scholarly journals Whole-Transcriptome RNA Sequencing Reveals the Global Molecular Responses and CeRNA Regulatory Network of mRNAs, lncRNAs, miRNAs and circRNAs in Response to Salt Stress in Sugar Beet (Beta vulgaris)

2020 ◽  
Vol 22 (1) ◽  
pp. 289
Author(s):  
Junliang Li ◽  
Jie Cui ◽  
Cuihong Dai ◽  
Tianjiao Liu ◽  
Dayou Cheng ◽  
...  
Keyword(s):  
Salt Stress ◽  
Sugar Beet ◽  
Circular Rnas ◽  
Rna Seq ◽  
Plasma Membrane Permeability ◽  
Cerna Network ◽  
Mechanistic Basis ◽  
Whole Transcriptome ◽  
First Time ◽  
Competitive Endogenous Rna

Sugar beet is an important sugar-yielding crop with some tolerance to salt, but the mechanistic basis of this tolerance is not known. In the present study, we have used whole-transcriptome RNA-seq and degradome sequencing in response to salt stress to uncover differentially expressed (DE) mRNAs, microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in both leaves and roots. A competitive endogenous RNA (ceRNA) network was constructed with the predicted DE pairs, which revealed regulatory roles under salt stress. A functional analysis suggests that ceRNAs are implicated in copper redistribution, plasma membrane permeability, glycometabolism and energy metabolism, NAC transcription factor and the phosphoinositol signaling system. Overall, we conducted for the first time a full transcriptomic analysis of sugar beet under salt stress that involves a potential ceRNA network, thus providing a basis to study the potential functions of lncRNAs/circRNAs.

scholarly journals Roles of ncRNAs as ceRNAs in Gastric Cancer

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1036
Author(s):  
Junhong Ye ◽  
Jifu Li ◽  
Ping Zhao
Keyword(s):  
Gastric Cancer ◽  
Research Strategy ◽  
Circular Rnas ◽  
Messenger Rnas ◽  
Cerna Network ◽  
Degree Of Malignancy ◽  
High Degree ◽  
Competitive Endogenous Rna ◽  
Made In

Although ignored in the past, with the recent deepening of research, significant progress has been made in the field of non-coding RNAs (ncRNAs). Accumulating evidence has revealed that microRNA (miRNA) response elements regulate RNA. Long ncRNAs, circular RNAs, pseudogenes, miRNAs, and messenger RNAs (mRNAs) form a competitive endogenous RNA (ceRNA) network that plays an essential role in cancer and cardiovascular, neurodegenerative, and autoimmune diseases. Gastric cancer (GC) is one of the most common cancers, with a high degree of malignancy. Considerable progress has been made in understanding the molecular mechanism and treatment of GC, but GC’s mortality rate is still high. Studies have shown a complex ceRNA crosstalk mechanism in GC. lncRNAs, circRNAs, and pseudogenes can interact with miRNAs to affect mRNA transcription. The study of the involvement of ceRNA in GC could improve our understanding of GC and lead to the identification of potential effective therapeutic targets. The research strategy for ceRNA is mainly to screen the different miRNAs, lncRNAs, circRNAs, pseudogenes, and mRNAs in each sample through microarray or sequencing technology, predict the ceRNA regulatory network, and, finally, conduct functional research on ceRNA. In this review, we briefly discuss the proposal and development of the ceRNA hypothesis and the biological function and principle of ceRNAs in GC, and briefly introduce the role of ncRNAs in the GC’s ceRNA network.

scholarly journals Identification and characterization of circRNAs in the skin during the wool follicle development of Aohan fine wool sheep

2019 ◽  
Author(s):  
Ranran Zhao ◽  
Nan Liu ◽  
Fuhui Han ◽  
Hegang Li ◽  
Jifeng Liu ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Circular Rnas ◽  
Follicle Development ◽  
Rna Seq ◽  
Ampk Signaling ◽  
Wool Follicle ◽  
Solid Foundation ◽  
Sheep Shoulder ◽  
Competitive Endogenous Rna

