scholarly journals Tr-milRNA1 Contributes to Lignocellulase Secretion under Heat Stress by Regulating the Lectin-Type Cargo Receptor Gene Trvip36 in Trichoderma guizhouence NJAU 4742

2021 ◽  
Vol 7 (12) ◽  
pp. 997
Author(s):  
Tuo Li ◽  
Jinding Liu ◽  
Qin Wang ◽  
Yang Liu ◽  
Ting Li ◽  
...  
Keyword(s):  
Heat Stress ◽  
Target Gene ◽  
Target Genes ◽  
Bioinformatics Analysis ◽  
Receptor Gene ◽  
Biological Processes ◽  
Overexpression Strain ◽  
Cargo Receptor ◽  
Lignocellulose Utilization ◽  
Lignocellulase Secretion

Background: MicroRNA plays an important role in multifarious biological processes by regulating their corresponding target genes. However, the biological function and regulatory mechanism of fungal microRNA-like RNAs (milRNAs) remain poorly understood. Methods: In this study, combined with deep sequencing and bioinformatics analysis, milRNAs and their targets from Trichoderma guizhouence NJAU 4742 were isolated and identified under solid-state fermentation (SSF) by using rice straw as the sole carbon source at 28 °C and 37 °C, respectively. Results: A critical milRNA, TGA1_S04_31828 (Tr-milRNA1), was highly expressed under heat stress (37 °C) and adaptively regulated lignocellulase secretion. Overexpression of Tr-milRNA1 (OE-Tr-milRNA1) did not affect vegetative growth, but significantly increased lignocellulose utilization under heat stress. Based on the bioinformatics analysis and qPCR validation, a target of Tr-milRNA1 was identified as Trvip36, a lectin-type cargo receptor. The expression of Tr-milRNA1 and Trvip36 showed a divergent trend under SSF when the temperature was increased from 28 °C to 37 °C. In addition, the expression of Trvip36 was suppressed significantly in Tr-milRNA1 overexpression strain (OE-Tr-milRNA1). Compared with the wild type, deletion of Trvip36 (ΔTrvip36) significantly improved the secretion of lignocellulases by reducing the retention of lignocellulases in the ER under heat stress. Conclusions: Tr-milRNA1 from NJAU 4742 improved lignocellulose utilization under heat stress by regulating the expression of the corresponding target gene Trvip36. These findings might open avenues for exploring the mechanism of lignocellulase secretion in filamentous fungi.

M6A2Target: a comprehensive database for targets of m6A writers, erasers and readers

2020 ◽  
Author(s):  
Shuang Deng ◽  
Hongwan Zhang ◽  
Kaiyu Zhu ◽  
Xingyang Li ◽  
Ying Ye ◽  
...  
Keyword(s):  
High Throughput ◽  
Target Gene ◽  
Target Genes ◽  
Biological Processes ◽  
Public Repository ◽  
Reversible Process ◽  
Comprehensive Database ◽  
Dynamic Modification ◽  
Gene Database ◽  
User Friendly

Abstract N6-methyladenosine (m6A) is the most abundant posttranscriptional modification in mammalian mRNA molecules and has a crucial function in the regulation of many fundamental biological processes. The m6A modification is a dynamic and reversible process regulated by a series of writers, erasers and readers (WERs). Different WERs might have different functions, and even the same WER might function differently in different conditions, which are mostly due to different downstream genes being targeted by the WERs. Therefore, identification of the targets of WERs is particularly important for elucidating this dynamic modification. However, there is still no public repository to host the known targets of WERs. Therefore, we developed the m6A WER target gene database (m6A2Target) to provide a comprehensive resource of the targets of m6A WERs. M6A2Target provides a user-friendly interface to present WER targets in two different modules: ‘Validated Targets’, referred to as WER targets identified from low-throughput studies, and ‘Potential Targets’, including WER targets analyzed from high-throughput studies. Compared to other existing m6A-associated databases, m6A2Target is the first specific resource for m6A WER target genes. M6A2Target is freely accessible at http://m6a2target.canceromics.org.

scholarly journals Exploring Heat-Response Mechanisms of MicroRNAs Based on Microarray Data of Rice Post-meiosis Panicle

