Identification and study of differentially expressed miRNAs in aged NAFLD rats based on high-throughput sequencing

Abstract Objective: This study screened the differentially expressed miRNAs in the mouse cochlea during hearing loss and explored the relationship between miR-224-5p and Neuritin.Methods: The combination of kanamycin sulfate and furosemide was used to establish a mouse hearing loss model. High-throughput sequencing was used to screen the differentially expressed miRNAs during hearing loss. qRT-PCR was used to identify the expression of differential miRNAs in hearing loss. Western Blot was used to detect the expression of Neuritin protein. Luciferase was used to identify the binding site of miRNA and Neuritin.Results: The expression of miR-224-5p in the mouse cochlea increased during hearing loss (p<0.05). MiR-224-5p mimics can reduce Neuritin protein expression in 293T cells (p<0.05). MiR-224-5p can specifically bind to Neuritin (p<0.05).Conclusion: The expression of miR-224-5p increases in hearing loss and targets the expression of Neuritin

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Identification of Differentially Expressed Circular RNAs in Keloid and Normal Skin Tissue by High‐throughput Sequencing

Dermatologic Therapy ◽

10.1111/dth.14745 ◽

2021 ◽

Author(s):

Jing Zhang ◽

Ninghua Liu ◽

Xiufa Wu ◽

Peixuan Wu ◽

Nan Song ◽

...

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Normal Skin ◽

Differentially Expressed ◽

Skin Tissue ◽

Circular Rnas

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Identification of Exogenous Nitric Oxide-Responsive miRNAs from Alfalfa (Medicago sativa L.) under Drought Stress by High-Throughput Sequencing

Genes ◽

10.3390/genes11010030 ◽

2019 ◽

Vol 11 (1) ◽

pp. 30

Author(s):

Yaodong Zhao ◽

Wenjing Ma ◽

Xiaohong Wei ◽

Yu Long ◽

Ying Zhao ◽

...

Keyword(s):

Nitric Oxide ◽

Drought Stress ◽

Medicago Sativa ◽

High Throughput ◽

Drought Resistance ◽

High Throughput Sequencing ◽

Target Genes ◽

Expression Profiles ◽

Differentially Expressed ◽

Medicago Sativa L

Alfalfa (Medicago sativa L.) is a high quality leguminous forage. Drought stress is one of the main factors that restrict the development of the alfalfa industry. High-throughput sequencing was used to analyze the microRNA (miRNA) profiles of alfalfa plants treated with CK (normal water), PEG (polyethylene glycol-6000; drought stress), and PEG + SNP (sodium nitroprusside; nitric oxide (NO) sprayed externally under drought stress). We identified 90 known miRNAs belonging to 46 families and predicted 177 new miRNAs. Real-time quantitative fluorescent PCR (qRT-PCR) was used to validate high-throughput expression analysis data. A total of 32 (14 known miRNAs and 18 new miRNAs) and 55 (24 known miRNAs and 31 new miRNAs) differentially expressed miRNAs were identified in PEG and PEG + SNP samples. This suggested that exogenous NO can induce more new miRNAs. The differentially expressed miRNA maturation sequences in the two treatment groups were targeted by 86 and 157 potential target genes, separately. The function of target genes was annotated by gene ontology (GO) enrichment and kyoto encyclopedia of genes and genomes (KEGG) analysis. The expression profiles of nine selected miRNAs and their target genes verified that their expression patterns were opposite. This study has documented that analysis of miRNA under PEG and PEG + SNP conditions provides important insights into the improvement of drought resistance of alfalfa by exogenous NO at the molecular level. This has important scientific value and practical significance for the improvement of plant drought resistance by exogenous NO.

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Identification of MicroRNAs That Respond to Soybean Cyst Nematode Infection in Early Stages in Resistant and Susceptible Soybean Cultivars

International Journal of Molecular Sciences ◽

10.3390/ijms20225634 ◽

2019 ◽

Vol 20 (22) ◽

pp. 5634 ◽

Cited By ~ 3

Author(s):

Piao Lei ◽

Bing Han ◽

Yuanyuan Wang ◽

Xiaofeng Zhu ◽

Yuanhu Xuan ◽

...