Abstract Background Aohan fine wool sheep (AFWS) is an early fine wool variety breed cultivated in China. The wool has excellent quality and good textile performance. Investigating the molecular mechanisms that regulate wool growth is important for improving wool quality and yield. Circular RNAs (circRNAs) are non-coding RNAs which are widely expressed and can act as a competitive endogenous RNA (ceRNA) to bind to miRNA. Although circRNA has been studied in many fields, research in sheep wool follicles is limited. To understand the regulation of circRNA in the growth of fine wool sheep, we used RNA-seq to identify circRNAs in sheep shoulder skin at three stages, embryonic day 90 (E90d), embryonic day 120 (E120d), and Birth.Results We identified 8,753circRNAs and found that 1,351 were differentially expressed. We also analyzed the classification and characteristic of the circRNAs in sheep shoulder skin. GO and KEGG were used for source genes of circRNAs, and these were mainly enriched in cellular component organization, regulation of primary metabolic process, tight junctions, and the cGMP-PKG and AMPK signaling pathways. In addition, we predicted interactions between 17 circRNAs and 8 miRNAs using miRanda ( http://www.microrna.org/microrna/home.do ). Based on the significant pathways, we speculate the circ-0005720, circ-0001754, circ-0008036, circ-0004032, circ-0005174, circ-0005519, circ-0007826 may play an important role in regulating wool follicle growth in AFWS. 5 circRNAs were randomly selected to validate the results of the RNA-seq by qRT-PCR.Conclusion Our results provide more information about circRNAs in regulating wool follicle development in AFWS and provide a solid foundation for future experiments.

scholarly journals Reverse complementary matches simultaneously promote both back-splicing and exon-skipping

2021 ◽  
Author(s):  
Dong Cao
Keyword(s):  
Larval Stage ◽  
Large Scale ◽  
Exon Skipping ◽  
The Other ◽  
Circular Rnas ◽  
Branch Points ◽  
Rna Seq ◽  
C Elegans ◽  
Neuronal Genes ◽  
Whole Transcriptome

Circular RNAs (circRNAs) play diverse roles in different biological and physiological environments. Understanding circRNA expression profile and how circRNAs are regulated help make better use of them. Here, using large-scale neuron isolation from the first larval stage (L1) of Caenorhabditis elegans (C. elegans) followed by whole-transcriptome RNA sequencing (RNA-seq), we provide the first neuronal circRNA data in C. elegans. We show that circRNAs are highly expressed in the neurons of C. elegans and are preferably derived from neuronal genes. More importantly, reverse complementary matches (RCMs) in circRNA-flanking introns are not only required for back-splicing but also promote the skipping of exon(s) to be circularized. Finally, through one-by-one mutagenesis of all the splicing sites and branch points required for exon-skipping and back-splicing, we show that exon-skipping is not absolutely required for back-splicing, neither the other way. Instead, the coupled exon-skipping and back-splicing are happening at the same time and the two pathways work together to regulate the levels of the circular and the skipped transcripts.

scholarly journals Study of Neuronal Apoptosis ceRNA Network in Hippocampal Sclerosis of Human Temporal Lobe Epilepsy by RNA-Seq

2021 ◽  
Vol 15 ◽  
Author(s):  
Shengkun Yu ◽  
Yifei Gu ◽  
Tianyu Wang ◽  
Long Mu ◽  
Haiyang Wang ◽  
...  
Keyword(s):  
Temporal Lobe Epilepsy ◽  
Temporal Lobe ◽  
Neuronal Apoptosis ◽  
Molecular Mechanisms ◽  
Hippocampal Sclerosis ◽  
Rna Seq ◽  
Cerna Network ◽  
Reverse Transcription Quantitative Pcr ◽  
New Perspective ◽  
Competitive Endogenous Rna

