scholarly journals The Effect of Different Pollination on the Expression of Dangshan Su Pear MicroRNA

2017 ◽  
Vol 2017 ◽  
pp. 1-18 ◽  
Author(s):  
Xi Cheng ◽  
Chongchong Yan ◽  
Jinyun Zhang ◽  
Chenhui Ma ◽  
Shumei Li ◽  
...  
Keyword(s):  
High Throughput ◽  
Fruit Quality ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Cell Content ◽  
Qrt Pcr ◽  
Stone Cell ◽  
Negative Effect

The high-throughput sequencing of pear “Dangshan Su” × “Yali” (whose fruits lignin and stone cell content are high and quality is poor) and pear “Dangshan Su” × “Wonhwang” (whose fruits with low content of lignin and stone cell and the quality are better ) found that the expressions of these two miRNAs (pyr-1809 and pyr-novel-miR-144-3p) were significantly different; their corresponding target genes encode two kinds of laccase (Pbr018935.1 and Pbr003857.1). qRT-PCR results showed that these two enzymes are involved in the formation of lignin and stone cells and the existence of these two miRNAs has a negative effect on them. It was concluded that the effect of pollination on the development of stone cells may affect the synthesis of lignin, through the regulation of laccase controlled by miRNAs, and ultimately affect the formation of stone cell and fruit quality.

scholarly journals Identification of copper (Cu) stress-responsive grapevine microRNAs and their target genes by high-throughput sequencing

2019 ◽  
Vol 6 (1) ◽  
pp. 180735 ◽  
Author(s):  
Songtao Jiu ◽  
Xiangpeng Leng ◽  
Muhammad Salman Haider ◽  
Tianyu Dong ◽  
Le Guan ◽  
...  
Keyword(s):  
Plant Growth ◽  
High Throughput ◽  
Stress Responses ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Patterns ◽  
Qrt Pcr ◽  
Cu Stress ◽  
Gene Information

MicroRNAs (miRNAs) are a class of single-stranded non-coding small RNAs (sRNAs) that are 20–24 nucleotides (nt) in length. Extensive studies have indicated that miRNAs play important roles in plant growth, development and stress responses. With more copper (Cu) and copper containing compounds used as bactericides and fungicides in plants, Cu stress has become one of the serious environmental problems that affect plant growth and development. In order to uncover the hidden response mechanisms of Cu stress, two small RNA libraries were constructed from Cu-treated and water-treated (Control) leaves of ‘Summer Black’ grapevine. Following high-throughput sequencing and filtering, a total of 158 known and 98 putative novel miRNAs were identified in the two libraries. Among these, 100 known and 47 novel miRNAs were identified as differentially expressed under Cu stress. Subsequently, the expression patterns of nine Cu-responsive miRNAs were validated by quantitative real-time PCR (qRT-PCR). There existed some consistency in expression levels of Cu-responsive miRNAs between high throughput sequencing and qRT-PCR assays. The targets prediction of miRNAs indicates that miRNA may regulate some transcription factors, including AP2, SBP, NAC, MYB and ARF during Cu stress. The target genes for two known and two novel miRNAs showed specific cleavage sites at the 10th and/or 11th nucleotide from the 5′-end of the miRNA corresponding to their miRNA complementary sequences. The findings will lay the foundation for exploring the role of the regulation of miRNAs in response to Cu stress and provide valuable gene information for breeding some Cu-tolerant grapevine cultivars.

scholarly journals High-throughput sequencing analysis identified microRNAs associated with egg production in ducks ovaries

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8440
Author(s):  
Mohan Qiu ◽  
Zengrong Zhang ◽  
Xia Xiong ◽  
Huarui Du ◽  
Qingyun Li ◽  
...  
Keyword(s):  
High Throughput ◽  
Egg Production ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Patterns ◽  
Egg Laying ◽  
Sequencing Analysis ◽  
Pathway Network ◽  
Qrt Pcr ◽  
Meat Type