Keyword(s):

Small Rna ◽

Soybean Cyst Nematode ◽

High Throughput Sequencing ◽

Target Genes ◽

Cyst Nematode ◽

Differentially Expressed ◽

Early Stages ◽

Differentially Expressed Mirnas ◽

Plant Pathogen Interactions ◽

Insight Into

Soybean cyst nematode (SCN) causes heavy losses to soybean yield. In order to investigate the roles of soybean miRNAs during the early stages of infection (1 and 5 dpi), 24 small RNA libraries were constructed from SCN resistant cultivar Huipizhi (HPZ) and the susceptible Williams 82 (W82) cultivar for high-throughput sequencing. By sequencing the small RNA libraries, a total of 634 known miRNAs were identified, and 252 novel miRNAs were predicted. Altogether, 14 known miRNAs belonging to 13 families, and 26 novel miRNAs were differentially expressed and may respond to SCN infection in HPZ and W82. Similar expression results were also confirmed by qRT-PCR. Further analysis of the biological processes that these potential target genes of differentially expressed miRNAs regulate found that they may be strongly related to plant–pathogen interactions. Overall, soybean miRNAs experience profound changes in early stages of SCN infection in both HPZ and W82. The findings of this study can provide insight into miRNAome changes in both HPZ and W82 at the early stages of infection, and may provide a stepping stone for future SCN management.

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Construction of miRNA-target networks using microRNA profiles of CVB3-infected HeLa cells

Scientific Reports ◽

10.1038/s41598-019-54188-w ◽

2019 ◽

Vol 9 (1) ◽

Author(s):

Hai Lan Yao ◽

Mi Liu ◽

Wen Jun Wang ◽

Xin Ling Wang ◽

Juan Song ◽

...

Keyword(s):

Hela Cells ◽

Regulatory Networks ◽

Cellular Differentiation ◽

High Throughput Sequencing ◽

Target Genes ◽

Expression Profiles ◽

Differentially Expressed ◽

Mirna Regulation ◽

Cvb3 Infection ◽

Differentially Expressed Mirnas

AbstractMicroRNAs (miRNAs) play an important role in regulating gene expression in multiple biological processes and diseases. Thus, to understand changes in miRNA during CVB3 infection, specific miRNA expression profiles were investigated at 3 h, 6 h, and 9 h postinfection in HeLa cells by small-RNA high-throughput sequencing. Biological implications of 68 differentially expressed miRNAs were analyzed through GO and KEGG pathways. Interaction networks between 34 known highly differentially expressed miRNAs and targets were constructed by mirDIP and Navigator. The predicted targets showed that FAM135A, IKZF2, PLAG1, ZNF148, PHC3, LCOR and DYRK1A, which are associated with cellular differentiation and transcriptional regulation, were recognized by 8 miRNAs or 9 miRNAs through interactional regulatory networks. Seven target genes were confirmed by RT-qPCR. The results showed that the expression of DYRK1A, FAM135A, PLAG1, ZNF148, and PHC3 were obviously inhibited at 3 h, 6 h, and 9 h postinfection. The expression of LCOR did not show a significant change, and the expression of IKZF2 increased gradually with prolonged infection time. Our findings improve the understanding of the pathogenic mechanism of CVB3 infection on cellular differentiation and development through miRNA regulation, which has implications for interventional approaches to CVB3-infection therapy. Our results also provide a new method for screening target genes of microRNA regulation in virus-infected cells.

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

10.21203/rs.2.15327/v1 ◽

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.

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High-Throughput Sequencing Identification of Differentially Expressed microRNAs in Metastatic Ovarian Cancer with experimental validations

10.21203/rs.2.23093/v3 ◽

2020 ◽

Author(s):

Yang Gu ◽

Shulan Zhang

Keyword(s):