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Yan Peng ◽  
Xianwen Zhang ◽  
Yuewu Liu ◽  
Xinbo Chen
Keyword(s):  
Heat Stress ◽  
Target Genes ◽  
Expression Profiles ◽  
Time Lag ◽  
Interaction Network ◽  
Biological Processes ◽  
Functional Identification ◽  
Protein Protein Interaction ◽  
Heat Response ◽  
Protein Protein Interaction Network

To explore heat response mechanisms of mircoRNAs (miRNAs) in rice post-meiosis panicle, microarray analysis was performed on RNA isolated from rice post-meiosis panicles which were treated at 40°C for 0 min, 10 min, 20 min, 60 min, and 2 h. By integrating paired differentially expressed (DE) miRNAs and mRNA expression profiles, we found that the expression levels of 29 DE-miRNA families were negatively correlated to their 178 DE-target genes. Further analysis showed that the majority of miRNAs in 29 DE-miRNA families resisted the heat stress by downregulating their target genes and a time lag existed between expression of miRNAs and their target genes. Then, GO-Slim classification and functional identification of these 178 target genes showed that (1) miRNAs were mainly involved in a series of basic biological processes even under heat conditions; (2) some miRNAs might play important roles in the heat resistance (such as osa-miR164, osa-miR166, osa-miR169, osa-miR319, osa-miR390, osa-miR395, and osa-miR399); (3) osa-miR172 might play important roles in protecting the rice panicle under the heat stress, but osa-miR437, osa-miR418, osa-miR164, miR156, and miR529 might negatively affect rice fertility and panicle flower; and (4) osa-miR414 might inhibit the flowering gene expression by downregulation of LOC_Os 05g51830 to delay the heading of rice. Finally, a heat-induced miRNA-PPI (protein-protein interaction) network was constructed, and three miRNA coregulatory modules were discovered.

scholarly journals MicroRNA-381 Negatively Regulates TLR4 Signaling in A549 Cells in Response to LPS Stimulation

2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
Zhihao Xu ◽  
Dapeng Dong ◽  
Xiaofei Chen ◽  
Huaqiong Huang ◽  
Shenglan Wen
Keyword(s):  
Target Gene ◽  
Target Genes ◽  
Bioinformatics Analysis ◽  
Respiratory Infections ◽  
A549 Cells ◽  
Luciferase Reporter ◽  
Reporter Assay ◽  
Elisa Kit ◽  
Cox 2

It is widely reported that miR-381 is dysregulated in various tumors. However, the specific role of miR-381 in respiratory infections has not been reported. To probe this role, A549 cells were pretreated with 1 μg/mL LPS for 24 h. The level of miR-381 was detected using RT-qPCR. The expression of proinflammatory cytokines was determined using an ELISA kit and western blotting. Bioinformatics analysis was used to predict the target genes of miR-381, and a luciferase reporter assay was used to validate the expression of the target genes. miR-381 expression was increased in A549 cells treated with LPS, which is a ligand of TLRs. Further study revealed that the overexpression of miR-381 increased the activity of NF-κB signaling, thereby increasing the expression of IL-6, TNFα, and COX-2. Further study revealed that IκBα was a target gene of miR-381. The upregulation of miR-381 under LPS stimulation contributes to respiratory infections mainly by targeting IκBα.

scholarly journals Identification of miRNA and Their Regulatory Effects Induced by Total Flavonoids From Dracocephalum moldavica in the Treatment of Vascular Dementia

2021 ◽  
Vol 12 ◽  
Author(s):  
Mimin Liu ◽  
Guangzhi Shan ◽  
Hailun Jiang ◽  
Li Zeng ◽  
Kaiyue Zhao ◽  
...  
Keyword(s):  
Vascular Dementia ◽  
Target Gene ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Bioinformatics Analysis ◽  
Gene Profiling ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Total Flavonoids ◽  
Compound Target

