Expression Profile Analysis and Target Gene Prediction of Three Conserved MicroRNAs in Resistant Gossypium hirsutum Cv. KV-1 Responding to Verticillium dahliae

2014 ◽  
Vol 884-885 ◽  
pp. 441-445
Author(s):  
Xiao Hong He ◽  
Min Shi ◽  
Quan Sun ◽  
Ying Fan Cai
Keyword(s):  
Verticillium Wilt ◽  
Deep Sequencing ◽  
Verticillium Dahliae ◽  
Upland Cotton ◽  
Target Genes ◽  
Gene Prediction ◽  
Interaction Mechanism ◽  
Sequencing Data ◽  
Qrt Pcr ◽  
Two Samples

Plant microRNAs (miRNAs) play important roles in the post-transcriptional regulation of plant growth, development, flowering, metabolism, and responses to stress. Verticillium wilt is a vascular disease in plants caused by the fungal pathogen Verticillium dahliae. In order to find and investigate miRNAs related to the upland cotton variety Zhongzhimian KV-1 resistant Verticillium wilt, deep sequencing technology was used to construct small RNA libraries of two samples, which from seedlings of KV-1 cotton by different pathogenicity strains Verticillium wilt pathogen infections. The V. dahliae strains D07038 and V991 were used in this study and are moderately virulent and virulent, respectively. miRNAs with differential expression among the samples were obtained through analysis of sequencing data and three miRNAs (miR1423a-5p, miR3444a-5p and miR5562) were chosen to be identified by quantitative real-time RT-PCR (qRT-PCR). At the same time, their target genes were predicted. The results of qRT-PCR were consistent, which indicated 3444a-5p and miR5562 were with the highest expression level in virulent condition, but miR1423a-5p was a low-level expression. The results of experiments agreed with deep sequencing data basically. Analysis of the transcript data for target genes of three conserved miRNAs indicated that they play an important role in plant-pathogen interaction mechanism. The identification and characterisation of miRNAs from upland cotton may help to further the study of miRNA regulatory mechanisms that are involved in resistance to Verticillium wilt.

scholarly journals GhKWL1 Upregulates GhERF105 but Its Function Is Impaired by Binding with VdISC1, a Pathogenic Effector of Verticillium dahliae

2021 ◽  
Vol 22 (14) ◽  
pp. 7328
Author(s):  
Yang Chen ◽  
Mi Zhang ◽  
Lei Wang ◽  
Xiaohan Yu ◽  
Xianbi Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transgenic Plants ◽  
Gossypium Hirsutum ◽  
Verticillium Wilt ◽  
Verticillium Dahliae ◽  
Defense Response ◽  
Upland Cotton ◽  
Effector Protein ◽  
Positive Regulator ◽  
Its Gene

Verticillium wilt, caused by Verticillium dahliae, is a devastating disease for many important crops, including cotton. Kiwellins (KWLs), a group of cysteine-rich proteins synthesized in many plants, have been shown to be involved in response to various phytopathogens. To evaluate genes for their function in resistance to Verticillium wilt, we investigated KWL homologs in cotton. Thirty-five KWL genes (GhKWLs) were identified from the genome of upland cotton (Gossypium hirsutum). Among them, GhKWL1 was shown to be localized in nucleus and cytosol, and its gene expression is induced by the infection of V. dahliae. We revealed that GhKWL1 was a positive regulator of GhERF105. Silencing of GhKWL1 resulted in a decrease, whereas overexpression led to an increase in resistance of transgenic plants to Verticillium wilt. Interestingly, through binding to GhKWL1, the pathogenic effector protein VdISC1 produced by V. dahliae could impair the defense response mediated by GhKWL1. Therefore, our study suggests there is a GhKWL1-mediated defense response in cotton, which can be hijacked by V. dahliae through the interaction of VdISC1 with GhKWL1.

scholarly journals Transcriptome Analysis of Responses to Dengue Virus 2 Infection in Aedes albopictus (Skuse) C6/36 Cells

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 343
Author(s):  
Manjin Li ◽  
Dan Xing ◽  
Duo Su ◽  
Di Wang ◽  
Heting Gao ◽  
...  
Keyword(s):  
Dengue Virus ◽  
Aedes Albopictus ◽  
Bioinformatics Analysis ◽  
Interaction Mechanism ◽  
Transcriptional Analysis ◽  
Functional Verification ◽  
Mosquito Vector ◽  
Rna Seq ◽  
Sequencing Data ◽  
Qrt Pcr

