scholarly journals Discovery of MicroRNAs and Their Target Genes Related to Drought in Paulownia “Yuza 1” by High-Throughput Sequencing

2017 ◽  
Vol 2017 ◽  
pp. 1-11 ◽  
Author(s):  
Minjie Deng ◽  
Yabing Cao ◽  
Zhenli Zhao ◽  
Lu Yang ◽  
Yanfang Zhang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Plant Hormone ◽  
Target Genes ◽  
Reference Data ◽  
Relevant Information ◽  
Putative Target

Understanding the role of miRNAs in regulating the molecular mechanisms responsive to drought stress was studied in Paulownia “yuza 1.” Two small RNA libraries and two degradome libraries were, respectively, constructed and sequenced in order to detect miRNAs and their target genes associated with drought stress. A total of 107 miRNAs and 42 putative target genes were identified in this study. Among them, 77 miRNAs were differentially expressed between drought-treated Paulownia “yuza 1” and the control (60 downregulated and 17 upregulated). The predicted target genes were annotated using the GO, KEGG, and Nr databases. According to the functional classification of the target genes, Paulownia “yuza 1” may respond to drought stress via plant hormone signal transduction, photosynthesis, and osmotic adjustment. Furthermore, the expression levels of seven miRNAs (ptf-miR157b, ptf-miR159b, ptf-miR398a, ptf-miR9726a, ptf-M2153, ptf-M2218, and ptf-M24a) and their corresponding target genes were validated by quantitative real-time PCR. The results provide relevant information for understanding the molecular mechanism of Paulownia resistance to drought and reference data for researching drought resistance of other trees.

scholarly journals Identification of Drought-Responsive microRNAs from Roots and Leaves of Alfalfa by High-Throughput Sequencing

2017 ◽  
Author(s):  
Yue Li ◽  
Liqiang Wan ◽  
Shuyi Bi ◽  
Xiufu Wan ◽  
Zhenyi Li ◽  
...  
Keyword(s):  
Drought Stress ◽  
High Throughput ◽  
Stress Responses ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Plant Stress ◽  
Online Tool ◽  
Bioenergy Plant ◽  
Plant Stress Responses

Alfalfa, an important legume forage, is an ideal crop for sustainable agriculture and a potential bioenergy plant. Drought, one of the most common environmental stresses, substantially affects plants’ growth, development and productivity. MicroRNAs (miRNAs) are newly discovered gene expression regulators that have been linked to several plant stress responses. To elucidate the role of miRNAs in drought stress regulation of alfalfa, a high-throughput sequencing approach was used to analyze 12 small RNA libraries comprising of 4 samples, each with 3 biological replicates. We identified 348 known miRNAs, belonging to 80 miRNA families, from the 12 libraries and 281 novel miRNAs using Mireap software. 18 known miRNAs in roots and 12 known miRNAs in leaves were screened out as drought-responsive miRNAs. Except for miR319d and miR157a which were upregulated under drought stress, the expression pattern of drought-responsive miRNAs were different between roots and leaves in alfalfa. This is the first study discovering miR157a, miR1507, miR3512, miR3630, miR5213, miR5294, miR5368 and miR6173 are drought-responsive miRNAs. Target transcripts of drought-responsive miRNAs were computationally predicted. All 447 target genes for the known miRNAs were predicted using an online tool. This study provides a significant insight on understanding drought-responsive mechanisms of alfalfa.

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.

scholarly journals The role of m6A modification in the biological functions and diseases

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Xiulin Jiang ◽  
Baiyang Liu ◽  
Zhi Nie ◽  
Lincan Duan ◽  
Qiuxia Xiong ◽  
...  
Keyword(s):  
Cancer Progression ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Rna Modification ◽  
Biological Functions ◽  
Rna Methylation ◽  
Downstream Target ◽  
Different Types ◽  
M6a Rna Methylation

