway ◽  
Small Rnas ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Mapk Signaling ◽  
Pcr Analysis ◽  
Clinical Indicators ◽  
Qrt Pcr

Objective Lupus nephritis (LN) is a major end-organ complication of systemic lupus erythematosus (SLE), and the molecular mechanism of LN is not completely clear. Accumulating pieces of evidence indicate the potential vital role of tRNA-derived small RNAs (tsRNAs) in human diseases. Current study aimed to investigate the potential roles of tsRNAs in LN. Methods We herein employed high‐throughput sequencing to screen the expression profiles of tsRNAs in renal tissues of the LN and control groups. To validate the sequencing data, we performed quantitative real-time PCR (qRT-PCR) analysis. Correlational analysis of verified tsRNAs expression and clinical indicators was conducted using linear regression. The potential target genes were also predicted. The biological functions of tsRNAs were annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Results Our findings revealed that the expression profiles of tsRNAs were significantly altered in the kidney tissues from LN patients compared with control. Overall, 160 tsRNAs were significantly dysregulated in the LN group, of which 79 were upregulated, whereas 81 were downregulated. Subsequent qRT-PCR results confirmed the different expression of candidate tsRNAs. Correlation analysis results found that expression of verified tsRNAs were correlated to clinical indicators. The target prediction results revealed that verified tsRNAs might act on 712 target genes. Further bioinformatics analysis uncovered tsRNAs might participate in the pathogenesis of LN through several associated pathways, including cell adhesion molecules, MAPK signaling pathway, PI3K-Akt signaling pathway and B cell receptor signaling pathway. Conclusion This study provides a novel insight for studying the mechanism of LN.

scholarly journals miR-615 Fine-Tunes Growth and Development and Has a Role in Cancer and in Neural Repair

Cells ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 1566 ◽  
Author(s):  
Marisol Godínez-Rubí ◽  
Daniel Ortuño-Sahagún
Keyword(s):  
Growth And Development ◽  
Target Genes ◽  
Noncoding Rnas ◽  
Tumor Promoter ◽  
Neural Repair ◽  
Small Noncoding Rnas ◽  
Physiological Processes ◽  
And Migration ◽  
Migration Of Cells ◽  
Regulation Of Growth

MicroRNAs (miRNAs) are small noncoding RNAs that function as epigenetic modulators regulating almost any gene expression. Similarly, other noncoding RNAs, as well as epigenetic modifications, can regulate miRNAs. This reciprocal interaction forms a miRNA-epigenetic feedback loop, the deregulation of which affects physiological processes and contributes to a great diversity of diseases. In the present review, we focus on miR-615, a miRNA highly conserved across eutherian mammals. It is involved not only during embryogenesis in the regulation of growth and development, for instance during osteogenesis and angiogenesis, but also in the regulation of cell growth and the proliferation and migration of cells, acting as a tumor suppressor or tumor promoter. It therefore serves as a biomarker for several types of cancer, and recently has also been found to be involved in reparative processes and neural repair. In addition, we present the pleiad of functions in which miR-615 is involved, as well as their multiple target genes and the multiple regulatory molecules involved in its own expression. We do this by introducing in a comprehensible way the reported knowledge of their actions and interactions and proposing an integral view of its regulatory mechanisms.

scholarly journals MicroRNAs in Uteroplacental Vascular Dysfunction

Cells ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 1344 ◽  
Author(s):  
Hu ◽  
Zhang
Keyword(s):  
Intrauterine Growth Restriction ◽  
Target Genes ◽  
Vascular Dysfunction ◽  
Neonatal Morbidity ◽  
Trophoblast Invasion ◽  
Transcriptional Level ◽  
Regulate Gene Expression ◽  
Rna Molecules ◽  
Expression Of Genes ◽  
Differentially Expressed Mirnas

Pregnancy complications of preeclampsia and intrauterine growth restriction (IUGR) are major causes of maternal and perinatal/neonatal morbidity and mortality. Although their etiologies remain elusive, it is generally accepted that they are secondary to placental insufficiency conferred by both failure in spiral artery remodeling and uteroplacental vascular malfunction. MicroRNAs (miRNAs) are small no-coding RNA molecules that regulate gene expression at the post-transcriptional level. Increasing evidence suggests that miRNAs participate in virtually all biological processes and are involved in numerous human diseases. Differentially expressed miRNAs in the placenta are typical features of both preeclampsia and IUGR. Dysregulated miRNAs target genes of various signaling pathways in uteroplacental tissues, contributing to the development of both complications. In this review, we provide an overview of how aberrant miRNA expression in preeclampsia and IUGR impacts the expression of genes involved in trophoblast invasion and uteroplacental vascular adaptation.