Dengue virus (DENV), a member of the Flavivirus genus of the Flaviviridae family, can cause dengue fever (DF) and more serious diseases and thus imposes a heavy burden worldwide. As the main vector of DENV, mosquitoes are a serious hazard. After infection, they induce a complex host–pathogen interaction mechanism. Our goal is to further study the interaction mechanism of viruses in homologous, sensitive, and repeatable C6/36 cell vectors. Transcriptome sequencing (RNA-Seq) technology was applied to the host transcript profiles of C6/36 cells infected with DENV2. Then, bioinformatics analysis was used to identify significant differentially expressed genes and the associated biological processes. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was performed to verify the sequencing data. A total of 1239 DEGs were found by transcriptional analysis of Aedes albopictus C6/36 cells that were infected and uninfected with dengue virus, among which 1133 were upregulated and 106 were downregulated. Further bioinformatics analysis showed that the upregulated DEGs were significantly enriched in signaling pathways such as the MAPK, Hippo, FoxO, Wnt, mTOR, and Notch; metabolic pathways and cellular physiological processes such as autophagy, endocytosis, and apoptosis. Downregulated DEGs were mainly enriched in DNA replication, pyrimidine metabolism, and repair pathways, including BER, NER, and MMR. The qRT-PCR results showed that the concordance between the RNA-Seq and RT-qPCR data was very high (92.3%). The results of this study provide more information about DENV2 infection of C6/36 cells at the transcriptome level, laying a foundation for further research on mosquito vector–virus interactions. These data provide candidate antiviral genes that can be used for further functional verification in the future.

scholarly journals Expression Profiles of tRNA-Derived Small RNAs and Their Potential Roles in Primary Nasopharyngeal Carcinoma

2021 ◽  
Vol 8 ◽  
Author(s):  
Zhaoyi Lu ◽  
Kai Su ◽  
Xiaomin Wang ◽  
Mingjie Zhang ◽  
Shiyin Ma ◽  
...  
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
Small Rnas ◽  
Target Genes ◽  
Expression Profiles ◽  
Target Prediction ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Diagnostic Efficiency ◽  
Sequencing Data ◽  
Qrt Pcr

Introduction: tRNA-derived small RNAs (tsRNAs), a class of small non-coding RNAs, are divided into two categories: tRNA-related fragments (tRFs) and tRNA halves (tiRNAs). Abnormal expression of tsRNAs has been found in diverse cancers, which indicates that further understanding of the function of tsRNAs will help identify new biomarkers and potential therapeutic targets. Until now, the underlying roles of tsRNAs in primary nasopharyngeal carcinoma (NPC) are still unknown.Methods: tRF and tiRNA sequencing was performed on four pairs of NPC tissues and healthy controls. Thirty pairs of NPC samples were used for quantitative real-time polymerase chain reaction (qRT-PCR) verification, and the ROC analysis was used to evaluate the diagnostic efficiency initially. Target prediction and bioinformatics analysis of validated tRFs and tiRNAs were conducted to explore the mechanisms of tsRNAs in NPC’s pathogenesis.Results: A total of 158 differentially expressed tRFs and tiRNAs were identified, of which 88 are upregulated and 70 are downregulated in NPC. Three validated tRFs in the results of qRT-PCR were consistent with the sequencing data: two upregulations (tRF-1:28-Val-CAC-2 and tRF-1:24-Ser-CGA-1-M3) and one downregulation (tRF-55:76-Arg-ACG-1-M2). The GO and KEGG pathway enrichment analysis showed that the potential target genes of validated tRFs are widely enriched in cancer pathways. The related modules may play an essential role in the pathogenesis of NPC.Conclusions: The tsRNAs may become a novel class of biological diagnostic indicators and possible targets for NPC.

scholarly journals Hsa-circ-0064636 regulation of the target gene VDAC1/UBE4A by hsa-miR-326/hsa-miR-503-5 in osteosarcoma

2021 ◽  
Author(s):  
Guohua Yan ◽  
Hanji Huang ◽  
Kanglu Li ◽  
Mingjun Zheng ◽  
Jiagang Qin ◽  
...  
Keyword(s):  
Cancer Progression ◽  
Target Gene ◽  
Target Genes ◽  
Gene Prediction ◽  
Critical Role ◽  
Regulation Of Gene Expression ◽  
Circular Rnas ◽  
Qrt Pcr ◽  
Eukaryotic Organisms