AbstractN6-methyladenosine (m6A) is the most prevalent, abundant and conserved internal cotranscriptional modification in eukaryotic RNAs, especially within higher eukaryotic cells. m6A modification is modified by the m6A methyltransferases, or writers, such as METTL3/14/16, RBM15/15B, ZC3H3, VIRMA, CBLL1, WTAP, and KIAA1429, and, removed by the demethylases, or erasers, including FTO and ALKBH5. It is recognized by m6A-binding proteins YTHDF1/2/3, YTHDC1/2 IGF2BP1/2/3 and HNRNPA2B1, also known as “readers”. Recent studies have shown that m6A RNA modification plays essential role in both physiological and pathological conditions, especially in the initiation and progression of different types of human cancers. In this review, we discuss how m6A RNA methylation influences both the physiological and pathological progressions of hematopoietic, central nervous and reproductive systems. We will mainly focus on recent progress in identifying the biological functions and the underlying molecular mechanisms of m6A RNA methylation, its regulators and downstream target genes, during cancer progression in above systems. We propose that m6A RNA methylation process offer potential targets for cancer therapy in the future.

scholarly journals Genome-wide miRNA analysis and integrated network for flavonoid biosynthesis in Osmanthus fragrans

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yong Shi ◽  
Heng Xia ◽  
Xiaoting Cheng ◽  
Libin Zhang
Keyword(s):  
Secondary Metabolites ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Flavonoid Biosynthesis ◽  
Integrated Network ◽  
Osmanthus Fragrans ◽  
Flavonoid Synthesis ◽  
Genome Wide

AbstractBackgroundOsmanthus fragransis an important economical plant containing multiple secondary metabolites including flavonoids and anthocyanins. During the past years, the roles of miRNAs in regulating the biosynthesis of secondary metabolites in plants have been widely investigated. However, few studies on miRNA expression profiles and the potential roles in regulating flavonoid biosynthesis have been reported inO. fragrans.ResultsIn this study, we used high-throughput sequencing technology to analyze the expression profiles of miRNAs in leaf and flower tissues ofO. fragrans. As a result, 106 conserved miRNAs distributed in 47 families and 88 novel miRNAs were identified. Further analysis showed there were 133 miRNAs differentially expressed in leaves and flowers. Additionally, the potential target genes of miRNAs as well as the related metabolic pathways were predicted. In the end, flavonoid content was measured in flower and leaf tissues and potential role of miR858 in regulating flavonoid synthesis was illustrated inO. fragrans.ConclusionsThis study not only provided the genome-wide miRNA profiles in the flower and leaf tissue ofO. fragrans, but also investigated the potential regulatory role of miR858a in flavonoid synthesis inO. fragrans. The results specifically indicated the connection of miRNAs to the regulation of secondary metabolite biosynthesis in non-model economical plant.

Abstract W MP86: Microrna-146a Modulates Neurogenesis And Oligodendrogenesis After Stroke

Stroke ◽  
2015 ◽  
Vol 46 (suppl_1) ◽  
Author(s):  
Xianshuang Liu ◽  
Chopp Michael ◽  
Xinli Wang ◽  
Li Zhang ◽  
Yisheng Cui ◽  
...  
Keyword(s):  
Progenitor Cells ◽  
Molecular Mechanisms ◽  
Neural Progenitor Cells ◽  
Target Genes ◽  
Artery Occlusion ◽  
Locked Nucleic Acid ◽  
Myelin Proteins ◽  
Oligodendrocyte Progenitor Cells ◽  
Marker Proteins