Vascular dementia (VaD) is a general term used to describe difficulties in memory, reasoning, judgment, and planning caused by a reduced blood flow to the brain and consequent brain damage, in which microRNAs (miRNAs) are involved. Dracocephalum moldavica L. (D. moldavica) is traditionally used in the treatment of cardiovascular diseases as well as VaD, but the biomolecular mechanisms underlying its therapeutic effect are obscure. In the present study, the molecular mechanisms involved in the treatment of VaD by the total flavonoids from Dracocephalum moldavica L. (TFDM) were explored by the identification of miRNA profiling using bioinformatics analysis and experimental verification. A total of 2,562 differentially expressed miRNAs (DEMs) and 3,522 differentially expressed genes (DEGs) were obtained from the GSE120584 and GSE122063 datasets, in which the gene functional enrichment and protein-protein interaction network of 93 core targets, originated from the intersection of the top DEM target genes and DEGs, were established for VaD gene profiling. One hundred and eighty-five targets interacting with 42 flavonoids in the TFDM were included in a compound-target network, subsequently found that they overlapped with potential targets for VaD. These 43 targets could be considered in the treatment of VaD by TFDM, and included CaMKII, MAPK, MAPT, PI3K, and KDR, closely associated with the vascular protective effect of TFDM, as well as anti-oxidative, anti-inflammatory, and anti-apoptotic properties. The subsequent analysis of the compound-target gene-miRNA network indicated that eight miRNAs that mediated 43 targets had a close interaction with TFDM, suggesting that the neuroprotective effects were principally due to kaempferol, apigenin, luteolin, and quercetin, which were mostly associated with the miR-3184-3p/ESR1, miR-6762-3p/CDK1, miR-6777-3p/ESRRA, and other related axes. Furthermore, the in vitro oxygen-glucose deprivation (OGD) model demonstrated that the dysregulation of miR-3184-3p and miR-6875-5p found by qRT-PCR was consistent with the changes in the bioinformatics analysis. TFDM and its active compounds involving tilianin, luteolin, and apigenin showed significant effects on the upregulation of miR-3184-3p and downregulation of miR-6875-5p in OGD-injured cells, in line with the improved cell viability. In conclusion, our findings revealed the underlying miRNA-target gene network and potential targets of TFDM in the treatment of VaD.

scholarly journals Analysis of Long Noncoding RNA and mRNA Expression Profiles of Testes with High and Low Sperm Motility in Domestic Pigeons (Columba livia)

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 349
Author(s):  
Xiuli Xu ◽  
Yuge Tan ◽  
Haiguang Mao ◽  
Honghua Liu ◽  
Xinyang Dong ◽  
...  
Keyword(s):  
Sperm Motility ◽  
Noncoding Rna ◽  
Target Gene ◽  
Target Genes ◽  
Semen Quality ◽  
Expression Profiles ◽  
Columba Livia ◽  
Ion Binding ◽  
Biological Processes ◽  
Domestic Pigeons

Sperm motility is one of the most important indicators in assessing semen quality, and it is used to evaluate poultry fertility. Many long noncoding RNAs (lncRNAs) and mRNAs are involved in regulating testis development and spermatogenesis. In this study, we employed RNA sequencing to analyse the testis transcriptome (lncRNA and mRNA) of ten pigeons with high and low sperm motility. In total, 46,117 mRNAs and 17,463 lncRNAs were identified, of which 2673 mRNAs and 229 lncRNAs (P < 0.05) were significantly differentially expressed (DE) between the high and low sperm motility groups. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analysis showed that target genes of DE lncRNAs and DE mRNAs were related to calcium ion binding, ATP binding, and spermatogenesis. Moreover, we found that UBB, a target gene of lncRNA MSTRG.7787.5, was involved in germ cell development. Our study provided a catalogue of lncRNAs and mRNAs associated with sperm motility, and they deserve further study to deepen the understanding of biological processes in the pigeon testis.

scholarly journals A novel miRNA-4484 is up-regulated on microarray and associated with increased MMP-21 expression in serum of systemic sclerosis patients

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Marta Rusek ◽  
Małgorzata Michalska-Jakubus ◽  
Małgorzata Kowal ◽  
Jerzy Bełtowski ◽  
Dorota Krasowska
Keyword(s):  
Systemic Sclerosis ◽  
Signaling Pathways ◽  
Target Gene ◽  
Target Genes ◽  
Bioinformatics Analysis ◽  
Chromosomal Location ◽  
Receptor Interaction ◽  
Control Group ◽  
Internal Organs ◽  
Novel Mirna