Abstract Background: Circular RNAs (circRNAs) are a subclass of noncoding RNAs that play a critical role in the regulation of gene expression in eukaryotic organisms. Recent studies have revealed the critical role of circRNAs in cancer progression. Yet, little is not well understood of hsa-circ-0064636 in osteosarcoma (OS).Methods: The differential expression of hsa-circ-0064636 in OS cell lines was verified by quantitative real-time PCR (qRT-PCR). Differentially expressed mRNAs and miRNAs were screened in OS mRNA and miRNA expression datasets. miRNAs that interacted with hsa-circ-0064636 were predicted by RNAhybrid, TargetScan and miRanda. and were further detected using RNAhybrid, TargetScan and miRanda. miRWalk, miRMap, and miRNAMap were used to perform target gene prediction on the intersected miRNAs to construct a circ-miRNA-mRNA interactor network. The target genes were then subjected to survival analysis using PROGgeneV2, which resulted in a circ-miRNA-mRNA interaction subnetwork with prognostic impact.Results: The qRT-PCR experiments successfully verified that hsa-circ-0064636 was significantly overexpressed in the OS cell line. Hsa-mir-326(miR-326) and hsa-mir-503-5p(miR-503-5p) are target miRNAs of hsa-circ-0064636 in the target genes obtained from the miR-326 and miR-503-5p screens. UBE4A and VDAC1 had a significant effect on prognosis. UBE4A is a target gene for miR-326, while VDAC1 is a target gene for miR-503-5p .Conclusion: hsa-circ-0064636 may be involved in OS development through acting as a sponge to inhibit miR-326 and miR-503-5p , thus regulating the expression of VDAC1 and UBE4A.

scholarly journals Antifungal activity of plant essential oils against Verticillium dahliae Klebahn, the causal agent of verticillium wilt of pepper

2019 ◽  
Vol 34 (1) ◽  
pp. 39-46
Author(s):  
Jelena Lukovic ◽  
Biljana Todorovic ◽  
Svetlana Milijasevic-Marcic ◽  
Emil Rekanovic ◽  
Miroslav Kostic ◽  
...  
Keyword(s):  
Essential Oils ◽  
Verticillium Wilt ◽  
Verticillium Dahliae ◽  
Harmful Effect ◽  
Causal Agent ◽  
Mentha Piperita ◽  
Black Pine ◽  
Plant Essential Oils ◽  
Two Samples

Biofungicides based on plant oils have some advantages compared to chemical fungicides, especially considering their harmful effect on the environment. Twenty-two essential oils from Germany and Albania were assayed for inhibitory and fungicidal activity against Verticillium dahliae Klebahn, the causal agent of Verticillium wilt of pepper, using the macrodilution fumigant method. The concentrations of oils obtained in the vapour phase were: 0.02, 0.04, 0.08, 0.16 and 0.32 ?l ml-1 with determined minimum inhibitory and fungicidal concentrations. The strongest activity was shown by two samples of mint oil (Mentha piperita L.) at 0.02 ?l ml-1 of air, both from Germany and Albania, followed by plant essential oils of eucalyptus (Eucalyptus globulus Labilardie), black pine (Pinus nigra L.) and cade (Juniperus oxycedrus L.), and all of them were lethal to the pathogen. Nine oils: two samples of mint, cade, eucalyptus, black pine, lavender (Lavandula angustifolia Mill.), sage (Salvia officinalis L.) and rosemary (Rosmarinus officinalis L.) inhibited the growth of Verticillium dahliae, while five oils (two samples of mint, eucalyptus, black pine and cade) showed fungicidal effects on the pathogen. These results showed that mint, eucalyptus, black pine and cade essential oils have a potential for further in vivo experiments against Verticillium dahliae.

scholarly journals Abnormal expression of rno_circRNA_014900 and rno_circRNA_005442 induced by ketamine in the rat hippocampus

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Jing Mao ◽  
Tianmei Li ◽  
Di Fan ◽  
Hongli Zhou ◽  
Jianguo Feng ◽  
...  
Keyword(s):  
Target Genes ◽  
Circular Rna ◽  
Fold Change ◽  
Rat Hippocampus ◽  
Antidepressant Effect ◽  
Signal Pathways ◽  
Qrt Pcr ◽  
Abnormal Expression ◽  
Reverse Transcription Pcr ◽  
Pathway Analyses