Background: Neurogenesis and oligodendrogenesis are associated with functional recovery after stroke. However, the molecules that regulate the generation of new neurons and oligodendrocytes have not been fully investigated. MicroRNAs (miRNAs) post-transcriptionally regulate gene expression. MiR-146a has been reported to regulate the immune response in cells, but the role of miR-146a in neural (NPCs) and oligodendrocyte progenitor cells (OPCs) remains unexplored. Methods and Results: Adult Wistar rats were subjected to right middle cerebral artery occlusion (MCAo). In situ hybridization using locked nucleic acid (LNA)probes against miR-146a showed that stroke considerably increased miR-146a density in the subventricular zone (SVZ, 19 ± 1 vs 6 ± 0.1 area/mm2 in non-MCAo group, p<0.05, n=4/group) and corpus callosum (24 ± 3 vs 8±1 area/mm2 in non-MCAo group) of the ischemic hemisphere. Quantitative RT-PCR also demonstrated a marked upregulation of miR-146a transcript in ischemic NPCs (8.5 fold), suggesting an important role in stroke-induced neurogenesis and oligodendrogenesis. To test its biological function, we over-expressed miR-146a in neural progenitor cells by transfection of miR-146a mimics using nucleofector and found that elevation of miR-146a significantly increased the percentage of Tuj1+ neuroblasts (5 ± 0.3 vs 1 ± 0.2%, p<0.05, n=6/group) and O4+ OPCs (10 ± 1 vs 4 ± 0.4%, p<0.05). Moreover, over-expression of miR-146a in primary cultured OPCs significantly increased several myelin proteins including MBP and PLP, and decreased levels of OPC marker proteins including PDGFRα and NG2, whereas attenuation of miR-146a by siRNA against miR-146a suppressed myelin proteins and augmented OPC marker proteins. Furthermore, miR-146a levels in the OPCs were inversely related to IRAK1 proteins, one of miR-146a target genes. Attenuation of IRAK1 in OPCs substantially increased myelin proteins, indicating that miR-146a mediates oligodendrocyte maturation via targeting IRAK1. Conclusion: Our data provide new insight into molecular mechanisms underlying stroke-induced neurogenesis and oligodendrogenesis by revealing a novel role of miR-146a in NPCs and OPCs, which has potential to be used as a new therapy for neurorecovery after stroke.

scholarly journals Transcriptome Analysis of Watermelon Leaves Reveals Candidate Genes Responsive to Cucumber green mottle mosaic virus Infection

2019 ◽  
Vol 20 (3) ◽  
pp. 610 ◽  
Author(s):  
Yuyan Sun ◽  
Min Fan ◽  
Yanjun He
Keyword(s):  
Mosaic Virus ◽  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Plant Hormone ◽  
Pcr Analysis ◽  
Whole Plant ◽  
Plant Pathogen Interactions ◽  
Differently Expressed Genes

Cucumber green mottle mosaic virus (CGMMV) is a member of the genus Tobamovirus, which cause diseases in cucurbits, especially watermelon. In watermelon, symptoms develop on the whole plant, including leaves, stems, peduncles, and fruit. To better understand the molecular mechanisms of watermelon early responses to CGMMV infection, a comparative transcriptome analysis of 24 h CGMMV-infected and mock-inoculated watermelon leaves was performed. A total of 1641 differently expressed genes (DEGs) were identified, with 886 DEGs upregulated and 755 DEGs downregulated after CGMMV infection. A functional analysis indicated that the DEGs were involved in photosynthesis, plant–pathogen interactions, secondary metabolism, and plant hormone signal transduction. In addition, a few transcription factor families, including WRKY, MYB, HLH, bZIP and NAC, were responsive to the CGMMV-induced stress. To confirm the high-throughput sequencing results, 15 DEGs were validated by qRT-PCR analysis. The results provide insights into the identification of candidate genes or pathways involved in the responses of watermelon leaves to CGMMV infection.

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 STAT3 and STAT5 Activation in Solid Cancers

Cancers ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 1428 ◽  
Author(s):  
Sebastian Igelmann ◽  
Heidi Neubauer ◽  
Gerardo Ferbeyre
Keyword(s):  
Tumor Suppressor ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Critical Role ◽  
Control Cell ◽  
Cytokine Signaling ◽  
Specific Gene ◽  
Mitochondrial Functions ◽  
Context Dependent

The Signal Transducer and Activator of Transcription (STAT)3 and 5 proteins are activated by many cytokine receptors to regulate specific gene expression and mitochondrial functions. Their role in cancer is largely context-dependent as they can both act as oncogenes and tumor suppressors. We review here the role of STAT3/5 activation in solid cancers and summarize their association with survival in cancer patients. The molecular mechanisms that underpin the oncogenic activity of STAT3/5 signaling include the regulation of genes that control cell cycle and cell death. However, recent advances also highlight the critical role of STAT3/5 target genes mediating inflammation and stemness. In addition, STAT3 mitochondrial functions are required for transformation. On the other hand, several tumor suppressor pathways act on or are activated by STAT3/5 signaling, including tyrosine phosphatases, the sumo ligase Protein Inhibitor of Activated STAT3 (PIAS3), the E3 ubiquitin ligase TATA Element Modulatory Factor/Androgen Receptor-Coactivator of 160 kDa (TMF/ARA160), the miRNAs miR-124 and miR-1181, the Protein of alternative reading frame 19 (p19ARF)/p53 pathway and the Suppressor of Cytokine Signaling 1 and 3 (SOCS1/3) proteins. Cancer mutations and epigenetic alterations may alter the balance between pro-oncogenic and tumor suppressor activities associated with STAT3/5 signaling, explaining their context-dependent association with tumor progression both in human cancers and animal models.