Hippocampal sclerosis (HS) is one of the most common pathological type of intractable temporal lobe epilepsy (TLE), often characterized by hippocampal atrophy, neuronal apoptosis, and gliogenesis. However, the molecular mechanisms of neuronal apoptosis in patients with HS are still not fully understood. We therefore conducted a pilot study focusing on the neuronal apoptosis ceRNA network in the sclerotic hippocampus of intractable TLE patients. In this research, RNA sequencing (RNA-seq) was utilized to quantify the expression levels of lncRNAs, miRNAs, and mRNAs in TLE patients with HS (HS-TLE) and without HS (non-HS-TLE), and reverse transcription-quantitative PCR (qRT-PCR). The interactions of differential expression (DE) lncRNAs-miRNAs or DEmiRNAs-mRNAs were integrated by StarBase v3.0, and visualized using Cytoscape. Subsequently, we annotate the functions of lncRNA-associated competitive endogenous RNA (ceRNA) network through analysis of their interactions with mRNAs. RNA-seq analyses showed 381 lncRNAs, 42 miRNAs, and 457 mRNAs were dysregulated expression in HS-TLE compared to non-HS-TLE. According to the ceRNA hypothesis, 5 HS-specific ceRNA network were constructed. Among them, the core ceRNA regulatory network involved in neuronal apoptosis was constituted by 10 DElncRNAs (CDKN2B-AS1, MEG3, UBA6-AS1, etc.), 7 DEmiRNAs (hsa-miR-155-5p, hsa-miR-195-5p, hsa-miR-200c-3p, etc.), and 3 DEmRNAs (SCN2A, DYRK2, and MAPK8), which belonging to apoptotic and epileptic terms. Our findings established the first ceRNA network of lncRNA-mediated neuronal apoptosis in HS-TLE based on transcriptome sequencing, which provide a new perspective on the disease pathogenesis and precise treatments of HS.

scholarly journals Comprehensive Analysis of REST/NRSF Gene in Glioma and Its ceRNA Network Identification

2021 ◽  
Vol 8 ◽  
Author(s):  
Yulian Zhang ◽  
Qi Wang ◽  
Zai Wang ◽  
Chuanpeng Zhang ◽  
Xiaoli Xu ◽  
...  
Keyword(s):  
The Cancer Genome Atlas ◽  
Rna Seq ◽  
Regulatory Interaction ◽  
Cerna Network ◽  
Free Interval ◽  
Clinical Relationship ◽  
Network Identification ◽  
Cancer Genome Atlas ◽  
Molecular Regulatory Mechanisms ◽  
Competitive Endogenous Rna

We sought to clarify the clinical relationship between REST/NRSF expression and the prognosis of glioma and explore the REST-associated competitive endogenous RNA (ceRNA) network in glioma. We downloaded RNA-seq, miRNA-seq and correlated clinical data of 670 glioma patients from The Cancer Genome Atlas and analyzed the correlation between REST expression, clinical characteristics and prognosis. Differentially expressed genes (DEGs) were identified with DESeq2 and analyzed with Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) using the Profiler package. Starbase was used to explore the regulatory interaction between REST and miRNAs or LncRNAs. The lncRNA-miRNA-REST ceRNA network was constructed with Cytoscape. RT-qPCR, WB, CCK8, wound-healing, and luciferase assays were performed to validate the ceRNA network. Results showed that REST expression was significantly higher in glioma patients than normal samples. Higher REST expression was significantly associated with worse overall survival, progression-free interval, and worse disease-specific survival in glioma patients. The DEGs of mRNA, miRNA, and lncRNA were identified, and GO and KEGG enrichment analyses were performed. Finally, REST-associated ceRNA networks, including NR2F2-AS1-miR129-REST and HOTAIRM1-miR137-REST, were experimentally validated. Thus, REST may be a prognostic biomarker and therapeutic target in glioma, and its regulatory network validated in this study may provide insights into glioma's molecular regulatory mechanisms.

scholarly journals Conprehensive Analysis of circRNA-microRNA-mRNA Network Revealed Novel Regulatory Mechanism in Trichosposon Asahii Infection

2020 ◽  
Author(s):  
Ming-Wang Zhang ◽  
Zhi-Hong Zhu ◽  
Zhi-Kuan Xia ◽  
Xin Yang ◽  
Wan-Ting Luo ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Expression Profiles ◽  
Luciferase Reporter ◽  
Circular Rnas ◽  
Invasive Infection ◽  
Rna Seq ◽  
Kegg Analysis ◽  
Cerna Network ◽  
Go Enrichment ◽  
Receptor Signaling Pathway