Abstract Background Recent studies have shown that circular RNA (circRNA) is rich in microRNA (miRNA) binding sites. We have previously demonstrated that the antidepressant effect of ketamine is related to the abnormal expression of various miRNAs in the brain. This study determined the expression profile of circRNAs in the hippocampus of rats treated with ketamine. Methods The aberrantly expressed circRNAs in rat hippocampus after ketamine injection were analyzed by microarray chip, and we further validated these circRNAs by quantitative reverse-transcription PCR (qRT-PCR). The target genes of the different circRNAs were predicted using bioinformatic analyses, and the functions and signal pathways of these target genes were investigated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Results Microarray analysis showed that five circRNAs were aberrantly expressed in rat hippocampus after ketamine injection (fold change > 2.0, p < 0.05). The results from the qRT-PCR showed that one of the circRNAs was significantly increased (rno_circRNA_014900; fold change = 2.37; p = 0.03), while one was significantly reduced (rno_circRNA_005442; fold change = 0.37; p = 0.01). We discovered a significant enrichment in several GO terms and pathways associated with depression. Conclusion Our findings showed the abnormal expression of ketamine-induced hippocampal circRNAs in rats.

scholarly journals Improvement, identification, and target prediction for miRNAs in the porcine genome by using massive, public high-throughput sequencing data

2021 ◽  
Vol 99 (2) ◽  
Author(s):  
Yuhua Fu ◽  
Pengyu Fan ◽  
Lu Wang ◽  
Ziqiang Shu ◽  
Shilin Zhu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Target Prediction ◽  
Large Data ◽  
Sequencing Data ◽  
Regulate Gene Expression ◽  
High Throughput Sequencing Data ◽  
Annotation Information ◽  
Public Data ◽  
Broad Variety

Abstract Despite the broad variety of available microRNA (miRNA) research tools and methods, their application to the identification, annotation, and target prediction of miRNAs in nonmodel organisms is still limited. In this study, we collected nearly all public sRNA-seq data to improve the annotation for known miRNAs and identify novel miRNAs that have not been annotated in pigs (Sus scrofa). We newly annotated 210 mature sequences in known miRNAs and found that 43 of the known miRNA precursors were problematic due to redundant/missing annotations or incorrect sequences. We also predicted 811 novel miRNAs with high confidence, which was twice the current number of known miRNAs for pigs in miRBase. In addition, we proposed a correlation-based strategy to predict target genes for miRNAs by using a large amount of sRNA-seq and RNA-seq data. We found that the correlation-based strategy provided additional evidence of expression compared with traditional target prediction methods. The correlation-based strategy also identified the regulatory pairs that were controlled by nonbinding sites with a particular pattern, which provided abundant complementarity for studying the mechanism of miRNAs that regulate gene expression. In summary, our study improved the annotation of known miRNAs, identified a large number of novel miRNAs, and predicted target genes for all pig miRNAs by using massive public data. This large data-based strategy is also applicable for other nonmodel organisms with incomplete annotation information.

scholarly journals miR-21-5p Regulates the Proliferation and Differentiation of Skeletal Muscle Satellite Cells by Targeting KLF3 in Chicken

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 814
Author(s):  
Donghao Zhang ◽  
Jinshan Ran ◽  
Jingjing Li ◽  
Chunlin Yu ◽  
Zhifu Cui ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Satellite Cells ◽  
Muscle Development ◽  
Target Genes ◽  
Cell Number ◽  
Sequencing Data ◽  
Proliferation Markers ◽  
Muscle Satellite Cells ◽  
Skeletal Muscle Satellite Cells ◽  
Proliferation And Differentiation

The proliferation and differentiation of skeletal muscle satellite cells (SMSCs) play an important role in the development of skeletal muscle. Our previous sequencing data showed that miR-21-5p is one of the most abundant miRNAs in chicken skeletal muscle. Therefore, in this study, the spatiotemporal expression of miR-21-5p and its effects on skeletal muscle development of chickens were explored using in vitro cultured SMSCs as a model. The results in this study showed that miR-21-5p was highly expressed in the skeletal muscle of chickens. The overexpression of miR-21-5p promoted the proliferation of SMSCs as evidenced by increased cell viability, increased cell number in the proliferative phase, and increased mRNA and protein expression of proliferation markers including PCNA, CDK2, and CCND1. Moreover, it was revealed that miR-21-5p promotes the formation of myotubes by modulating the expression of myogenic markers including MyoG, MyoD, and MyHC, whereas knockdown of miR-21-5p showed the opposite result. Gene prediction and dual fluorescence analysis confirmed that KLF3 was one of the direct target genes of miR-21-5p. We confirmed that, contrary to the function of miR-21-5p, KLF3 plays a negative role in the proliferation and differentiation of SMSCs. Si-KLF3 promotes cell number and proliferation activity, as well as the cell differentiation processes. Our results demonstrated that miR-21-5p promotes the proliferation and differentiation of SMSCs by targeting KLF3. Collectively, the results obtained in this study laid a foundation for exploring the mechanism through which miR-21-5p regulates SMSCs.