Ovarian Cancer ◽

High Throughput Sequencing ◽

Human Cancer ◽

Quantitative Polymerase Chain Reaction ◽

Gynecological Cancer ◽

Metastatic Potential ◽

Differentially Expressed ◽

Luciferase Reporter ◽

Downstream Target ◽

Differentially Expressed Mirnas

Abstract Background: Ovarian cancer (OC) is a common gynecological cancer and characterized by high metastatic potential. MicroRNAs (miRNAs, miRs) have the promise to be harnessed as prognostic and therapeutic biomarkers for OC. Herein, we sought to identify differentially expressed miRNAs and mRNAs in metastatic OC, and to validate them with functional experiments. Methods: Differentially expressed miRNAs and miRNAs were screened from six pairs of primary OC tissues and metastatic tissues using an miRStar™ Human Cancer Focus miRNA & Target mRNA PCR Array. Then, gene expression profiling results were verified by reverse transcription quantitative polymerase chain reaction (RT-qPCR) and western blot assays. The binding affinity between miR-7-5p and TGFβ2 was validated by dual-luciferase reporter assay. Expression of miR-7-5p and TGFβ2 was manipulated to assess their roles in malignant phenotypes of highly metastatic HO-8910PM cells. Results: MiRNA profiling and sequencing identified 12 miRNAs and 10 mRNAs that were differentially expressed in metastatic tissues. Gene ontology and Pathway analyses determined that 3 differentially expressed mRNAs (ITGB3, TGFβ2 and TNC) were related to OC metastasis. The results of RT-qPCR confirmed that the decrease of miR-7-5p was most significant in OC metastasis, while TGFβ2 was up-regulated in OC metastasis. Moreover, miR-7-5p targeted and negatively regulated TGFβ2. MiR-7-5p overexpression accelerated HO-8910PM cell viability and invasion, and TGFβ2 overexpression reversed the results. Meanwhile, simultaneous miR-7-5p and TGFβ2 overexpression rescued the cell activities. Conclusions: This study characterizes differentially expressed miRNAs and mRNAs in metastatic OC, where miR-7-5p and its downstream target were most closely associated with metastatic OC. Overexpression of miR-7-5p targets and inhibits TGFβ2 expression, thereby inhibiting the growth and metastasis of OC.

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Immune-related miRNA-mRNA regulation network in the livers of DHAV-3-infected ducklings

10.21203/rs.2.13422/v3 ◽

2019 ◽

Author(s):

Fengyao Wu ◽

Fengying Lu ◽

Xin Fan ◽

Jin Chao ◽

Chuanmin Liu ◽

...

Keyword(s):

Signaling Pathways ◽

High Throughput Sequencing ◽

Expression Patterns ◽

Differentially Expressed ◽

Receptor Interaction ◽

Integrated Analysis ◽

Mrna Regulation ◽

Duck Hepatitis ◽

Differentially Expressed Mirnas ◽

Regulation Network

Abstract Background: Duck hepatitis A virus type 3 (DHAV-3) is one of the most harmful pathogens in the duck industry. However, the molecular mechanism underlying DHAV-3 infection in ducklings is remain poorly understood. To elucidate the genetic regulatory network for miRNA-mRNA and the signaling pathways involved in DHAV-3 infection in ducklings, we conducted global miRNA and mRNA expression profiling of duckling liver tissues infected with lethal DHAV-3 using high-throughput sequencing. Results: We found 156 differentially expressed miRNAs (DEMs) and 7717 differentially expressed miRNAs (DEGs) between mock-infected and DHAV-3-infected duckling livers. A total of 19,606 miRNA-mRNA pairs with negatively correlated expression patterns were identified in miRNA-mRNA networks constructed on the basis of these DEMs and DEGs. Moreover, immune-related pathways including the cytokine-cytokine receptor interaction, apoptosis, Toll-like receptor, Jak-STAT, and RIG-I-like receptor signaling pathway were significantly enriched through analyzing functions of mRNAs in the network in response to DHAV-3 infection. Besides, apl-miR-32-5p, apl-miR-125-5p, apl-miR-128-3p, apl-miR-460-5p, and novel-m0012-3p were identified as potential regulators in the immune-related signaling pathways during the DHAV-3 infection. Conclusions: To our knowledge, this is the first report on integrated analysis of miRNA-seq and mRNA-seq in DHAV-3-infected ducklings. The results indicated the important roles of miRNAs in regulating immune response genes and revealed the immune related miRNA-mRNA regulation network in the DHAV-3-infected duckling liver. Our findings may provide valuable information to further investigate the roles of miRNAs and their target genes in DHAV-3 replication and pathogenesis; additionally, they may offer clues for further understanding host-virus interactions.

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