scholarly journals Functional Analysis of Three miRNAs in Agropyron mongolicum Keng under Drought Stress

Agronomy ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 661 ◽  
Author(s):  
Xuting Zhang ◽  
Bobo Fan ◽  
Zhuo Yu ◽  
Lizhen Nie ◽  
Yan Zhao ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Northern China ◽  
Bioinformatic Analysis ◽  
Pcr Analysis ◽  
Rna Molecules ◽  
Natural Pasture ◽  
Non Coding Rna

Agropyron mongolicum Keng, a perennial diploid grass with high drought tolerance, belongs to the genus Agropyron, tribe Triticeae. It has made tremendous contributions toward reseeding natural pasture and seeding artificial grassland in China, especially in the arid and semi-arid area of northern China. As a wild relative of wheat, A. mongolicum is also a valuable resource for the genetic improvement of wheat crops. MicroRNAs are small non-coding RNA molecules ubiquitous in plants, which have been involved in responses to a wide variety of stresses including drought, salinity, chilling temperature. To date, little research has been done on drought-responsive miRNAs in A. mongolicum. In this study, two miRNA libraries of A. mongolicum under drought and normal conditions were constructed, and drought-responsive miRNAs were screened via Solexa high throughput sequencing and bioinformatic analysis. A total of 114 new miRNAs were identified in A. mongolicum including 53 conservative and 61 unconservative miRNAs, and 1393 target genes of 98 miRNAs were predicted. Seventeen miRNAs were found to be differentially expressed under drought stress, seven (amo-miR21, amo-miR62, amo-miR82, amo-miR5, amo-miR77, amo-miR44 and amo-miR17) of which were predicted to target on genes involved in drought tolerance. QRT-PCR analysis confirmed the expression changes of the seven drought related miRNAs in A. mongolicum. We then transformed the seven miRNAs into Arabidopsis thaliana plants, and three of them (amo-miR21, amo-miR5 and amo-miR62) were genetically stable. The three miRNAs demonstrated the same expression pattern in A. thaliana as that in A. mongolicum under drought stress. Findings from this study will better our understanding of the molecular mechanism of miRNAs in drought tolerance and promote molecular breeding of forage grass with improved adaption to drought.

scholarly journals Dietary Melatonin Supplementation Could Be a Promising Preventing/Therapeutic Approach for a Variety of Liver Diseases

Nutrients ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 1135 ◽  
Author(s):  
Francesca Bonomini ◽  
Elisa Borsani ◽  
Gaia Favero ◽  
Luigi Rodella ◽  
Rita Rezzani
Keyword(s):  
Liver Diseases ◽  
Molecular Mechanisms ◽  
Antioxidant Properties ◽  
Therapeutic Strategies ◽  
Beneficial Effects ◽  
Pathological Conditions ◽  
Positive Effect ◽  
And Oxidative Stress

In the therapeutic strategies, the role of diet is a well-established factor that can also have an important role in liver diseases. Melatonin, identified in animals, has many antioxidant properties and it was after discovered also in plants, named phytomelatonin. These substances have a positive effect during aging and in pathological conditions too. In particular, it is important to underline that the amount of melatonin produced by pineal gland in human decreases during lifetime and its reduction in blood could be related to pathological conditions in which mitochondria and oxidative stress play a pivotal role. Moreover, it has been indicated that melatonin/phytomelatonin containing foods may provide dietary melatonin, so their ingestion through balanced diets could be sufficient to confer health benefits. In this review, the classification of liver diseases and an overview of the most important aspects of melatonin/phytomelatonin, concerning the differences among their synthesis, their presence in foods and their role in health and diseases, are summarized. The findings suggest that melatonin/phytomelatonin supplementation with diet should be considered important in preventing different disease settings, in particular in liver. Currently, more studies are needed to strengthen the potential beneficial effects of melatonin/phytomelatonin in liver diseases and to better clarify the molecular mechanisms of action.

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