scholarly journals Dynamic characteristics and functional analysis provide new insights into long non-coding RNA responsive to Verticillium dahliae infection in Gossypium hirsutum

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Guoning Wang ◽  
Xingfen Wang ◽  
Yan Zhang ◽  
Jun Yang ◽  
Zhikun Li ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Verticillium Wilt ◽  
Dynamic Characteristics ◽  
Target Genes ◽  
Acid Metabolism ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Alpha Linolenic Acid ◽  
Non Coding Rna ◽  
Long Non Coding Rna

Abstract Background Verticillium wilt is a widespread and destructive disease, which causes serious loss of cotton yield and quality. Long non-coding RNA (lncRNA) is involved in many biological processes, such as plant disease resistance response, through a variety of regulatory mechanisms, but their possible roles in cotton against Verticillium dahliae infection remain largely unclear. Results Here, we measured the transcriptome of resistant G. hirsutum following infection by V. dahliae and 4277 differentially expressed lncRNAs (delncRNAs) were identified. Localization and abundance analysis revealed that delncRNAs were biased distribution on chromosomes. We explored the dynamic characteristics of disease resistance related lncRNAs in chromosome distribution, induced expression profiles, biological function, and these lncRNAs were divided into three categories according to their induced expression profiles. For the delncRNAs, 687 cis-acting pairs and 14,600 trans-acting pairs of lncRNA-mRNA were identified, which indicated that trans-acting was the main way of Verticillium wilt resistance-associated lncRNAs regulating target mRNAs in cotton. Analyzing the regulation pattern of delncRNAs revealed that cis-acting and trans-acting lncRNAs had different ways to influence target genes. Gene Ontology (GO) enrichment analysis revealed that the regulatory function of delncRNAs participated significantly in stimulus response process, kinase activity and plasma membrane components. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that delncRNAs participated in some important disease resistance pathways, such as plant-pathogen interaction, alpha-linolenic acid metabolism and plant hormone signal transduction. Additionally, 21 delncRNAs and 10 target genes were identified as being involved in alpha-linolenic acid metabolism associated with the biosynthesis of jasmonic acid (JA). Subsequently, we found that GhlncLOX3 might regulate resistance to V. dahliae through modulating the expression of GhLOX3 implicated in JA biosynthesis. Further functional analysis showed that GhlncLOX3-silenced seedlings displayed a reduced resistance to V. dahliae, with down-regulated expression of GhLOX3 and decreased content of JA. Conclusion This study shows the dynamic characteristics of delncRNAs in multiaspect, and suggests that GhlncLOX3-GhLOX3-JA network participates in response to V. dahliae invasion. Our results provide novel insights for genetic improvement of Verticillium wilt resistance in cotton using lncRNAs.

scholarly journals miR-373-3p Regulates Invasion and Migration Abilities of Trophoblast Cells via Targeted CD44 and Radixin

2021 ◽  
Vol 22 (12) ◽  
pp. 6260
Author(s):  
Hyun-Jung Lee ◽  
Seung Mook Lim ◽  
Hee Yeon Jang ◽  
Young Ran Kim ◽  
Joon-Seok Hong ◽  
...  
Keyword(s):  
Preterm Labor ◽  
Target Genes ◽  
Gene Array ◽  
Migration And Invasion ◽  
Trophoblast Cells ◽  
Invasion And Migration ◽  
Mirna Array ◽  
Qrt Pcr ◽  
Putative Target ◽  
And Migration

Preterm labor (PTL) is one of the obstetric complications, and is known to be associated with abnormal maternal inflammatory response and intrauterine inflammation and/or infection. However, the expression of specific miRNAs associated with PTL is not clear. In this study, we performed combination analysis of miRNA array and gene array, and then selected one miRNA (miR-373-3p) and its putative target genes (CD44 and RDX) that exhibited large expression differences in term and PTL placentas with or without inflammation. Using qRT-PCR and luciferase assays, we confirmed that miR-373-3p directly targeted CD44 and RDX. Overexpression of miR-373-3p reduced the migration and invasion of trophoblast cells, while inhibition of miR-373-3p restored the migration and invasion abilities of trophoblast cells. Finally, we validated the expression of miR-373-3p and its target genes in clinical patients’ blood. miR-373-3p was increased in PTL patients’ blood, and was the most expressed in PTL patients’ blood with inflammation. In addition, by targeting the miR-373-3p, CD44 and RDX was decreased in PTL patients’ blood, and their expression were the lowest in PTL patients’ blood with inflammation. Taken together, these findings suggest that miR-373-3p and its target genes can be potential biomarkers for diagnosis of PTL.

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