Background MicroRNAs (miRNAs) exist widely and are involved in multiple biological processes in ducks, whereas the regulatory mechanism of miRNAs in egg laying of ducks has remained unclear. This study aims to reveal key miRNAs involved in the regulation of egg production in duck ovaries. Methods High-throughput sequencing was performed on four egg-type duck ovaries and four egg-meat-type duck ovaries at the start of the egg-laying stage. Quantitative reverse transcription PCR (qRT-PCR) validation was performed on differentially expressed miRNAs (DE miRNAs). Gene network of DEmiRNA-mRNA-pathway was constructed by Cytoscape. Results A total of 251 know miRNAs and 1,972 novel miRNAs were obtained from whole clean reads. Among the known miRNAs, we identified 21 DEmiRNAs, including eight down-regulated and 13 up-regulated miRNAs in egg-type ducks compared with egg-meat-type ducks. Among the novel miRNAs, we identified 70 DEmiRNAs, including 58 down-regulated and 12 up-regulated in egg-type ducks compared with egg-meat-type ducks. The expression patterns of four miRNAs were verified by qRT-PCR. The DEmiRNAs were involved in the function of response to folic acid and the pathway of valine, leucine and isoleucine degradation. Specific target genes of DEmiRNAs enrichment was found in some egg-laying regulation pathways, such as dopaminergic synapse, ovarian steroidogenesis and oocyte meiosis. The DEmiRNA-mRNA-pathway network including three DEmiRNAs, nine mRNAs and 11 pathways. apl-miR-194-5p and apl-miR-215-5p may be potential key miRNAs in regulating egg laying. Conclusions This study provided miRNAs profiles in ducks about egg laying and establish a theoretical basis for subsequent selection or modification of duck phenotypes at the molecular level.

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

Genes ◽  
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.

scholarly journals Identification of MicroRNAs in Response to Different Day Lengths in Soybean Using High-Throughput Sequencing and qRT-PCR

PLoS ONE ◽  
2015 ◽  
Vol 10 (7) ◽  
pp. e0132621 ◽  
Author(s):  
Wenbin Li ◽  
Pengpeng Wang ◽  
Yongguang Li ◽  
Kexin Zhang ◽  
Fuquan Ding ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Qrt Pcr

scholarly journals Analysis of the Differential Exosomal miRNAs of DC2.4 Dendritic Cells Induced by Toxoplasma gondii Infection

2019 ◽  
Vol 20 (21) ◽  
pp. 5506
Author(s):  
Dong-Liang Li ◽  
Wei-Hao Zou ◽  
Sheng-Qun Deng ◽  
Hong-Juan Peng
Keyword(s):  
Dendritic Cells ◽  
Toxoplasma Gondii ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Quantitative Polymerase Chain Reaction ◽  
Biologically Active ◽  
Transferase Activity ◽  
Bioinformatics Analyses ◽  
Exosomal Mirnas

Toxoplasma gondii is an intracellular parasite that infects humans and other warm-blooded animals. Exosomes are endocytic-derived vesicles released by cells, representing an important mode of intercellular communication. In exosomes, specific molecules of proteins, lipids, and mRNAs or miRNAs have been detected, some of which are capable of transferring biologically active molecules to recipient cells. Dendritic cells (DCs) are the only antigen-presenting cells (APCs) that activate the initial immune response. In this study, high-throughput sequencing was used to analyze the exosomal miRNA profile of DC2.4 cells infected with Toxoplasma gondii for 28 h, compared with those of uninfected DC2.4 cells. Differential exosomal miRNAs (DEmiRs) from these two cell groups were analyzed. Through high-throughput sequencing, 3434 DEmiRs were obtained, and 12 stably enriched DEmiRNAs were verified by Reverse Transcription-quantitative Polymerase Chain Reaction (RT-qPCR) and selected for further analysis. The target genes of these 12 miRNAs were predicted with online analysis software and subjected to bioinformatics analyses including protein–protein interaction (PPI) network analysis, key driver analysis (KDA), gene ontology (GO) enrichment, and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis. These DEmiRs were found to be associated with a variety of biological processes and signaling pathways involved in host ubiquitin system, innate immunity, biosynthesis, and transferase activity and could be potential biomarkers for T. gondii infection.

Sign in / Sign up

Export Citation Format

Share Document