Abstract Systemic sclerosis (SSc) is a complex, heterogeneous connective tissue disease, characterized by fibrosis and ECM deposition in skin and internal organs, autoimmunity, and changes in the microvasculature. Profiling of circulating miRNAs in serum has been found to be changed in pathological states, creating new possibilities for molecular diagnostics as blood-based biomarkers. This study was designed to identify miRNAs that are differentially expressed in SSc and might be potentially contributing to the disease etiopathogenesis or be used for diagnostic purposes. Thus, we compared the expression pattern of multiple miRNAs in serum of 10 SSc patients to 6 healthy controls using microarray analysis, and RT-qPCR to confirm the obtained results. In addition, bioinformatics analysis was performed to explore miRNAs target genes and the signaling pathways that may be potentially involved in SSc pathogenesis. Our study shows a different expression of 15 miRNAs in SSc patients. We identified that miR-4484, located on chromosome 10q26.2, was an 18-fold up-regulated in SSc patients compared to a control group. Bioinformatics analysis of the miR-4484 target genes and the signaling pathways showed that it might be potentially involved in the TGF-β signaling pathway, ECM-receptor interaction, and metalloproteinases expression. Based on the chromosomal location, the most interesting target gene of miR-4484 may be MMP-21. We found that the expression of MMP-21 significantly increased in SSc patients compared to healthy subjects (P < 0.05). Our results suggest that miR-4484, and MMP-21 might be novel serum biomarkers that may correspond to pathological fibrosis in SSc, but it needs to be validated in further studies.

scholarly journals Long non-coding RNA LINC00488 facilitates thyroid cancer cell progression through miR-376a-3p/PON2

2021 ◽  
Vol 41 (3) ◽  
Author(s):  
Fuyuan Xie ◽  
Longgen Li ◽  
Yuting Luo ◽  
Rensheng Chen ◽  
Jinhong Mei
Keyword(s):  
Thyroid Cancer ◽  
Cancer Cell ◽  
Target Gene ◽  
Target Genes ◽  
Bioinformatics Analysis ◽  
Cell Counting ◽  
Luciferase Reporter ◽  
Migration And Invasion ◽  
Thyroid Cancer Cell ◽  
Gene Assay

Abstract Objective: Long non-coding RNAs (lncRNAs) recently have been identified as influential indicators in a variety of malignancies. The aim of the present study was to identify a functional lncRNA LINC00488 and its effects on thyroid cancer in the view of cell proliferation and apoptosis. Methods: In order to evaluate the effects of LINC00488 on the cellular process of thyroid cancer, we performed a series of in vitro experiments, including cell counting kit-8 (CCK-8) assay, EdU (5-ethynyl-2′-deoxyuridine) assay, flow cytometry, transwell chamber assay, Western blot and RT-qPCR. The target gene of LINC00488 was then identified by bioinformatics analysis (DIANA and TargetScan). Finally, a series of rescue experiments was conducted to validate the effect of LINC00488 and its target genes on proliferation, migration, invasion and apoptosis of thyroid cancer. Results: Our findings revealed that LINC00488 was highly expressed in thyroid cancer cell lines (BCPAP, BHP5-16, TPC-1 and CGTH-W3) and promoted the proliferation, migration and invasion, while inhibited the apoptosis of thyroid cancer cells (BCPAP and TPC-1). The results of bioinformatics analysis and dual luciferase reporter gene assay showed that LINC00488 could directly bind to miR-376a-3p and down-regulated the expression level of miR-376a-3p. In addition, Paraoxonase-2 (PON2) was a target gene of miR-376a-3p and negatively regulated by miR-376a-3p. Rescue experiment indicated that LINC00488 might enhance PON2 expression by sponging miR-376a-3p in thyroid cancer. Conclusion: Taken together, our study revealed that lncRNA LINC00488 acted as an oncogenic gene in the progression of thyroid cancer via regulating miR-376a-3p/PON2 axis, which indicated that LINC00488-miR-376a-3p-PON2 axis could serve as novel biomarkers or potential targets for the treatment of thyroid cancer.

scholarly journals Identification of Circulating miR-210 as a Promising Biomarker for Lung Adenocarcinoma

2019 ◽  
Author(s):  
Jinru Xue ◽  
Hua Xin ◽  
Erna Jia ◽  
Na Ren
Keyword(s):  
Early Detection ◽  
Early Diagnosis ◽  
Lung Adenocarcinoma ◽  
Target Genes ◽  
Bioinformatics Analysis ◽  
Meta Analysis ◽  
Biological Processes ◽  
Circulating Mirnas ◽  
Diagnostic Efficacy ◽  
Kegg Pathways