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 Development of a tRNA-Derived Small RNA Prognostic Panel and Their Potential Functions in Osteosarcoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Zhenming Tang ◽  
Shuhui Zhang ◽  
Zhougui Ling
Keyword(s):  
Small Rna ◽  
Target Genes ◽  
Cox Model ◽  
Expression Profiles ◽  
Survival Rates ◽  
Low Risk ◽  
Validation Dataset ◽  
Therapeutic Outcomes ◽  
Risk Patients ◽  
Geo Database

BackgroundTherapeutic outcomes of osteosarcoma treatment have not significantly improved in several decades. Therefore, strong prognostic biomarkers are urgently needed.MethodsWe first extracted the tRNA-derived small RNA (tsRNA) expression profiles of osteosarcoma from the GEO database. Then, we performed a unique module analysis and use the LASSO-Cox model to select survival-associated tsRNAs. Model effectiveness was further verified using an independent validation dataset. Target genes with selected tsRNAs were predicted using RNAhybrid.ResultsA LASSO-Cox model was established to select six prognostic tsRNA biomarkers: tRF-33-6SXMSL73VL4YDN, tRF-32-6SXMSL73VL4YK, tRF-32-M1M3WD8S746D2, tRF-35-RPM830MMUKLY5Z, tRF-33-K768WP9N1EWJDW, and tRF-32-MIF91SS2P46I3. We developed a prognostic panel for osteosarcoma patients concerning their overall survival by high-low risk. Patients with a low-risk profile had improved survival rates in training and validation dataset.ConclusionsThe suggested prognostic panel can be utilized as a reliable biomarker to predict osteosarcoma patient survival rates.

scholarly journals Identification of miRNA-mRNA Crosstalk in Respiratory Syncytial Virus- (RSV-) Associated Pediatric Pneumonia through Integrated miRNAome and Transcriptome Analysis

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Xu Zhang ◽  
Feng Huang ◽  
Diyuan Yang ◽  
Tao Peng ◽  
Gen Lu
Keyword(s):  
Respiratory Syncytial Virus ◽  
Signaling Pathway ◽  
Whole Blood ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Expression Profiles ◽  
Mapk Signaling ◽  
Design Strategies ◽  
Pediatric Pneumonia ◽  
Syncytial Virus

Respiratory syncytial virus (RSV) is the most common respiratory virus and is associated with pediatric pneumonia, causing bronchiolitis and significant mortality in infants and young children. MicroRNAs (miRNAs) are endogenous noncoding small RNAs that function in gene regulation and are associated with host immune response and disease progression. In the present study, we profiled the global transcriptome and miRNAome of whole blood samples from children with mild or severe RSV-associated pneumonia, aiming to identify the potential biomarkers and investigate the molecular mechanisms of severe RSV-associated pediatric pneumonia. We found that expression profiles of whole blood microRNAs and mRNAs were altered and distinctly different in children with severe RSV-associated pneumonia. In particular, the four most significantly upregulated miRNAs in children with severe RSV-associated pneumonia were hsa-miR-1271-5p, hsa-miR-10a-3p, hsa-miR-125b-5p, and hsa-miR-30b-3p. The severe RSV-associated pneumonia-specific differentially expressed miRNA target interaction network was also contrasted. These target genes were further analyzed with Gene Ontology enrichment analysis. We found that most of the target genes were involved in inflammatory and immune responses, including the NF-κB signaling pathway, the MAPK signaling pathway, and T cell receptor signaling. Our findings will contribute to the identification of biomarkers and new drug design strategies to treat severe RSV-associated pediatric pneumonia.

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.

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