Abstract Background: Trichosporon asahii (T. asahii) invasive infection frequently occurs in immunodeficient hosts with high mortality, but the pathogenesis of T. asahii infection remains elusive. Circular RNAs (circRNAs) are a type of endogenous noncoding RNAs that participant various disease processes. However, the mechanism of circRNAs in T. asahii infection are still completely unknown.Methods: RNA sequencing (RNA-seq) was performed to analyse the expression profiles of circRNA, microRNA (miRNA), and mRNA in THP-1 cells infected with T. asahii or uninfected samples. Part of the RNA-seq results were verified by RT-qPCR. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were used to analyse the differentially expressed (DE) mRNA. The circRNA-miRNA-mRNA network was constructed and verified with dual-luciferase reporter assay and overexpression experiment.Results: A total of 46 circRNAs , 412 mRNAs and 47 miRNAs were DE after T. asahii infection at 12 h. GO and KEGG analysis showed that the DE mRNAs were primary linked to the leukocyte migration involved in inflammatory response, Toll-like receptor signaling pathway, and TNF signaling pathway. A competing endogenous RNA (ceRNA) network was constructed with five DE circRNAs, five DE miRNAs and 42 DE mRNAs. Among them, we verified that hsa_circ_0065336 indirectly regulate PTPN11 expression by sponging miR-505-3p.Conclusions: These data revealed a comprehensive circRNA-associated ceRNA network during T. asahii infection, thus providing new insights to clarify the pathogenesis between T. asahii-host interation.

scholarly journals Transcriptome analyses of β-thalassemia -28 (A>G) mutation using isogenic cell models generated by CRISPR/Cas9 and asymmetric single-stranded oligodeoxynucleotides (assODN)

2020 ◽  
Author(s):  
Jing Li ◽  
Ziheng Zhou ◽  
Hai-Xi Sun ◽  
Wenjie Ouyang ◽  
Guoyi Dong ◽  
...  
Keyword(s):  
Cell Model ◽  
Genetic Diseases ◽  
Erk Pathway ◽  
Globin Genes ◽  
Rna Seq ◽  
Cell Models ◽  
Pathogenesis Related ◽  
Whole Transcriptome ◽  
First Time ◽  
Transcriptome Level

Abstractβ-thalassemia, caused by mutations in the human hemoglobin (HBB) gene, is one of the most common genetic diseases in the world. HBB –28 (A>G) mutation is one of the five most common mutations in China patients with β-thalassemia. However, few studies have been conducted to understand how this mutation affects the expression of pathogenesis related genes including globin genes due to limited homologous clinical materials. Therefore, we first developed an efficient technique using CRISPR/Cas9 combined with asymmetric single-stranded oligodeoxynucleotides (assODN) to generate a K562 cell model of HBB −28 (A>G) named K562−28 (A>G). Then, we systematically analyzed the differences between K562−28 (A>G) and K562 at the transcriptome level by high-throughput RNA-seq pre- and post-erythrogenic differentiation. We found that HBB −28 (A>G) mutation not only disturbed the transcription of HBB but also decreased the expression of HBG, which may further aggravate the thalassemia phenotype and partially explain the severer clinical outcome of β-thalassemia patients with HBB −28 (A>G) mutation. Moreover, we found K562−28 (A>G) cell line is more sensitive to hypoxia and showed a defective erythrogenic program compared with K562 before differentiation. In agreement, p38MAPK and ERK pathway are hyperactivated in K562−28 (A>G) after differentiation. Importantly, all above mentioned abnormalities in K562−28 (A>G) were reversed after correction of this mutation with CRISPR/Cas and assODN, confirming the specificity of these phenotypes. Overall, this is the first time to analyze the effects of the HBB - 28 (A>G) mutation at whole-transcriptome level based on isogenic cell lines, providing a landscape for further investigation of the mechanism of β-thalassemia with HBB −28 (A>G) mutation.

scholarly journals Comprehensive circRNA-microRNA-mRNA network analysis revealed the novel regulatory mechanism of Trichosporon asahii infection

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Ming-Wang Zhang ◽  
Zhi-Hong Zhu ◽  
Zhi-Kuan Xia ◽  
Xin Yang ◽  
Wan-Ting Luo ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Noncoding Rna ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Luciferase Reporter ◽  
Circular Rnas ◽  
Rna Seq ◽  
Trichosporon Asahii ◽  
Cerna Network ◽  
Pathway Analyses