Abstract Background: Lung adenocarcinoma (LUAD), with an increasing morbidity and mortality globally, is the most common histological subtype of lung cancer (LC). Early diagnosis of LUAD can significantly prolong survival time. Multiple researches have revealed that circulating miRNAs might be used as promising biomarkers for early detection of LUAD Material and Methods: A meta-analysis was conducted to find circulating miRNAs for early diagnosis of LUAD and summarized their diagnostic values based on GEO database. Further, by bioinformatics analysis we predicted the target genes of circulating miRNAs owning statistically significant, and explored the molecular regulation mechanisms and biological processes of the target genes in the pathogenetic of LUAD. Results: overall, six datasets were eligible, information on original expression levels of circulating miR-21, miR-155, miR-210, miR-126, miR-486, miR-182, and miR-17 extracted independently by two reviewers. Finally, we found circulating miR-210 had good diagnostic efficacy for LUAD detection, the combined AUC value was 0.83. We then predicted 480 overlapped genes of miR-210 at least 5 of 11 databases. Bioinformatics analysis showed statistically significant GO analysis 38 items and KEGG pathways 21 items. Response to hypoxia may be the mainly involved biological process of miR-210 in LUAD. Nine hub genes (FBXO, FBXL, MGRN1, ATG7, CUL3, RAB, ADAMTS, SEMA, THBS2) were obtained by construct PPI network. Conclusions: our study implied that circulating miR-210 may be a promising noninvasive biomarker for early detection of LUAD, but further researches are needed to validate the promising results and to identify specific biological processes and target genes.

scholarly journals The Divergent Orphan Nuclear Receptor ODR-7 Regulates Olfactory Neuron Gene Expression via Multiple Mechanisms in Caenorhabditis elegans

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 1779-1791
Author(s):  
Marc E Colosimo ◽  
Susan Tran ◽  
Piali Sengupta
Keyword(s):  
Nuclear Receptors ◽  
Nuclear Receptor ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Receptor Gene ◽  
Biological Processes ◽  
Orphan Nuclear Receptor ◽  
Olfactory Neurons ◽  
C Elegans

Abstract Nuclear receptors regulate numerous critical biological processes. The C. elegans genome is predicted to encode ∼270 nuclear receptors of which &gt;250 are unique to nematodes. ODR-7 is the only member of this large divergent family whose functions have been defined genetically. ODR-7 is expressed in the AWA olfactory neurons and specifies AWA sensory identity by promoting the expression of AWA-specific signaling genes and repressing the expression of an AWC-specific olfactory receptor gene. To elucidate the molecular mechanisms of action of a divergent nuclear receptor, we have identified residues and domains required for different aspects of ODR-7 function in vivo. ODR-7 utilizes an unexpected diversity of mechanisms to regulate the expression of different sets of target genes. Moreover, these mechanisms are distinct in normal and heterologous cellular contexts. The odr-7 ortholog in the closely related nematode C. briggsae can fully substitute for all ODR-7-mediated functions, indicating conservation of function across 25–120 million years of divergence.

Cytoplasmic HYL1 modulates miRNA-mediated translational repression

2021 ◽  
Author(s):  
Xi Yang ◽  
Weiguo Dong ◽  
Wenqing Ren ◽  
Qiuxia Zhao ◽  
Feijie Wu ◽  
...  
Keyword(s):  
Target Gene ◽  
Target Genes ◽  
Mrna Translation ◽  
Gene Repression ◽  
Translational Repression ◽  
Mirna Biogenesis ◽  
Biological Processes ◽  
Core Component ◽  
Plant Gene Regulation ◽  
Insight Into

Abstract MicroRNAs (miRNAs) control various biological processes by repressing target mRNAs. In plants, miRNAs mediate target gene repression via both mRNA cleavage and translational repression. However, the mechanism underlying this translational repression is poorly understood. Here, we found that Arabidopsis thaliana HYPONASTIC LEAVES1 (HYL1), a core component of the miRNA processing machinery, regulates miRNA-mediated mRNA translation but not miRNA biogenesis when it localized in the cytoplasm. Cytoplasmic HYL1 localizes to the endoplasmic reticulum and associates with ARGONAUTE1 (AGO1) and ALTERED MERISTEM PROGRAM1 (AMP1). In the cytoplasm, HYL1 monitors the distribution of AGO1 onto polysomes, binds to the mRNAs of target genes, represses their translation, and partially rescues the phenotype of the hyl1 null mutant. This study uncovered another function of HYL1 and provides insight into the mechanism of plant gene regulation.

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