Abstract Background Invasive Trichosporon asahii (T. asahii) infection frequently occurs with a high mortality in immunodeficient hosts, but the pathogenesis of T. asahii infection remains elusive. Circular RNAs (circRNAs) are a type of endogenous noncoding RNA that participate in various disease processes. However, the mechanism of circRNAs in T. asahii infection remains completely unknown. Methods RNA sequencing (RNA-seq) was performed to analyze the expression profiles of circRNAs, microRNAs (miRNAs), and mRNAs in THP-1 cells infected with T. asahii or uninfected samples. Some of the RNA-seq results were verified by RT-qPCR. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were used to analyze the differentially expressed mRNAs. A circRNA-miRNA-mRNA network was constructed and verified by dual-luciferase reporter assay and overexpression experiments. Results A total of 46 circRNAs, 412 mRNAs and 47 miRNAs were differentially expressed at 12 h after T. asahii infection. GO and KEGG analyses showed that the differentially expressed mRNAs were primarily linked to the leukocyte migration involved in the inflammatory response, the Toll-like receptor signaling pathway, and the TNF signaling pathway. A competing endogenous RNA (ceRNA) network was constructed with 5 differentially expressed circRNAs, 5 differentially expressed miRNAs and 42 differentially expressed mRNAs. Among them, hsa_circ_0065336 was found to indirectly regulate PTPN11 expression by sponging miR-505-3p. Conclusions These data revealed a comprehensive circRNA-associated ceRNA network during T. asahii infection, thus providing new insights into the pathogenesis of the T. asahii-host interactions.

scholarly journals Comprehensive analysis of competitive endogenous RNA associated with immune infiltration in lung adenocarcinoma

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wenjie Chen ◽  
Wen Li ◽  
Zhenkun Liu ◽  
Guangzhi Ma ◽  
Yunfu Deng ◽  
...  
Keyword(s):  
Prognostic Factors ◽  
Mast Cells ◽  
Correlation Analysis ◽  
Lung Adenocarcinoma ◽  
Molecular Mechanisms ◽  
Cox Regression ◽  
The Cancer Genome Atlas ◽  
Cerna Network ◽  
Monocytes And Macrophages ◽  
Competitive Endogenous Rna

AbstractTo identify the prognostic biomarker of the competitive endogenous RNA (ceRNA) and explore the tumor infiltrating immune cells (TIICs) which might be the potential prognostic factors in lung adenocarcinoma. In addition, we also try to explain the crosstalk between the ceRNA and TIICs to explore the molecular mechanisms involved in lung adenocarcinoma. The transcriptome data of lung adenocarcinoma were obtained from The Cancer Genome Atlas (TCGA) database, and the hypergeometric correlation of the differently expressed miRNA-lncRNA and miRNA-mRNA were analyzed based on the starBase. In addition, the Kaplan–Meier survival and Cox regression model analysis were used to identify the prognostic ceRNA network and TIICs. Correlation analysis was performed to analysis the correlation between the ceRNA network and TIICs. In the differently expressed RNAs between tumor and normal tissue, a total of 190 miRNAs, 224 lncRNAs and 3024 mRNAs were detected, and the constructed ceRNA network contained 5 lncRNAs, 92 mRNAs and 10 miRNAs. Then, six prognostic RNAs (FKBP3, GPI, LOXL2, IL22RA1, GPR37, and has-miR-148a-3p) were viewed as the key members for constructing the prognostic prediction model in the ceRNA network, and three kinds of TIICs (Monocytes, Macrophages M1, activated mast cells) were identified to be significantly related with the prognosis in lung adenocarcinoma. Correlation analysis suggested that the FKBP3 was associated with Monocytes and Macrophages M1, and the GPI was obviously related with Monocytes and Macrophages M1. Besides, the LOXL2 was associated with Monocytes and Activated mast cells, and the IL22RA1 was significantly associated with Monocytes and Macrophages M1, while the GPR37 and Macrophages M1 was closely related. The constructed ceRNA network and identified Monocytes, Macrophages M1 and activated Mast cells are all prognostic factors for lung adenocarcinoma. Moreover, the crosstalk between the ceRNA network and TIICs might be a potential molecular mechanism involved.

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